Bobik K, Burch-Smith TM. Chloroplast signaling within, between and beyond cells. Front Plant Sci. 2015;6:781.
Article
PubMed
PubMed Central
Google Scholar
Daniell H, Chan H-T, Pasoreck EK. Vaccination through chloroplast genetics: affordable protein drugs for the prevention and treatment of inherited or infectious human diseases. Annu Rev Genet. 2016. In Press.
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 1986;5:2043–9.
CAS
PubMed
PubMed Central
Google Scholar
Wambugu P, Brozynska M, Furtado A, Waters D, Henry R. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences. Sci Rep. 2015;5:13957.
Article
PubMed
PubMed Central
Google Scholar
Brozynska M, Furtado A, Henry RJ. Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnol J. 2016;14:1070–85.
Article
CAS
PubMed
Google Scholar
Su J, Zhu L, Sherman A, Wang X, Lin S, Kamesh A, et al. Low cost industrial production of coagulation factor IX bioencapsulated in lettuce cells for oral tolerance induction in hemophilia B. Biomaterials. 2015;70:84–93.
Article
CAS
PubMed
Google Scholar
Jansen RK, Wojciechowski MF, Sanniyasi E, Lee SB, Daniell H. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol Phylogenet Evol. 2008;48:1204–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK, Luo H, et al. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet. 2007;115:571–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H. Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics. 2006;7:222.
Article
PubMed
PubMed Central
CAS
Google Scholar
Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H. The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. Plant Biotechnol J. 2007;5:339–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H. The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics. 2006;7:61.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H. The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms. BMC Plant Biol. 2006;6:21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Daniell H, Lee SB, Grevich J, Saski C, Quesada-Vargas T, Guda C, et al. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet. 2006;112:1503–18.
Article
CAS
PubMed
Google Scholar
Jansen RK, Saski C, Lee SB, Hansen AK, Daniell H. Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol. 2011;28:835–47.
Article
CAS
PubMed
Google Scholar
Wolfe KH, Morden CW, Palmer JD. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci U S A. 1992;89:10648–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bortiri E, Coleman-Derr D, Lazo GR, Anderson OD, Gu YQ. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Res Notes. 2008;1:61.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 1999;6:283–90.
Article
CAS
PubMed
Google Scholar
Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, Jansen RK. Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Mol Biol. 2005;59:309–22.
Article
CAS
PubMed
Google Scholar
Jansen RK, Kaittanis C, Saski C, Lee SB, Tomkins J, Alverson AJ, Daniell H. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol. 2006;6:32.
Article
PubMed
PubMed Central
CAS
Google Scholar
Daniell H, Wurdack KJ, Kanagaraj A, Lee SB, Saski C, Jansen RK. The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron. Theor Appl Genet. 2008;116:723–37.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu J, Liu B, Cheng F, Ramchiary N, Choi SR, Lim YP, Wang X-W. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology. Front Plant Sci. 2012;3:234.
Google Scholar
Grivet D, Heinze B, Vendramin G, Petit R. Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Mol Ecol Notes. 2001;1:345–9.
Article
CAS
Google Scholar
Goremykin V, Hirsch-Ernst K, Wölfl S, Hellwig F. The chloroplast genome of the 'basal' angiosperm Calycanthus fertilis–structural and phylogenetic analyses. Plant Syst Evol. 2003;242:119–35.
Article
CAS
Google Scholar
Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol Biol Evol. 2004;21:1445–54.
Article
CAS
PubMed
Google Scholar
Goremykin VV, Hirsch-Ernst KI, Wölfl S, Hellwig FH. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol Biol Evol. 2003;20:1499–505.
Article
CAS
PubMed
Google Scholar
Dhingra A, Folta KM. ASAP: amplification, sequencing & annotation of plastomes. BMC Genomics. 2005;6:176.
Article
PubMed
PubMed Central
CAS
Google Scholar
Heinze B. A database of PCR primers for the chloroplast genomes of higher plants. Plant Methods. 2007;3:4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu FH, Kan DP, Lee SB, Daniell H, Lee YW, Lin CC, et al. Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol. 2009;29:847–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leseberg CH, Duvall MR. The complete chloroplast genome of Coix lacryma-jobi and a comparative molecular evolutionary analysis of plastomes in cereals. J Mol Evol. 2009;69:311–8.
Article
CAS
PubMed
Google Scholar
Dong W, Xu C, Cheng T, Lin K, Zhou S. Sequencing angiosperm plastid genomes made easy: a complete set of universal primers and a case study on the phylogeny of saxifragales. Genome Biol Evol. 2013;5:989–97.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mardanov AV, Ravin NV, Kuznetsov BB, Samigullin TH, Antonov AS, Kolganova TV, Skyabin KG. Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms. J Mol Evol. 2008;66:555–64.
Article
CAS
PubMed
Google Scholar
Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, et al. The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family. Sci Rep. 2015;5:9040.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moore MJ, Dhingra A, Soltis PS, Shaw R, Farmerie WG, Folta KM, Soltis DE. Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol. 2006;6:17.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang W, Messing J. High-throughput sequencing of three Lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS One. 2011;6, e24670.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cronn R, Liston A, Parks M, Gernandt DS, Shen R, Mockler T. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res. 2008;36, e122.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pan IC, Liao DC, Wu FH, Daniell H, Singh ND, Chang C, et al. Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical oncidium breeding. PLoS One. 2012;7, e34738.
Article
CAS
PubMed
PubMed Central
Google Scholar
Atherton RA, McComish BJ, Shepherd LD, Berry LA, Albert NW, Lockhart PJ. Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform. Plant Methods. 2010;6:22.
Article
PubMed
PubMed Central
CAS
Google Scholar
Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, et al. Organellar genomes of white spruce (Picea glauca): assembly and annotation. Genome Biol Evol. 2016;8:29–41.
Article
Google Scholar
Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, et al. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics. 2013;14:670.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu Z, Gui S, Quan Z, Pan L, Wang S, Ke W, et al. A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots. BMC Plant Biol. 2014;14:289.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li Q, Li Y, Song J, Xu H, Xu J, Zhu Y, et al. High‐accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy. New Phytol. 2014;204:1041–9.
Article
CAS
PubMed
Google Scholar
Redwan R, Saidin A, Kumar S. Complete chloroplast genome sequence of MD-2 pineapple and its comparative analysis among nine other plants from the subclass Commelinidae. BMC Plant Biol. 2015;15:196.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen X, Li Q, Li Y, Qian J, Han J. Chloroplast genome of Aconitum barbatum var. puberulum (Ranunculaceae) derived from CCS reads using the PacBio RS platform. Frontiers Plant Sci. 2015;6:42.
Google Scholar
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133–8.
Article
CAS
PubMed
Google Scholar
English AC, Richards S, Han Y, Wang M, Vee V, Qu J, et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One. 2012;7, e47768.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10:563–9.
Article
CAS
PubMed
Google Scholar
Oldenburg DJ, Bendich AJ. DNA maintenance in plastids and mitochondria of plants. Frontiers Plant Sci. 2015;6:883.
Article
Google Scholar
Oldenburg DJ, Bendich AJ. The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication. Curr Genet. 2016;62:431–42.
Article
CAS
PubMed
Google Scholar
Jansen RK, Cai Z, Raubeson LA, Daniell H, Leebens-Mack J, Müller KF, et al. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci U S A. 2007;104:19369–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pillon Y, Chase MW. Taxonomic exaggeration and its effects on orchid conservation. Conserv Biol. 2007;21:263–5.
Article
PubMed
Google Scholar
Chang CC, Lin HC, Lin IP, Chow TY, Chen HH, Chen WH, et al. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol. 2006;23:279–91.
Article
CAS
PubMed
Google Scholar
Jheng CF, Chen TC, Lin JY, Chen TC, Wu WL, Chang CC. The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Sci. 2012;190:62–73.
Article
CAS
PubMed
Google Scholar
Kim GB, Kwon Y, Yu HJ, Lim KB, Seo JH, Mun JH. The complete chloroplast genome of Phalaenopsis 'Tiny Star'. Mitochondrial DNA. 2016;27:1300–2.
Article
CAS
PubMed
Google Scholar
Wu FH, Chan MT, Liao DC, Hsu CT, Lee YW, Daniell H, et al. Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol. 2010;10:68.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yang JB, Tang M, Li HT, Zhang ZR, Li DZ. Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evol Biol. 2013;13:84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luo J, Hou BW, Niu ZT, Liu W, Xue QY, Ding XY. Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications. PLoS One. 2014;9, e99016.
