The Amborellagenome: an evolutionary reference for plant biology
© BioMed Central Ltd 2008
Published: 10 March 2008
The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.
The origin and evolution of the angiosperms is one of the great terrestrial radiations and has had manifold effects on the global biota. Today, flowering plants generate the vast majority of human food, either directly or indirectly as animal feed, and account for a huge proportion of land-based photosynthesis and carbon sequestration. With a fossil record that extends back to just over 130 million years ago, flowering plants have diversified to include 250,000 to possibly 400,000 species occupying nearly every habitable terrestrial environment, and many aquatic ones. Understanding how angiosperms have accomplished this feat over a relatively short span of evolutionary time will elucidate many of the key processes underlying the assembly of Earth's plant/animal associations and entire ecosystems.
Many scientists have understood the importance of broad, comparative genome sequencing since the beginning of the Arabidopsis thaliana and rice (Oryyza sativa) genome sequencing projects [1–4]. Arabidopsis, a relative of cabbage, had already become the premier model for plant genetics, and half the world's dependence on rice for food makes that crop plant an important model for the genetic architecture of traits important to humanity. More recently, poplar (Populus trichocarpa), grapevine (Vitis vinifera) and papaya (Carica papaya) have been sequenced as genomic models for woody crop plants [5–12]. These advances have been motivated by the realization that understanding the structure and evolution of plant genomes would contribute to society through enhancements to agriculture and forestry .
Recent phylogenetic analyses [14, 15, 17, 22] have identified Amborella trichopoda, a large shrub known only from the island of New Caledonia, as the single 'sister species' to all other living flowering plants. Amborella therefore offers the unparalleled potential to 'root' analyses of all angiosperm features, from gene families to genome structure, and from physiology to morphology. Furthermore, as the branching-point for Amborella is situated 'between' gymnosperms and all other angiosperms, a genome sequence for Amborella would help characterize processes that distinguish these two lineages of extant seed plants. The nuclear genome sequence of Amborella would contribute uniquely to efforts to reconstruct characteristics of the 'ancestral angiosperm'. The importance of Amborella in this regard is already widely appreciated [19, 23]. Two recent papers, in fact, point specifically to basal angiosperms, including Amborella, as obvious choices for future nuclear genome sequencing efforts [24, 25].
In addition, two features of Amborella's truly extraordinary mitochondrial gen-ome raise compelling questions that warrant the sequencing of the Amborella nuclear genome. First, the Amborella mitochondrial genome is extraordinarily rich in 'foreign' genes acquired by horizontal gene transfer, far richer than any other plant mitochondrial genome . These foreign genes were acquired from a wide range of donors. These findings raise important questions that can best be addressed with a complete nuclear genome sequence. For instance, is the Amborella nuclear genome also exceptionally rich in foreign sequences, and were these sequences acquired from the same donors as the foreign mitochondrial sequences? The Amborella nuclear genome sequence will enable subsequent experiments to determine what roles, if any, foreign nuclear genes play in Amborella. Second, the Amborella mitochondrial genome is exceptionally large, and much of the extra DNA is of unknown origin (Rice DW, Richardson AO, Young GJ, Sanchez-Puerta MV, Zhang Y, CWD, Knox EB, Munzinger J, Boore J, JDP, unpublished observations). We suspect that much of this unknown DNA was probably acquired from Amborella's nuclear genome, a hypothesis that can only be tested once a complete nuclear sequence is available.
Given the available genomic infrastructure, the importance of Amborella as the sister to all other extant angiosperms, the large community of plant biologists who require a universal evolutionary reference for their studies, and the availability of cost-effective, ultra-high-throughput DNA sequencing technologies, it is our opinion that the Amborella genome is in an extremely strong position to warrant complete sequencing in the near future. Thus, the stage is set for a large-scale international Amborella genome sequencing initiative in support of fundamental and applied plant sciences, and we enthusiastically advocate such an endeavor.
This work was supported in part by NSF grant PGR-0638595, DBI-207202 and NIH grant RO1-GM-70612.
- Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408: 796-815. 10.1038/35048692.View ArticleGoogle Scholar
- The Arabidopsis Information Resource. [http://www.arabidopsis.org]
- International Rice Genome Sequencing Project: The map-based sequence of the rice genome. Nature. 2001, 441: 337-340.Google Scholar
- Rice Annotation Database. [http://rad.dna.affrc.go.jp]
- Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, et al: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006, 313: 1596-1604. 10.1126/science.1128691.PubMedView ArticleGoogle Scholar
- The International Populus Genome Consortium. [http://www.ornl.gov/sci/ipgc]
- JGI Populus trichocarpa v1.1. [http://genome.jgi-psf.org/Poptr1_1]
- Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyère C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, et al: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007, 449: 463-U465. 10.1038/nature06148.PubMedView ArticleGoogle Scholar
- International Grape Genome Program - IGGP. [http://www.vitaceae.org]
- Grape Genome Browser. [http://www.genoscope.cns.fr/externe/English/Projets/Projet_ML]
- Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, Malacarne G, Iliev D, Coppola G, Wardell B, Micheletti D, Macalma T, Facci M, Mitchell JT, Perazzolli M, Eldredge G, Gatto P, Oyzerski R, Moretto M, Gutin N, Stefanini M, Chen Y, Segala C, Davenport C, Demattè L, Mraz A, et al: A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE. 2007, 2: e1326-10.1371/journal.pone.0001326.PubMedPubMed CentralView ArticleGoogle Scholar
- Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang M-L, Zhu YJ, et al: The draft genome of the transgenic tropical fruit tree papaya (Carica papayaLinnaeus). Nature. Google Scholar
- Committee on Objectives for the National Plant Genome Initiative: 2003-2008 National Research Council: The National Plant Genome Initiative: Objectives for 2003-2008. 2002, Washington, DC, USA: National Academies PressGoogle Scholar
- Jansen RK, Cai Z, Raubeson LA, Daniell H, dePamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL: Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA. 2007, 104: 19369-19374. 10.1073/pnas.0709121104.PubMedPubMed CentralView ArticleGoogle Scholar
- Moore MJ, Bell CD, Soltis PS, Soltis DE: Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA. 2007, 104: 19363-19368. 10.1073/pnas.0708072104.PubMedPubMed CentralView ArticleGoogle Scholar
- Soltis DE, Soltis PS, Albert VA, Oppenheimer DG, dePamphilis CW, Ma H, Frohlich MW, Theissen G, Floral Genome Project Research Group: Missing links: the genetic architecture of flower and floral diversification. Trends Plant Sci. 2002, 7: 22-31. 10.1016/S1360-1385(01)02098-2.PubMedView ArticleGoogle Scholar
- Soltis DE, Soltis PS, Endress PK, Chase MW: Phylogeny and Evolution of Angiosperms. 2005, Sunderland, MA, USA: SinauerGoogle Scholar
- Williams JH, Friedman WE: Identification of diploid endosperm in an early angiosperm lineage. Nature. 2002, 415: 522-526. 10.1038/415522a.PubMedView ArticleGoogle Scholar
- Friedman WE: Embryological evidence for developmental lability during early angiosperm evolution. Nature. 2006, 441: 337-340. 10.1038/nature04690.PubMedView ArticleGoogle Scholar
- Duarte JM, Wall PK, Zahn LM, Soltis PS, Soltis DE, Leebens-Mack J, Ma H, Carlson JE, dePamphilis CW: Utility of Amborella trichopoda and Nuphar advenaESTs for phylogeny and comparative sequence analysis. Taxon. Google Scholar
- Committee on the National Plant Genome Initiative: Achievements and Future Directions, National Research Council. Achievements of the National Plant Genome Initiative and New Horizons in Plant Biology. 2008, Washington, DC, USA: National Academies Press, [http://www.nap.edu/catalog.php?record_id=12054]Google Scholar
- Soltis PS, Soltis DE, Chase MW: Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature. 1999, 402: 402-404. 10.1038/46528.PubMedView ArticleGoogle Scholar
- Fourquin C, Vinauger-Douard M, Fogliani B, Dumas C, Scutt CP: Evidence that CRABS CLAW and TOUSLED have conserved their roles in carpel development since the ancestor of the extant angiosperms. Proc Natl Acad Sci USA. 2005, 102: 4649-4654. 10.1073/pnas.0409577102.PubMedPubMed CentralView ArticleGoogle Scholar
- Pryer KM, Schneider H, Zimmer EA, Banks JA: Deciding among green plants for whole genome studies. Trends Plant Sci. 2002, 7: 550-554. 10.1016/S1360-1385(02)02375-0.PubMedView ArticleGoogle Scholar
- Jackson S, Rounsley S, Purugganan M: Comparative sequencing of plant genomes: choices to make. Plant Cell. 2006, 18: 1100-1104. 10.1105/tpc.106.042192.PubMedPubMed CentralView ArticleGoogle Scholar
- Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA, Ma H, dePamphilis CW: Widespread genome duplications throughout the history of flowering plants. Genome Res. 2006, 16: 738-749. 10.1101/gr.4825606.PubMedPubMed CentralView ArticleGoogle Scholar
- AMBORELLA. [http://www.amborella.org]
- Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD: Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA. 2004, 101: 17747-17752. 10.1073/pnas.0408336102.PubMedPubMed CentralView ArticleGoogle Scholar
- Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, Schlarbaum SE, Bliss BJ, Zhang X, Tanksley SD, Oppenheimer DG, Soltis PS, Ma H, dePamphilis CW, Leebens-Mack JH: Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol. 2005, 5: 5-10.1186/1471-2229-5-5.PubMedPubMed CentralView ArticleGoogle Scholar
- Soltis DE, Ma H, Frohlich MW, Soltis PS, Albert VA, Oppenheimer DG, Altman NS, dePamphilis C, Leebens-Mack J: The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends Plant Sci. 2007, 12: 358-367. 10.1016/j.tplants.2007.06.012.PubMedView ArticleGoogle Scholar
- Kim S, Yoo MJ, Albert VA, Farris JS, Soltis PS, Soltis DE: Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am J Bot. 2004, 91: 2102-2118. 10.3732/ajb.91.12.2102.PubMedView ArticleGoogle Scholar
- Kim S, Soltis PS, Wall K, Soltis DE: Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol. 2006, 23: 107-120. 10.1093/molbev/msj014.PubMedView ArticleGoogle Scholar
- Zahn LM, King HZ, Leebens-Mack JH, Kim S, Soltis PS, Landherr LL, Soltis DE, dePamphilis CW, Ma H: The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history. Genetics. 2005, 169: 2209-2223. 10.1534/genetics.104.037770.PubMedPubMed CentralView ArticleGoogle Scholar
- Yoo MJ, Albert VA, Soltis PS, Soltis DE: Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants. BMC Plant Biol. 2006, 6: 3-10.1186/1471-2229-6-3.PubMedPubMed CentralView ArticleGoogle Scholar