Burns DM, Horn V, Paluh J, Yanofsky C. Evolution of the tryptophan synthetase of fungi. Analysis of experimentally fused Escherichia coli tryptophan synthetase alpha and beta chains. J Biol Chem. 1990;265(4):2060–9. https://doi.org/10.1016/S0021-9258(19)39940-5.
Article
CAS
PubMed
Google Scholar
Lang D, Thoma R, Henn-Sax M, Sterner R, Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science. 2000;289(5484):1546–50. https://doi.org/10.1126/science.289.5484.1546.
Article
CAS
PubMed
Google Scholar
Chen SD, Krinsky BH, Long MY: New genes as drivers of phenotypic evolution(vol 14, pg 645, 2013). Nat Rev Genet 2013, 14:745-745.
Long MY, VanKuren NW, Chen SD, Vibranovski MD. New gene evolution: little did we know. Annu Rev Genet. 2013;47:307–33.
Article
CAS
Google Scholar
Long MY: A new function evolved from gene fusion. Genome Res 2001, 11:308-308, 11, 1657, DOI: https://doi.org/10.1101/gr.165700.
Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, et al. Transcription-mediated gene fusion in the human genome. Genome Res. 2006;16(1):30–6. https://doi.org/10.1101/gr.4137606.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rogers RL, Bedford T, Hardl DL. Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics. 2009;181(1):313–22. https://doi.org/10.1534/genetics.108.091538.
Article
CAS
PubMed
PubMed Central
Google Scholar
Snel B, Bork P, Huynen M. Genome evolution - gene fusion versus gene fission. Trends Genet. 2000;16(1):9–11. https://doi.org/10.1016/S0168-9525(99)01924-1.
Article
CAS
PubMed
Google Scholar
Thomson TM, Lozano JJ, Loukili N, Carrio R, Serras F, Cormand B, et al. Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res. 2000;10(11):1743–56. https://doi.org/10.1101/gr.GR-1405R.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Lu SJ, Zhao SQ, Zheng XF, Long MY, Wei LP. Positive selection for the male functionality of a co-retroposed gene in the hominoids. BMC Evol Biol. 2009;9(1). https://doi.org/10.1186/1471-2148-9-252.
Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, et al. Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res. 2006;16(1):37–44. https://doi.org/10.1101/gr.4145906.
Article
CAS
PubMed
PubMed Central
Google Scholar
Goodstadt L, Ponting CP. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol. 2006;2(9):e133. https://doi.org/10.1371/journal.pcbi.0020133.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rogers RL, Hartl DL. Chimeric genes as a source of rapid evolution in Drosophila melanogaster. Mol Biol Evol. 2012;29(2):517–29. https://doi.org/10.1093/molbev/msr184.
Article
CAS
PubMed
Google Scholar
Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, et al. On the origin of new genes in Drosophila. Genome Res. 2008;18(9):1446–55. https://doi.org/10.1101/gr.076588.108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang CJ, Wang J, Marowsky NC, Long MY, Wing RA, Fan CZ. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biol Evol. 2013;5(5):1038–48. https://doi.org/10.1093/gbe/evt071.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang YE, Landback P, Vibranovski M, Long MY. New genes expressed in human brains: implications for annotating evolving genomes. Bioessays. 2012;34(11):982–91. https://doi.org/10.1002/bies.201200008.
Article
CAS
PubMed
Google Scholar
Tang L, Zou XH, Achoundong G, Potgieter C, Second G, Zhang DY, et al. Phylogeny and biogeography of the rice tribe (Oryzeae): evidence from combined analysis of 20 chloroplast fragments. Mol Phylogenet Evol. 2010;54(1):266–77. https://doi.org/10.1016/j.ympev.2009.08.007.
Article
CAS
PubMed
Google Scholar
Wang XY, Shi XL, Hao BL, Ge S, Luo JC. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 2005;165(3):937–46. https://doi.org/10.1111/j.1469-8137.2004.01293.x.
Article
CAS
PubMed
Google Scholar
Ma JX, Bennetzen JL. Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A. 2004;101(34):12404–10. https://doi.org/10.1073/pnas.0403715101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, et al. Domestication history and geographical adaptation inferred from a SNP map of African rice. Nat Genet. 2016;48(9):1083–8. https://doi.org/10.1038/ng.3633.
Article
CAS
PubMed
Google Scholar
Kaessmann H, Vinckenbosch N, Long MY. RNA-based gene duplication: mechanistic and evolutionary insights. Nat Rev Genet. 2009;10(1):19–31. https://doi.org/10.1038/nrg2487.
Article
CAS
PubMed
PubMed Central
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10(1):421. https://doi.org/10.1186/1471-2105-10-421.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vinckenbosch N, Dupanloup I, Kaessmann H. Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A. 2006;103(9):3220–5. https://doi.org/10.1073/pnas.0511307103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet. 2018;50(2):285–96. https://doi.org/10.1038/s41588-018-0040-0.