Article
PubMed
PubMed Central
CAS
Google Scholar
Li J, Chen C, Wang ZZ. The complete chloroplast genome of the Dendrobium strongylanthum (Orchidaceae: Epidendroideae). Mitochondrial DNA. 2016;27:3048–9.
PubMed
Google Scholar
da Rocha Perini V, Leles B, Furtado C, Prosdocimi F. Complete chloroplast genome of the orchid Cattleya crispata (Orchidaceae:Laeliinae), a Neotropical rupiculous species. Mitochondrial DNA. 2015. doi:10.3109/19401736.2014.1003850.
Tsitrone A, Kirkpatrick M, Levin DA. A model for chloroplast capture. Evolution. 2003;57:1776–82.
Article
PubMed
Google Scholar
Soltis DE, Kuzoff RK. Discordance between nuclear and chloroplast phylogenies in the heuchera group (Saxifragaceae). Evolution. 1995;49:727–42.
Article
Google Scholar
Rieseberg LH, Soltis DE. Phylogenetic consequences of cytoplasmic gene flow in plants. Evol Trends Plants. 1991;5:65–84.
Google Scholar
Maier RM, Neckermann K, Igloi GL, Kossel H. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol. 1995;251:614–28.
Article
CAS
PubMed
Google Scholar
Ogihara Y, Isono K, Kojima T, Endo A, Hanaoka M, Shiina T, et al. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics. 2002;266:740–6.
Article
CAS
PubMed
Google Scholar
Middleton CP, Senerchia N, Stein N, Akhunov ED, Keller B, Wicker T, Kilian B. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe. PLoS One. 2014;9, e85761.
Article
PubMed
PubMed Central
CAS
Google Scholar
Brozynska M, Omar ES, Furtado A, Crayn D, Simon B, Ishikawa R, Henry RJ. Chloroplast genome of novel rice germplasm identified in northern Australia. Tropical Plant Biol. 2014;7:111–20.
Article
CAS
Google Scholar
Waters DL, Nock CJ, Ishikawa R, Rice N, Henry RJ. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecol Evol. 2012;2:211–7.
Article
PubMed
PubMed Central
Google Scholar
Sotowa M, Ootsuka K, Kobayashi Y, Hao Y, Tanaka K, Ichitani K, et al. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms. Rice. 2013;6:26.
Article
PubMed
PubMed Central
Google Scholar
Xu Q, Xiong G, Li P, He F, Huang Y, Wang K, et al. Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids. PLoS One. 2012;7, e37128.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ibrahim RI, Azuma J, Sakamoto M. Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants. Genes Genet Syst. 2006;81:311–21.
Article
CAS
PubMed
Google Scholar
Li P, Li Z, Liu H, Hua J. Cytoplasmic diversity of the cotton genus as revealed by chloroplast microsatellite markers. Genet Resour Crop Evol. 2014;61:107–19.
Article
CAS
Google Scholar
Pickersgill B, Debouck DG. Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races. Theor Appl Genet. 2005;110:432–44.
Article
PubMed
CAS
Google Scholar
Palmer JD, Osorio B, Thompson WF. Evolutionary significance of inversions in legume chloroplast DNAs. Curr Genet. 1988;14:65–74.
Article
CAS
Google Scholar
Sherman-Broyles S, Bombarely A, Grimwood J, Schmutz J, Doyle J. Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean. G3 (Bethesda). 2014;4:2023–33.
Article
CAS
Google Scholar
Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen NA, Mutwakil M, et al. Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnol J. 2014;12:743–54.
Article
CAS
PubMed
Google Scholar
Cai Z, Guisinger M, Kim H-G, Ruck E, Blazier JC, McMurtry V, et al. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol. 2008;67:696–704.
Article
CAS
PubMed
Google Scholar
Magee AM, Aspinall S, Rice DW, Cusack BP, Semon M, Perry AS, et al. Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 2010;20:1700–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bogdanova VS, Zaytseva OO, Mglinets AV, Shatskaya NV, Kosterin OE, Vasiliev GV. Nuclear-cytoplasmic conflict in pea (Pisum sativum L.) is associated with nuclear and plastidic candidate genes encoding acetyl-CoA carboxylase subunits. PLoS One. 2015;10:e0119835.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guo X, Castillo-Ramírez S, González V, Bustos P, Fernández-Vázquez JL, Santamaría RI, et al. Rapid evolutionary change of common bean (Phaseolus vulgaris L.) plastome, and the genomic diversification of legume chloroplasts. BMC Genomics. 2007;8:228.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tangphatsornruang S, Sangsrakru D, Chanprasert J, Uthaipaisanwong P, Yoocha T, Jomchai N, Tragoonrung S. The chloroplast genome sequence of mungbean (Vigna radiata) determined by high-throughput pyrosequencing: structural organization and phylogenetic relationships. DNA Res. 2010;17:11–22.
Article
CAS
PubMed
Google Scholar
Martin GE, Rousseau-Gueutin M, Cordonnier S, Lima O, Michon-Coudouel S, Naquin D, et al. The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. Ann Bot. 2014;113:1197–210.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, et al. Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. PLoS One. 2012;7, e51687.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwarz EN, Ruhlman TA, Sabir JS, Hajrah NH, Alharbi NS, Al‐Malki AL, et al. Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids. J Syst Evol. 2015;53:458–68.
Article
Google Scholar
Su HJ, Hogenhout SA, Al-Sadi AM, Kuo CH. Complete chloroplast genome sequence of Omani Lime (Citrus aurantiifolia) and comparative analysis within the Rosids. PLoS One. 2014;9, e113049.
Article
PubMed
PubMed Central
CAS
Google Scholar
Carbonell-Caballero J, Alonso R, Ibañez V, Terol J, Talon M, Dopazo J. A phylogenetic analysis of 34 chloroplast genomes elucidates the relationships between wild and domestic species within the genus Citrus. Mol Biol Evol. 2015;32:2015–35.
Article
PubMed
PubMed Central
Google Scholar
Caspermeyer J. Most comprehensive study to date reveals evolutionary history of Citrus. Mol Biol Evol. 2015;32:2217–8.
Google Scholar
Chen SL, Xiao PG. Molecular evolution and positive Darwinian selection of the chloroplast maturase matK. J Plant Res. 2010;123:241–7.
Article
PubMed
CAS
Google Scholar
Peng L, Yamamoto H, Shikanai T. Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex. Biochim Biophys Acta. 1807;2011:945–53.
Google Scholar
Ma PF, Zhang YX, Guo ZH, Li DZ. Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus. Sci Rep. 2015;5:11608.
Article
PubMed
PubMed Central
Google Scholar
Zhang YJ, Ma PF, Li DZ. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS One. 2011;6, e20596.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burke SV, Grennan CP, Duvall MR. Plastome sequences of two New World bamboos–Arundinaria gigantea and Cryptochloa strictiflora (Poaceae)–extend phylogenomic understanding of Bambusoideae. Am J Bot. 2012;99:1951–61.
Article
CAS
PubMed
Google Scholar
Gao J, Li K, Gao LZ. The complete chloroplast genome sequence of the Bambusa multiplex (Poaceae: Bambusoideae). Mitochondrial DNA. 2014;18:1–3.
Google Scholar
Wysocki WP, Clark LG, Attigala L, Ruiz-Sanchez E, Duvall MR. Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis. BMC Evol Biol. 2015;15:50.
Article
PubMed
PubMed Central
Google Scholar
Ma PF, Zhang YX, Zeng CX, Guo ZH, Li DZ. Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe Arundinarieae (Poaceae). Syst Biol. 2014;63:933–50.
Article
PubMed
Google Scholar
Smith DR. Mitochondrion-to-plastid DNA, transfer: it happens. New Phytol. 2014;202:736–8.
Article
CAS
PubMed
Google Scholar
Timmis JN, Ayliffe MA, Huang CY, Martin W. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 2004;5:123–35.
Article
CAS
PubMed
Google Scholar
Li H, Chiu CC. Protein transport into chloroplasts. Annu Rev Plant Biol. 2010;61:157–80.
Article
CAS
PubMed
Google Scholar
Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Mol Biol Evol. 2014;31:3095–112.
Article
CAS
PubMed
Google Scholar
Tiller N, Bock R. The translational apparatus of plastids and its role in plant development. Mol Plant. 2014;7:1105–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hazkani-Covo E, Zeller RM, Martin W. Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 2010;6, e1000834.
Article
PubMed
PubMed Central
CAS
Google Scholar
Smith DR, Crosby K, Lee RW. Correlation between nuclear plastid DNA abundance and plastid number supports the limited transfer window hypothesis. Genome Biol Evol. 2011;3:365–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cummings HS, Hershey JWB. Translation initiation-factor IF1 is essential for cell viability in Escherichia coli. J Bacteriol. 1994;176:198–205.
CAS
PubMed
PubMed Central
Google Scholar
Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, et al. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell. 2001;13:645–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gantt JS, Baldauf SL, Calie PJ, Weeden NF, Palmer JD. Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 1991;10:3073–8.
CAS
PubMed
PubMed Central
Google Scholar
Park S, Jansen RK, Park S. Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae. BMC Plant Biol. 2015;15:40.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ueda M, Fujimoto M, Arimura S, Murata J, Tsutsumi N, Kadowaki K. Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene. 2007;402:51–6.
Article
CAS
PubMed
Google Scholar
Cusack BP, Wolfe KH. When gene marriages don’t work out: divorce by subfunctionalization. Trends Genet. 2007;23:270–2.
Article
CAS
PubMed
Google Scholar
Ueda M, Kuniyoshi T, Yamamoto H, Sugimoto K, Ishizaki K, Kohchi T, et al. Composition and physiological function of the chloroplast NADH dehydrogenase-like complex in Marchantia polymorpha. Plant J. 2012;72:683–93.
Article
CAS
PubMed
Google Scholar
Munekage Y, Hashimoto M, Miyake C, Tomizawa K-I, Endo T, Tasaka M, Shikanai T. Cyclic electron flow around photosystem I is essential for photosynthesis. Nature. 2004;429:579–82.
Article
CAS
PubMed
Google Scholar
Peltier G, Cournac L. Chlororespiration. Annu Rev Plant Biol. 2002;53:523–50.
Article
CAS
PubMed
Google Scholar
Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci U S A. 1994;91:9794–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanderson MJ, Copetti D, Búrquez A, Bustamante E, Charboneau JL, Eguiarte LE, et al. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): loss of the ndh gene suite and inverted repeat. Am J Bot. 2015;102:1115–27.
Article
PubMed
Google Scholar
McCoy SR, Kuehl JV, Boore JL, Raubeson LA. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol. 2008;8:130.
Article
PubMed
PubMed Central
CAS
Google Scholar
Braukmann TWA, Kuzmina M, Stefanović S. Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Curr Genet. 2009;55:323–37.
Article
CAS
PubMed
Google Scholar
Blazier J, Guisinger MM, Jansen RK. Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Mol Biol. 2011;76:263–72.
Article
CAS
Google Scholar
Weng M-L, Blazier JC, Govindu M, Jansen RK. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats and nucleotide substitution rates. Mol Biol Evol. 2014;31:645–59.
Article
CAS
PubMed
Google Scholar
Ranade SS, García-Gil MR, Rosselló JA. Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes. Mol Genet Genomics. 2016;291:935–41.
Article
CAS
PubMed
Google Scholar
Ruhlman TA, Chang WJ, Chen JJ, Huang YT, Chan MT, Zhang J, et al. NDH expression marks major transitions in plant evolution and reveals coordinate intracellular gene loss. BMC Plant Biol. 2015;15:100.
Article
PubMed
PubMed Central
CAS
Google Scholar
Takabayashi A, Endo T, Shikanai T, Sato F. Post-illumination reduction of the plastoquinone pool in chloroplast transformants in which chloroplastic NAD(P)H dehydrogenase was inactivated. Biosci Biotechnol Biochem. 2002;66:2107–11.
Article
CAS
PubMed
Google Scholar
Burrows PA, Sazanov LA, Svab Z, Maliga P, Nixon PJ. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO J. 1998;17:868–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kofer W, Koop H-U, Wanner G, Steinmüller K. Mutagenesis of the genes encoding subunits A, C, H, I, J and K of the plastid NAD(P)H-plastoquinone-oxidoreductase in tobacco by polyethylene glycol-mediated plastome transformation. Mol Gen Genet. 1998;258:166–73.
Article
CAS
PubMed
Google Scholar
Shikanai T, Endo T, Hashimoto T, Yamada Y, Asada K, Yokota A. Directed disruption of the tobacco ndhB gene impairs cyclic electron flow around photosystem I. Proc Natl Acad Sci U S A. 1998;95:9705–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin S, Daniell H. The engineered chloroplast genome just got smarter. Trends Plant Sci. 2015;20:622–40.
Article
CAS
PubMed
Google Scholar
Daniell H. Transgene containment by maternal inheritance: effective or elusive? Proc Natl Acad Sci U S A. 2007;104:6879–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dheeraj V, Daniell H. Chloroplast vector systems for biotechnology applications. Plant Physiol. 2007;145:1129–43.
Article
CAS
Google Scholar
Dunne A, Maple‐Grødem J, Gargano D, Haslam RP, Napier JA, Chua NH, et al. Modifying fatty acid profiles through a new cytokinin‐based plastid transformation system. Plant J. 2014;80:1131–8.
Article
CAS
PubMed
Google Scholar
Kavanagh TA, Thanh ND, Lao NT, McGrath N, Peter SO, Horváth EM, et al. Homeologous plastid DNA transformation in tobacco is mediated by multiple recombination events. Genetics. 1999;152:1111–22.
CAS
PubMed
PubMed Central
Google Scholar
Guda C, Lee SB, Daniell H. Stable expression of a biodegradable protein-based polymer in tobacco chloroplasts. Plant Cell Rep. 2000;19:257–62.
Article
CAS
Google Scholar
Ruhlman T, Verma D, Samson N, Daniell H. The role of heterologous chloroplast sequence elements in transgene integration and expression. Plant Physiol. 2010;152:2088–104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daniell H, Datta R, Varma S, Gray S, Lee SB. Containment of herbicide resistance through genetic engineering of the chloroplast genome. Nat Biotechnol. 1998;16:345–8.
Article
CAS
PubMed
Google Scholar
Krichevsky A, Meyers B, Vainstein A, Maliga P, Citovsky V. Autoluminescent plants. PLoS One. 2010;5, e15461.
Article
PubMed
PubMed Central
CAS
Google Scholar
Daniell H, Vivekananda J, Nielsen B, Ye G, Tewari K, Sanford J. Transient foreign gene expression in chloroplasts of cultured tobacco cells after biolistic delivery of chloroplast vectors. Proc Natl Acad Sci U S A. 1990;87:88–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Klein RR, Mullet JE. Control of gene expression during higher plant chloroplast biogenesis. Protein synthesis and transcript levels of psbA, psaA-psaB, and rbcL in dark-grown and illuminated barley seedlings. J Biol Chem. 1987;262:4341–8.
CAS
PubMed
Google Scholar
Wurbs D, Ruf S, Bock R. Contained metabolic engineering in tomatoes by expression of carotenoid biosynthesis genes from the plastid genome. Plant J. 2007;49:276–88.
Article
CAS
PubMed
Google Scholar
McBride KE, Schaaf DJ, Daley M, Stalker DM. Controlled expression of plastid transgenes in plants based on a nuclear DNA-encoded and plastid-targeted T7 RNA polymerase. Proc Natl Acad Sci U S A. 1994;91:7301–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar S, Dhingra A, Daniell H. Plastid-expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots, and leaves confers enhanced salt tolerance. Plant Physiol. 2004;136:2843–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dhingra A, Portis Jr AR, Daniell H. Enhanced translation of a chloroplast-expressed RbcS gene restores small subunit levels and photosynthesis in nuclear RbcS antisense plants. Proc Natl Acad Sci U S A. 2004;101:6315–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Cosa B, Moar W, Lee SB, Miller M, Daniell H. Overexpression of the Bt cry2Aa2 operon in chloroplasts leads to formation of insecticidal crystals. Nat Biotechnol. 2001;19:71–4.
Article
PubMed
PubMed Central
Google Scholar
Ruf S, Hermann M, Berger IJ, Carrer H, Bock R. Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit. Nat Biotechnol. 2001;19:870–5.
Article
CAS
PubMed
Google Scholar
Zhou F, Badillo-Corona JA, Karcher D, Gonzalez-Rabade N, Piepenburg K, Borchers AM, et al. High-level expression of human immunodeficiency virus antigens from the tobacco and tomato plastid genomes. Plant Biotechnol J. 2008;6:897–913.
Article
CAS
PubMed
Google Scholar
Lee SB, Li B, Jin S, Daniell H. Expression and characterization of antimicrobial peptides Retrocyclin-101 and Protegrin-1 in chloroplasts to control viral and bacterial infections. Plant Biotechnol J. 2011;9:100–15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin S, Kanagaraj A, Verma D, Lange T, Daniell H. Release of hormones from conjugates: chloroplast expression of beta-glucosidase results in elevated phytohormone levels associated with significant increase in biomass and protection from aphids or whiteflies conferred by sucrose esters. Plant Physiol. 2011;155:222–35.
Article
CAS
PubMed
Google Scholar
Jin S, Zhang X, Daniell H. Pinellia ternata agglutinin expression in chloroplasts confers broad spectrum resistance against aphid, whitefly, Lepidopteran insects, bacterial and viral pathogens. Plant Biotechnol J. 2012;10:313–27.
Article
CAS
PubMed
Google Scholar
Liu CW, Lin CC, Chen JJ, Tseng MJ. Stable chloroplast transformation in cabbage (Brassica oleracea L. var. capitata L.) by particle bombardment. Plant Cell Rep. 2007;26:1733–44.
Article
CAS
PubMed
Google Scholar
Dufourmantel N, Pelissier B, Garcon F, Peltier G, Ferullo JM, Tissot G. Generation of fertile transplastomic soybean. Plant Mol Biol. 2004;55:479–89.
Article
CAS
PubMed
Google Scholar
Dufourmantel N, Tissot G, Goutorbe F, Garcon F, Muhr C, Jansens S, et al. Generation and analysis of soybean plastid transformants expressing Bacillus thuringiensis Cry1Ab protoxin. Plant Mol Biol. 2005;58:659–68.
Article
CAS
PubMed
Google Scholar
Singh AK, Verma SS, Bansal KC. Plastid transformation in eggplant (Solanum melongena L.). Transgenic Res. 2010;19:113–9.
Article
CAS
PubMed
Google Scholar
Jin S, Singh ND, Li L, Zhang X, Daniell H. Engineered chloroplast dsRNA silences cytochrome p450 monooxygenase, V-ATPase and chitin synthase genes in the insect gut and disrupts Helicoverpa armigera larval development and pupation. Plant Biotechnol J. 2015;13:435–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Khan SA, Hasse C, Ruf S, Heckel DG, Bock R. Pest control. Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids. Science. 2015;347:991–4.
Article
CAS
PubMed
Google Scholar
Viitanen PV, Devine AL, Khan MS, Deuel DL, Van Dyk DE, Daniell H. Metabolic engineering of the chloroplast genome using the Echerichia coli ubiC gene reveals that chorismate is a readily abundant plant precursor for p-hydroxybenzoic acid biosynthesis. Plant Physiol. 2004;136:4048–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verma D, Kanagaraj A, Jin SX, Singh ND, Kolattukudy PE, Daniell H. Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars. Plant Biotechnol J. 2010;8:332–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schneider C. Chemistry and biology of vitamin E. Mol Nutr Food Res. 2005;49:7–30.
Article
CAS
PubMed
Google Scholar
Shintani D, DellaPenna D. Elevating the vitamin E content of plants through metabolic engineering. Science. 1998;282:2098–100.
Article
CAS
PubMed
Google Scholar
Jin S, Daniell H. Expression of gamma-tocopherol methyltransferase in chloroplasts results in massive proliferation of the inner envelope membrane and decreases susceptibility to salt and metal-induced oxidative stresses by reducing reactive oxygen species. Plant Biotechnol J. 2014;12:1274–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Apel W, Bock R. Enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin A conversion. Plant Physiol. 2009;151:59–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grabowski H, Cockburn I, Long G. The market for follow-on biologics: how will it evolve? Health Aff. 2006;25:1291–301.
Article
Google Scholar
Spök A, Karner S, Stein AJ, Rodríguez-Cerezo E. Plant molecular farming. Opportunities and challenges. JRC Scientific and Technical Reports 2008. http://ftp.jrc.es/EURdoc/JRC43873.pdf. Accessed 17 May 2016.
Holtz BR, Berquist BR, Bennett LD, Kommineni VJ, Munigunti RK, White EL, et al. Commercial‐scale biotherapeutics manufacturing facility for plant‐made pharmaceuticals. Plant Biotechnol J. 2015;13:1180–90.
Article
CAS
PubMed
Google Scholar
Kwon KC, Daniell H. Low‐cost oral delivery of protein drugs bioencapsulated in plant cells. Plant Biotechnol J. 2015;13:1017–22.
Article
PubMed
PubMed Central
Google Scholar
El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11:497–504.
Article
PubMed
CAS
Google Scholar
Kwon KC, Nityanandam R, New JS, Daniell H. Oral delivery of bioencapsulated exendin-4 expressed in chloroplasts lowers blood glucose level in mice and stimulates insulin secretion in beta-TC6 cells. Plant Biotechnol J. 2013;11:77–86.
Article
CAS
PubMed
Google Scholar
Shenoy V, Kwon KC, Rathinasabapathy A, Lin SN, Jin GY, Song CJ, et al. Oral delivery of angiotensin-converting enzyme 2 and angiotensin-(1–7) bioencapsulated in plant cells attenuates pulmonary hypertension. Hypertension. 2014;64:1248–59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kohli N, Westerveld DR, Ayache AC, Verma A, Shil P, Prasad T, et al. Oral delivery of bioencapsulated proteins across blood–brain and blood-retinal barriers. Mol Ther. 2014;22:535–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chan HT, Daniell H. Plant‐made oral vaccines against human infectious diseases—are we there yet? Plant Biotechnol J. 2015;13:1056–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davoodi-Semiromi A, Schreiber M, Nalapalli S, Verma D, Singh ND, Banks RK, et al. Chloroplast-derived vaccine antigens confer dual immunity against cholera and malaria by oral or injectable delivery. Plant Biotechnol J. 2010;8:223–42.
Article
CAS
PubMed
Google Scholar
Lakshmi PS, Verma D, Yang X, Lloyd B, Daniell H. Low cost tuberculosis vaccine antigens in capsules: expression in chloroplasts, bio-encapsulation, stability and functional evaluation in vitro. PLoS One. 2013;8, e54708.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hagelberg E, Hofreiter M, Keyser C. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci. 2015;370:20130371.
Article
PubMed
PubMed Central
CAS
Google Scholar
Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M, Henderson D, et al. Chloroplast DNA sequence from a Miocene Magnolia species. Nature. 1990;344:656–8.
Article
CAS
PubMed
Google Scholar
Rosselló JA. The never‐ending story of geologically ancient DNA: was the model plant Arabidopsis the source of Miocene Dominican amber? Biol J Linn Soc. 2014;111:234–40.
Article
Google Scholar
Zhu A, Guo W, Gupta S, Fan W, Mower JP. Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. New Phytol. 2016;209:1747–56.
Article
CAS
PubMed
Google Scholar
von Kohn C, Kielkowska A, Havey MJ. Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion. Genome. 2013;56:737–42.
Article
CAS
Google Scholar
Nashima K, Terakami S, Nishitani C, Kunihisa M, Shoda M, Takeuchi M, et al. Complete chloroplast genome sequence of pineapple (Ananas comosus). Tree Genet Genomes. 2015;11:60.
Article
Google Scholar
Downie SR, Jansen RK. A comparative analysis of whole plastid genomes from the Apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Syst Botany. 2015;40:336–51.
Article
Google Scholar
Liu Y, Huo N, Dong L, Wang Y, Zhang S, Young HA, et al. Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants. PLoS One. 2013;8, e57533.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM. The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol. 2002;19:1602–12.
Article
CAS
PubMed
Google Scholar
Hu Z-Y, Hua W, Huang S-M, Wang H-Z. Complete chloroplast genome sequence of rapeseed (Brassica napus L.) and its evolutionary implications. Genet Resour Crop Evol. 2011;58:875–87.
Article
CAS
Google Scholar
Yang JB, Li DZ, Li HT. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Mol Ecol Resour. 2014;14:1024–31.
Article
CAS
PubMed
Google Scholar
Oh H, Seo B, Lee S, Ahn D-H, Jo E, Park J-K, Min G-S. Two complete chloroplast genome sequences of Cannabis sativa varieties. Mitochondrial DNA. 2016;27:2835–7.
Article
PubMed
CAS
Google Scholar
Jo YD, Park J, Kim J, Song W, Hur CG, Lee YH, Kang BC. Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep. 2011;30:217–29.
Article
CAS
PubMed
Google Scholar
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, et al. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008;452:991–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ku C, Chung WC, Chen LL, Kuo CH. The complete plastid genome sequence of Madagascar periwinkle Catharanthus roseus (L.) G. Don: plastid genome evolution, molecular marker identification, and phylogenetic implications in asterids. PLoS One. 2013;8, e68518.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, et al. Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol Ecol Resour. 2014;14:1103–13.
Article
CAS
PubMed
Google Scholar
Ahmed I, Biggs PJ, Matthews PJ, Collins LJ, Hendy MD, Lockhart PJ. Mutational dynamics of aroid chloroplast genomes. Genome Biol Evol. 2012;4:1316–23.
Article
PubMed
PubMed Central
CAS
Google Scholar
Plader W, Yukawa Y, Sugiura M, Malepszy S. The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: its composition and comparative analysis. Cell Mol Biol Lett. 2007;12:584–94.
Article
CAS
PubMed
Google Scholar
Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI. Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)? Ann Bot. 2014;113:119–33.
Article
PubMed
Google Scholar
Wang B, Han L, Chen C, Wang Z. The complete chloroplast genome sequence of Dieffenbachia seguine (Araceae). Mitochondrial DNA. 2016;27:2913–4.
PubMed
Google Scholar
Ye CY, Lin Z, Li G, Wang YY, Qiu J, Fu F, Zhang H, et al. Echinochloa chloroplast genomes: insights into the evolution and taxonomic identification of two weedy species. PLoS One. 2014;9, e113657.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM. Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 2009;52:115–24.
Article
CAS
PubMed
Google Scholar
Logacheva MD, Samigullin TH, Dhingra A, Penin AA. Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale--a wild ancestor of cultivated buckwheat. BMC Plant Biol. 2008;8:59.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cahoon AB, Sharpe RM, Mysayphonh C, Thompson EJ, Ward AD, Lin A. The complete chloroplast genome of tall fescue (Lolium arundinaceum; Poaceae) and comparison of whole plastomes from the family Poaceae. Am J Bot. 2010;97:49–58.
Article
CAS
PubMed
Google Scholar
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, et al. The genome of woodland strawberry (Fragaria vesca). Nat Genet. 2011;43:109–16.
Article
CAS
PubMed
Google Scholar
Dempewolf H, Kane NC, Ostevik KL, Geleta M, Barker MS, Lai Z, et al. Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.–the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome. Mol Ecol Resour. 2010;10:1048–58.
Article
CAS
PubMed
Google Scholar
Timme RE, Kuehl JV, Boore JL, Jansen RK. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot. 2007;94:302–12.
Article
CAS
PubMed
Google Scholar
Barrett CF, Davis JI, Leebens‐Mack J, Conran JG, Stevenson DW. Plastid genomes and deep relationships among the commelinid monocot angiosperms. Cladistics. 2013;29:65–87.
Article
Google Scholar
Sanchez-Puerta MV, Abbona CC. The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae). PLoS One. 2014;9, e98353.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yan L, Lai X, Li X, Wei C, Tan X, Zhang Y. Analyses of the complete genome and gene expression of chloroplast of sweet potato (Ipomoea batata). PLoS One. 2015;10, e0124083.
Article
PubMed
PubMed Central
CAS
Google Scholar
McNeal JR, Kuehl JV, Boore JL, de Pamphilis CW. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol. 2007;7:57.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kanamoto H, Yamashita A, Asao H, Okumura S, Takase H, Hattori M, et al. Efficient and stable transformation of Lactuca sativa L. cv. Cisco (lettuce) plastids. Transgenic Res. 2006;15:205–17.
Article
CAS
PubMed
Google Scholar
Mennes CB, Lam VK, Rudall PJ, Lyon SP, Graham SW, Smets EF, Merckx VS. Ancient Gondwana break‐up explains the distribution of the mycoheterotrophic family Corsiaceae (Liliales). J Biogeogr. 2015;42:1123–36.
Article
Google Scholar
Hand ML, Spangenberg GC, Forster JW, Cogan NO. Plastome sequence determination and comparative analysis for members of the Lolium-Festuca grass species complex. G3 (Bethsada). 2013;3:607–16.
Article
CAS
Google Scholar
Kato T, Kaneko T, Sato S, Nakamura Y, Tabata S. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 2000;7:323–30.
Article
CAS
PubMed
Google Scholar
Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics. 2007;8:174.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, et al. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet. 1989;217:185–94.
Article
CAS
PubMed
Google Scholar
Kim KJ, Lee HL. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 2004;11:247–61.
Article
CAS
PubMed
Google Scholar
Young HA, Lanzatella CL, Sarath G, Tobias CM. Chloroplast genome variation in upland and lowland switchgrass. PLoS One. 2011;6, e23980.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kumar S, Hahn FM, McMahan CM, Cornish K, Whalen MC. Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines. BMC Plant Biol. 2009;9:131.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK. The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol. 2006;23:2175–90.
Article
CAS
PubMed
Google Scholar
Jeong YM, Chung WH, Mun JH, Kim N, Yu HJ. De novo assembly and characterization of the complete chloroplast genome of radish (Raphanus sativus L.). Gene. 2014;551:39–48.
Article
CAS
PubMed
Google Scholar
Rivarola M, Foster JT, Chan AP, Williams AL, Rice DW, Liu X, et al. Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One. 2011;6, e21743.
Article
CAS
PubMed
PubMed Central
Google Scholar
Calsa Junior T, Carraro DM, Benatti MR, Barbosa AC, Kitajima JP, Carrer H. Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr Genet. 2004;46:366–73.
Article
CAS
PubMed
Google Scholar
Qian J, Song J, Gao H, Zhu Y, Xu J, Pang X, et al. The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One. 2013;8, e57607.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yi DK, Kim KJ. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS One. 2012;7, e35872.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chung HJ, Jung JD, Park HW, Kim JH, Cha HW, Min SR, et al. The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep. 2006;25:1369–79.
Article
CAS
PubMed
Google Scholar
Schmitz-Linneweber C, Maier RM, Alcaraz JP, Cottet A, Herrmann RG, Mache R. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol Biol. 2001;45:307–15.
Article
CAS
PubMed
Google Scholar
Yi DK, Yang JC, So S, Joo M, Kim DK, Shin CH, et al. The complete plastid genome sequence of Abies koreana (Pinaceae: Abietoideae). Mitochondrial DNA. 2016;27:2351–3.
PubMed
Google Scholar
Yao X, Tang P, Li Z, Li D, Liu Y, Huang H. The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis. PLoS One. 2015;10, e0129347.
Article
PubMed
PubMed Central
Google Scholar
Hsu CY, Wu CS, Chaw SM. Ancient nuclear plastid DNA in the yew family (Taxaceae). Genome Biol Evol. 2014;6:2111–21.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ruhsam M, Rai HS, Mathews S, Ross TG, Graham SW, Raubeson LA, et al. Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria? Mol Ecol Resour. 2015;15:1067–78.
Article
CAS
PubMed
Google Scholar
Ma J, Yang B, Zhu W, Sun L, Tian J, Wang X. The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms. Gene. 2013;528:120–31.
Article
CAS
PubMed
Google Scholar
Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol. 2007;45:547–63.
Article
CAS
PubMed
Google Scholar
Wu CS, Chaw SM. Highly rearranged and size-variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers. Plant Biotechnol J. 2014;12:344–53.
Article
CAS
PubMed
Google Scholar
Shi C, Liu Y, Huang H, Xia EH, Zhang HB, Gao LZ. Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms. PLoS One. 2013;8, e59620.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang H, Shi C, Liu Y, Mao SY, Gao LZ. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evol Biol. 2014;14:151.
Article
PubMed
PubMed Central
Google Scholar
Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM. Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biol Evol. 2010;2:504–17.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu CS, Wang YN, Hsu CY, Lin CP, Chaw SM. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol Evol. 2011;3:1284–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Male PJ, Bardon L, Besnard G, Coissac E, Delsuc F, Engel J, et al. Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family. Mol Ecol Resour. 2014;14:966–75.
CAS
PubMed
Google Scholar
Huang YY, Matzke AJ, Matzke M. Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera). PLoS One. 2013;8, e74736.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, et al. Chloroplast genome analysis of Australian eucalypts--Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Mol Phylogenet Evol. 2013;69:704–16.
Article
CAS
PubMed
Google Scholar
Hirao T, Watanabe A, Kurita M, Kondo T, Takata K. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol. 2008;8:70.
Article
PubMed
PubMed Central
CAS
Google Scholar
Uthaipaisanwong P, Chanprasert J, Shearman JR, Sangsrakru D, Yoocha T, Jomchai N, et al. Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.). Gene. 2012;500:172–80.
Article
CAS
PubMed
Google Scholar
Steane D, Jones R, Vaillancourt R. A set of chloroplast microsatellite primers for Eucalyptus (Myrtaceae). Mol Ecol Notes. 2005;5:538–41.
Article
CAS
Google Scholar
Tangphatsornruang S, Uthaipaisanwong P, Sangsrakru D, Chanprasert J, Yoocha T, Jomchai N, Tragoonrung S. Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene. 2011;475:104–12.
Article
CAS
PubMed
Google Scholar
Lee HL, Jansen RK, Chumley TW, Kim KJ. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 2007;24:1161–80.
Article
CAS
PubMed
Google Scholar
Asif MH, Mantri SS, Sharma A, Srivastava A, Trivedi I, Gupta P, et al. Complete sequence and organisation of the Jatropha curcas (Euphorbiaceae) chloroplast genome. Tree Genet Genomes. 2010;6:941–52.
Article
Google Scholar
Guo W, Grewe F, Cobo-Clark A, Fan W, Duan Z, Adams RP, et al. Predominant and substoichiometric isomers of the plastid genome coexist within Juniperus plants and have shifted multiple times during cupressophyte evolution. Genome Biol Evol. 2014;6:580–90.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, de Pamphilis CW, et al. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol. 2006;6:77.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chen J, Hao Z, Xu H, Yang L, Liu G, Sheng Y, et al. The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng. Front Plant Sci. 2015;6:447.
PubMed
PubMed Central
Google Scholar
Ravi V, Khurana JP, Tyagi AK, Khurana P. The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet Genomes. 2006;3:49–59.
Article
Google Scholar
Straub SC, Moore MJ, Soltis PS, Soltis DE, Liston A, Livshultz T. Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Mol Phylogenet Evol. 2014;80:169–85.
Article
PubMed
Google Scholar
Besnard G, Hernández P, Khadari B, Dorado G, Savolainen V. Genomic profiling of plastid DNA variation in the Mediterranean olive tree. BMC Plant Biol. 2011;11:80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, et al. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One. 2010;5, e12762.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fang MF, Wang YJ, Zu YM, Dong WL, Wang RN, Deng TT, Li ZH. The complete chloroplast genome of the Taiwan red pine Pinus taiwanensis (Pinaceae). Mitochondrial DNA. 2016;27:2732–3.
Article
PubMed
CAS
Google Scholar
Vieira Ldo N, Faoro H, Rogalski M, Fraga HP, Cardoso RL, de Souza EM, et al. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection. PLoS One. 2014;9, e90618.
Article
PubMed
Google Scholar
Okumura S, Sawada M, Park YW, Hayashi T, Shimamura M, Takase H, Tomizawa K. Transformation of poplar (Populus alba) plastids and expression of foreign proteins in tree chloroplasts. Transgenic Res. 2006;15:637–46.
Article
CAS
PubMed
Google Scholar
Wang S, Shi C, Gao LZ. Plastid genome sequence of a wild woody oil species, Prinsepia utilis, provides insights into evolutionary and mutational patterns of Rosaceae chloroplast genomes. PLoS One. 2013;8, e73946.
Article
CAS
PubMed
PubMed Central
Google Scholar
Terakami S, Matsumura Y, Kurita K, Kanamori H, Katayose Y, Yamamoto T, Katayama H. Complete sequence of the chloroplast genome from pear (Pyrus pyrifolia): genome structure and comparative analysis. Tree Genet Genomes. 2012;8:841–54.
Article
Google Scholar
Alexander LW, Woeste KE. Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management. Tree Genet Genomes. 2014;10:803–12.
Article
Google Scholar
Yang B, Li M, Ma J, Fu Z, Xu X, Chen Q, et al. The complete chloroplast genome sequence of Sapindus mukorossi. Mitochondrial DNA. 2016;27:1825–6.
PubMed
Google Scholar
Fajardo D, Senalik D, Ames M, Zhu H, Steffan SA, Harbut R, et al. Complete plastid genome sequence of Vaccinium macrocarpon: structure, gene content, and rearrangements revealed by next generation sequencing. Tree Genet Genomes. 2013;9:489–98.
Article
Google Scholar
Yap JY, Rohner T, Greenfield A, Van Der Merwe M, McPherson H, Glenn W, et al. Complete chloroplast genome of the wollemi pine (Wollemia nobilis): structure and evolution. PLoS One. 2015;10, e0128126.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, et al. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot. 2005;92:142–66.
Article
CAS
PubMed
Google Scholar
Ruhlman TA, Rajasekaran K, Cary JW. Expression of chloroperoxidase from Pseudomonas pyrrocinia in tobacco plastids for fungal resistance. Plant Sci. 2014;228:98–106.
Article
CAS
PubMed
Google Scholar
Chakrabarti SK, Lutz KA, Lertwiriyawong B, Svab Z, Maliga P. Expression of the cry9Aa2 B.t. gene in tobacco chloroplasts confers resistance to potato tuber moth. Transgenic Res. 2006;15:481–8.
Article
CAS
PubMed
Google Scholar
DeGray G, Rajasekaran K, Smith F, Sanford J, Daniell H. Expression of an antimicrobial peptide via the chloroplast genome to control phytopathogenic bacteria and fungi. Plant Physiol. 2001;127:852–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen PJ, Senthilkumar R, Jane WN, He Y, Tian Z, Yeh KW. Transplastomic Nicotiana benthamiana plants expressing multiple defence genes encoding protease inhibitors and chitinase display broad-spectrum resistance against insects, pathogens and abiotic stresses. Plant Biotechnol J. 2014;12:503–15.
Article
CAS
PubMed
Google Scholar
Wang YP, Wei ZY, Zhang YY, Lin CJ, Zhong XF, Wang YL, et al. Chloroplast-expressed MSI-99 in tobacco improves disease resistance and displays inhibitory effect against rice blast fungus. Int J Mol Sci. 2015;16:4628–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
McBride KE, Svab Z, Schaaf DJ, Hogan PS, Stalker DM, Maliga P. Amplification of a chimeric Bacillus gene in chloroplasts leads to an extraordinary level of an insecticidal protein in tobacco. Biotechnology (N Y). 1995;13:362–5.
Article
CAS
Google Scholar
Kota M, Daniell H, Varma S, Garczynski SF, Gould F, Moar WJ. Overexpression of the Bacillus thuringiensis (Bt) Cry2Aa2 protein in chloroplasts confers resistance to plants against susceptible and Bt-resistant insects. Proc Natl Acad Sci U S A. 1999;96:1840–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee SB, Kwon HB, Kwon SJ, Park SC, Jeong MJ, Han SE, et al. Accumulation of trehalose within transgenic chloroplasts confers drought tolerance. Mol Breeding. 2003;11:1–13.
Article
CAS
Google Scholar
Ruiz ON, Hussein HS, Terry N, Daniell H. Phytoremediation of organomercurial compounds via chloroplast genetic engineering. Plant Physiol. 2003;132:1344–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruiz ON, Alvarez D, Torres C, Roman L, Daniell H. Metallothionein expression in chloroplasts enhances mercury accumulation and phytoremediation capability. Plant Biotechnol J. 2011;9:609–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lutz KA, Knapp JE, Maliga P. Expression of bar in the plastid genome confers herbicide resistance. Plant Physiol. 2001;125:1585–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ye GN, Hajdukiewicz PT, Broyles D, Rodriguez D, Xu CW, Nehra N, Staub JM. Plastid-expressed 5-enolpyruvylshikimate-3-phosphate synthase genes provide high level glyphosate tolerance in tobacco. Plant J. 2001;25:261–70.
Article
CAS
PubMed
Google Scholar
Shimizu M, Goto M, Hanai M, Shimizu T, Izawa N, Kanamoto H, et al. Selectable tolerance to herbicides by mutated acetolactate synthase genes integrated into the chloroplast genome of tobacco. Plant Physiol. 2008;147:1976–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iamtham S, Day A. Removal of antibiotic resistance genes from transgenic tobacco plastids. Nat Biotechnol. 2000;18:1172–6.
Article
CAS
PubMed
Google Scholar
Dufourmantel N, Dubald M, Matringe M, Canard H, Garcon F, Job C, et al. Generation and characterization of soybean and marker-free tobacco plastid transformants over-expressing a bacterial 4-hydroxyphenylpyruvate dioxygenase which provides strong herbicide tolerance. Plant Biotechnol J. 2007;5:118–33.
Article
CAS
PubMed
Google Scholar
Fouad WM, Altpeter F. Transplastomic expression of bacterial L-aspartate-alpha-decarboxylase enhances photosynthesis and biomass production in response to high temperature stress. Transgenic Res. 2009;18:707–18.
Article
CAS
PubMed
Google Scholar
Lu Y, Rijzaani H, Karcher D, Ruf S, Bock R. Efficient metabolic pathway engineering in transgenic tobacco and tomato plastids with synthetic multigene operons. Proc Natl Acad Sci U S A. 2013;110:E623–32.
Article
PubMed
PubMed Central
Google Scholar
Ruiz ON, Daniell H. Engineering cytoplasmic male sterility via the chloroplast genome by expression of beta-ketothiolase. Plant Physiol. 2005;138:1232–46.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yabuta Y, Tanaka H, Yoshimura S, Suzuki A, Tamoi M, Maruta T, Shigeoka S. Improvement of vitamin E quality and quantity in tobacco and lettuce by chloroplast genetic engineering. Transgenic Res. 2013;22:391–402.
Article
CAS
PubMed
Google Scholar
Harada H, Maoka T, Osawa A, Hattan J, Kanamoto H, Shindo K, et al. Construction of transplastomic lettuce (Lactuca sativa) dominantly producing astaxanthin fatty acid esters and detailed chemical analysis of generated carotenoids. Transgenic Res. 2014;23:303–15.
Article
CAS
PubMed
Google Scholar
Pengelly JJ, Forster B, von Caemmerer S, Badger MR, Price GD, Whitney SM. Transplastomic integration of a cyanobacterial bicarbonate transporter into tobacco chloroplasts. J Exp Bot. 2014;65:3071–80.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanz-Barrio R, Corral-Martinez P, Ancin M, Segui-Simarro JM, Farran I. Overexpression of plastidial thioredoxin f leads to enhanced starch accumulation in tobacco leaves. Plant Biotechnol J. 2013;11:618–27.
Article
CAS
PubMed
Google Scholar
Elghabi Z, Karcher D, Zhou F, Ruf S, Bock R. Optimization of the expression of the HIV fusion inhibitor cyanovirin-N from the tobacco plastid genome. Plant Biotechnol J. 2011;9:599–608.
Article
CAS
PubMed
Google Scholar
Agrawal P, Verma D, Daniell H. Expression of Trichoderma reesei beta-mannanase in tobacco chloroplasts and its utilization in lignocellulosic woody biomass hydrolysis. PLoS One. 2011;6, e29302.
Article
CAS
PubMed
PubMed Central
Google Scholar
Verma D, Jin S, Kanagaraj A, Singh ND, Daniel J, Kolattukudy PE, et al. Expression of fungal cutinase and swollenin in tobacco chloroplasts reveals novel enzyme functions and/or substrates. PLoS One. 2013;8, e57187.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saxena B, Subramaniyan M, Malhotra K, Bhavesh NS, Potlakayala SD, Kumar S. Metabolic engineering of chloroplasts for artemisinic acid biosynthesis and impact on plant growth. J Biosci. 2014;39:33–41.
Article
CAS
PubMed
Google Scholar
Yu LX, Gray BN, Rutzke CJ, Walker LP, Wilson DB, Hanson MR. Expression of thermostable microbial cellulases in the chloroplasts of nicotine-free tobacco. J Biotechnol. 2007;131:362–9.
Article
CAS
PubMed
Google Scholar
Petersen K, Bock R. High-level expression of a suite of thermostable cell wall-degrading enzymes from the chloroplast genome. Plant Mol Biol. 2011;76:311–21.
Article
CAS
PubMed
Google Scholar
Arai Y, Shikanai T, Doi Y, Yoshida S, Yamaguchi I, Nakashita H. Production of polyhydroxybutyrate by polycistronic expression of bacterial genes in tobacco plastid. Plant Cell Physiol. 2004;45:1176–84.
Article
CAS
PubMed
Google Scholar
Hasunuma T, Miyazawa SI, Yoshimura S, Shinzaki Y, Tomizawa KI, Shindo K, et al. Biosynthesis of astaxanthin in tobacco leaves by transplastomic engineering. Plant J. 2008;55:857–68.
Article
CAS
PubMed
Google Scholar
Nakahira Y, Ishikawa K, Tanaka K, Tozawa Y, Shiina T. Overproduction of hyperthermostable beta-1,4-endoglucanase from the archaeon Pyrococcus horikoshii by tobacco chloroplast engineering. Biosci Biotechnol Biochem. 2013;77:2140–3.
Article
CAS
PubMed
Google Scholar
Sherman A, Su J, Lin S, Wang X, Herzog RW, Daniell H. Suppression of inhibitor formation against FVIII in a murine model of hemophilia A by oral delivery of antigens bioencapsulated in plant cells. Blood. 2014;124:1659–68.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanz-Barrio R, Fernandez-San Millan A, Corral-Martinez P, Segui-Simarro JM, Farran I. Tobacco plastidial thioredoxins as modulators of recombinant protein production in transgenic chloroplasts. Plant Biotechnol J. 2011;9:639–50.
Article
CAS
PubMed
Google Scholar
Farran I, McCarthy-Suarez I, Rio-Manterola F, Mansilla C, Lasarte JJ, Mingo-Castel AM. The vaccine adjuvant extra domain A from fibronectin retains its proinflammatory properties when expressed in tobacco chloroplasts. Planta. 2010;231:977–90.
Article
CAS
PubMed
Google Scholar
Boyhan D, Daniell H. Low-cost production of proinsulin in tobacco and lettuce chloroplasts for injectable or oral delivery of functional insulin and C-peptide. Plant Biotechnol J. 2011;9:585–98.
Article
CAS
PubMed
Google Scholar
Fernandez-San Millan A, Mingo-Castel A, Miller M, Daniell H. A chloroplast transgenic approach to hyper-express and purify human serum albumin, a protein highly susceptible to proteolytic degradation. Plant Biotechnol J. 2003;1:71–9.
Article
CAS
PubMed
Google Scholar
Daniell H, Ruiz G, Denes B, Sandberg L, Langridge W. Optimization of codon composition and regulatory elements for expression of human insulin like growth factor-1 in transgenic chloroplasts and evaluation of structural identity and function. BMC Biotechnol. 2009;9:33.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang X, Su J, Sherman A, Rogers GL, Liao G, Hoffman BE, et al. Plant-based oral tolerance to hemophilia therapy employs a complex immune regulatory response including LAP+CD4+ T cells. Blood. 2015;125:2418–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Su J, Sherman A, Doerfler PA, Byrne BJ, Herzog RW, Daniell H. Oral delivery of Acid Alpha Glucosidase epitopes expressed in plant chloroplasts suppresses antibody formation in treatment of Pompe mice. Plant Biotechnol J. 2015;13:1023–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Youm JW, Jeon JH, Kim H, Min SR, Kim MS, Joung H, et al. High-level expression of a human beta-site APP cleaving enzyme in transgenic tobacco chloroplasts and its immunogenicity in mice. Transgenic Res. 2010;19:1099–108.
Article
CAS
PubMed
Google Scholar
Arlen PA, Falconer R, Cherukumilli S, Cole A, Cole AM, Oishi KK, Daniell H. Field production and functional evaluation of chloroplast-derived interferon-alpha2b. Plant Biotechnol J. 2007;5:511–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruhlman T, Ahangari R, Devine A, Samsam M, Daniell H. Expression of cholera toxin B-proinsulin fusion protein in lettuce and tobacco chloroplasts--oral administration protects against development of insulitis in non-obese diabetic mice. Plant Biotechnol J. 2007;5:495–510.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leelavathi S, Reddy VS. Chloroplast expression of His-tagged GUS-fusions: a general strategy to overproduce and purify foreign proteins using transplastomic plants as bioreactors. Mol Breeding. 2003;11:49–58.
Article
CAS
Google Scholar
Lim S, Ashida H, Watanabe R, Inai K, Kim YS, Mukougawa K, et al. Production of biologically active human thioredoxin 1 protein in lettuce chloroplasts. Plant Mol Biol. 2011;76:335–44.
Article
CAS
PubMed
Google Scholar
Nadai M, Bally J, Vitel M, Job C, Tissot G, Botterman J, Dubald M. High-level expression of active human alpha1-antitrypsin in transgenic tobacco chloroplasts. Transgenic Res. 2009;18:173–83.
Article
CAS
PubMed
Google Scholar
Gisby MF, Mellors P, Madesis P, Ellin M, Laverty H, O'Kane S, et al. A synthetic gene increases TGF beta 3 accumulation by 75-fold in tobacco chloroplasts enabling rapid purification and folding into a biologically active molecule. Plant Biotechnol J. 2011;9:618–28.
Article
CAS
PubMed
Google Scholar
Farran I, Rio-Manterola F, Iniguez M, Garate S, Prieto J, Mingo-Castel AM. High-density seedling expression system for the production of bioactive human cardiotrophin-1, a potential therapeutic cytokine, in transgenic tobacco chloroplasts. Plant Biotechnol J. 2008;6:516–27.
Article
CAS
PubMed
Google Scholar
Staub JM, Garcia B, Graves J, Hajdukiewicz PT, Hunter P, Nehra N, et al. High-yield production of a human therapeutic protein in tobacco chloroplasts. Nat Biotechnol. 2000;18:333–8.
Article
CAS
PubMed
Google Scholar
Oey M, Lohse M, Scharff LB, Kreikemeyer B, Bock R. Plastid production of protein antibiotics against pneumonia via a new strategy for high-level expression of antimicrobial proteins. Proc Natl Acad Sci U S A. 2009;106:6579–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koya V, Moayeri M, Leppla SH, Daniell H. Plant-based vaccine: mice immunized with chloroplast-derived anthrax protective antigen survive anthrax lethal toxin challenge. Infect Immun. 2005;73:8266–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Watson J, Koya V, Leppla SH, Daniell H. Expression of Bacillus anthracis protective antigen in transgenic chloroplasts of tobacco, a non-food/feed crop. Vaccine. 2004;22:4374–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Millan AFS, Ortigosa SM, Hervas-Stubbs S, Corral-Martinez P, Segui-Simarro JM, Gaetan J, et al. Human papillomavirus L1 protein expressed in tobacco chloroplasts self-assembles into virus-like particles that are highly immunogenic. Plant Biotechnol J. 2008;6:427–41.
Article
CAS
Google Scholar
Yacono MD, Farran I, Becher ML, Sander V, Sanchez VR, Martin V, et al. A chloroplast-derived Toxoplasma gondii GRA4 antigen used as an oral vaccine protects against toxoplasmosis in mice. Plant Biotechnol J. 2012;10:1136–44.
Article
CAS
Google Scholar
Kolotilin I, Kaldis A, Devriendt B, Joensuu J, Cox E, Menassa R. Production of a subunit vaccine candidate against porcine post-weaning diarrhea in high-biomass transplastomic tobacco. Plos One. 2012;7, e42405.
Article
CAS
PubMed
PubMed Central
Google Scholar
Arlen PA, Singleton M, Adamovicz JJ, Ding Y, Davoodi-Semiromi A, Daniell H. Effective plague vaccination via oral delivery of plant cells expressing F1-V antigens in chloroplasts. Infect Immun. 2008;76:3640–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Molina A, Hervas-Stubbs S, Daniell H, Mingo-Castel AM, Veramendi J. High-yield expression of a viral peptide animal vaccine in transgenic tobacco chloroplasts. Plant Biotechnol J. 2004;2:141–53.
Article
CAS
PubMed
Google Scholar
Lentz EM, Mozgovoj MV, Bellido D, Santos MJD, Wigdorovitz A, Bravo-Almonacid FF. VP8*antigen produced in tobacco transplastomic plants confers protection against bovine rotavirus infection in a suckling mouse model. J Biotechnol. 2011;156:100–7.
Article
CAS
PubMed
Google Scholar
Daniell H, Lee SB, Panchal T, Wiebe PO. Expression of the native cholera toxin B subunit gene and assembly as functional oligomers in transgenic tobacco chloroplasts. J Mol Biol. 2001;311:1001–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kang TJ, Loc NH, Jang MO, Jang YS, Kim YS, Seo JE, Yang MS. Expression of the B subunit of E. coli heat-labile enterotoxin in the chloroplasts of plants and its characterization. Transgenic Res. 2003;12:683–91.
Article
CAS
PubMed
Google Scholar
Chebolu S, Daniell H. Stable expression of Gal/GalNAc lectin of Entamoeba histolytica in transgenic chloroplasts and immunogenicity in mice towards vaccine development for amoebiasis. Plant Biotechnol J. 2007;5:230–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glenz K, Bouchon B, Stehle T, Wallich R, Simon MM, Warzecha H. Production of a recombinant bacterial lipoprotein in higher plant chloroplasts. Nat Biotechnol. 2006;24:76–7.
Article
CAS
PubMed
Google Scholar
Rosales-Mendoza S, Alpuche-Solis AG, Soria-Guerra RE, Moreno-Fierros L, Martinez-Gonzalez L, Herrera-Diaz A, Korban SS. Expression of an Escherichia coli antigenic fusion protein comprising the heat labile toxin B subunit and the heat stable toxin, and its assembly as a functional oligomer in transplastomic tobacco plants. Plant J. 2009;57:45–54.
Article
CAS
PubMed
Google Scholar
Soria-Guerra RE, Alpuche-Solis AG, Rosales-Mendoza S, Moreno-Fierros L, Bendik EM, Martinez-Gonzalez L, Korban SS. Expression of a multi-epitope DPT fusion protein in transplastomic tobacco plants retains both antigenicity and immunogenicity of all three components of the functional oligomer. Planta. 2009;229:1293–302.
Article
CAS
PubMed
Google Scholar
Rubio-Infante N, Govea-Alonso DO, Alpuche-Solis AG, Garcia-Hernandez AL, Soria-Guerra RE, Paz-Maldonado LMT, et al. A chloroplast-derived C4V3 polypeptide from the human immunodeficiency virus (HIV) is orally immunogenic in mice. Plant Mol Biol. 2012;78:337–49.
Article
CAS
PubMed
Google Scholar
Waheed MT, Thones N, Muller M, Hassan SW, Gottschamel J, Lossl E, et al. Plastid expression of a double-pentameric vaccine candidate containing human papillomavirus-16 L1 antigen fused with LTB as adjuvant: transplastomic plants show pleiotropic phenotypes. Plant Biotechnol J. 2011;9:651–60.
Article
CAS
PubMed
Google Scholar
Gonzalez-Rabade N, McGowan EG, Zhou F, McCabe MS, Bock R, Dix PJ, et al. Immunogenicity of chloroplast-derived HIV-1 p24 and a p24-Nef fusion protein following subcutaneous and oral administration in mice. Plant Biotechnol J. 2011;9:629–38.
Article
CAS
PubMed
Google Scholar
Zhou YX, Lee MYT, Ng JMH, Chye ML, Yip WK, Zee SY, Lam E. A truncated hepatitis E virus ORF2 protein expressed in tobacco plastids is immunogenic in mice. World J Gastroenterol. 2006;12:306–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shao HB, He DM, Qian KX, Shen GF, Su ZL. The expression of classical swine fever virus structural protein E2 gene in tobacco chloroplasts for applying chloroplasts as bioreactors. C R Biol. 2008;331:179–84.
Article
CAS
PubMed
Google Scholar
Tregoning JS, Nixon P, Kuroda H, Svab Z, Clare S, Bowe F, et al. Expression of tetanus toxin Fragment C in tobacco chloroplasts. Nucleic Acids Res. 2003;31:1174–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morgenfeld M, Lentz E, Segretin ME, Alfano EF, Bravo-Almonacid F. Translational fusion and redirection to thylakoid lumen as strategies to enhance accumulation of human papillomavirus E7 antigen in tobacco chloroplasts. Mol Biotechnol. 2014;56:1021–31.
Article
CAS
PubMed
Google Scholar