Article
CAS
PubMed
Google Scholar
Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5(7):621–8. https://doi.org/10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Zhang L, Ren Y, Yang T, Li G, Chen J, Gschwend AR, et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol. 2019;3(4):679–90. https://doi.org/10.1038/s41559-019-0822-5.
Article
PubMed
Google Scholar
Prince VE, Pickett FB. Splitting pairs: The diverging fates of duplicated genes. Nat Rev Genet. 2002;3(11):827–37. https://doi.org/10.1038/nrg928.
Article
CAS
PubMed
Google Scholar
Betran E, Thornton K, Long M. Retroposed new genes out of the X in Drosophila. Genome Res. 2002;12(12):1854–9. https://doi.org/10.1101/gr.604902.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vibranovski MD, Lopes HF, Karr TL, Long MY. Stage-specific expression profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives genomic relocation of testis-expressed genes. Plos Genet. 2009;5(11):e1000731. https://doi.org/10.1371/journal.pgen.1000731.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marques AC, Dupanloup I, Vinckenbosch N, Reymond A, Kaessmann H. Emergence of young human genes after a burst of retroposition in primates. Plos Biol. 2005;3(11):1970–9. https://doi.org/10.1371/journal.pbio.0030357.
Article
CAS
Google Scholar
Khodarahmpour Z. Effect of drought stress induced by polyethylene glycol (PEG) on germination indices in corn (Zea mays L.) hybrids. African J Biotechnol. 2011;10(79):18222–7. https://doi.org/10.5897/AJB11.2639.
Article
CAS
Google Scholar
Queiroz MS, Oliveira CE, Steiner F, Zuffo AM, Zoz T, Vendruscolo EP, et al. Drought stresses on seed germination and early growth of maize and sorghum. J Agricult Sci. 2019;11(2):310–8. https://doi.org/10.5539/jas.v11n2p310.
Article
Google Scholar
Wang W, Yu H, Long M. Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat Genet. 2004;36(5):523–7. https://doi.org/10.1038/ng1338.
Article
CAS
PubMed
Google Scholar
Wang W, Lan H. Rapid and parallel chromosomal number reductions in Muntjac deer inferred from mitochondrial DNA phylogeny. Mol Biol Evol. 2000;17(9):1326–33. https://doi.org/10.1093/oxfordjournals.molbev.a026416.
Article
CAS
PubMed
Google Scholar
Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, et al. FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol. 2010;11(10):R104. https://doi.org/10.1186/gb-2010-11-10-r104.
Article
CAS
PubMed
PubMed Central
Google Scholar
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol. 2011;7(5):e1001138. https://doi.org/10.1371/journal.pcbi.1001138.
Article
CAS
PubMed
PubMed Central
Google Scholar
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, et al. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res. 2011;39(15):e100. https://doi.org/10.1093/nar/gkr362.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang W, Zheng HK, Fan CZ, Li J, Shi JJ, Cai ZQ, et al. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell. 2006;18(8):1791–802. https://doi.org/10.1105/tpc.106.041905.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS. Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes. Genome Biology and Evolution. 2011;3:1357–68.
Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12(1). https://doi.org/10.1186/1471-2105-12-491.
Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, et al. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2014;164(2):513–24. https://doi.org/10.1104/pp.113.230144.
Article
CAS
PubMed
Google Scholar
Kaessmann H. Origins, evolution, and phenotypic impact of new genes. Genome Res. 2010;20(10):1313–26. https://doi.org/10.1101/gr.101386.109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Veltman MA, Flowers JM, van Andel TR, Schranz ME. Origins and geographic diversification of African rice (Oryza glaberrima). PLOS ONE. 2019;14(3):e0203508. https://doi.org/10.1371/journal.pone.0203508.
Article
CAS
PubMed
PubMed Central
Google Scholar
Semon M, Nielsen R, Jones MP, SR MC. The population structure of African cultivated rice Oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation. Genetics. 2005;169:1639–47. https://doi.org/10.1534/genetics.104.033175.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet. 2014;46(9):982–8. https://doi.org/10.1038/ng.3044.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nabholz B, Sarah G, Sabot F, Ruiz M, Adam H, Nidelet S, et al. Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (Oryza glaberrima). Mol Ecol. 2014;23(9):2210–27. https://doi.org/10.1111/mec.12738.
Article
CAS
PubMed
Google Scholar
Bai Y, Casola C, Feschotte C, Betran E. Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila. Genome Biol. 2007;8(1):R11. https://doi.org/10.1186/gb-2007-8-1-r11.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fu B, Chen M, Zou M, Long M, He S. The rapid generation of chimerical genes expanding protein diversity in zebrafish. BMC Genomics. 2010;11(1):657. https://doi.org/10.1186/1471-2164-11-657.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang CJ, Gschwend AR, Ouyang YD, Long MY. Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes. Plant Physiol. 2014;165(1):412–23. https://doi.org/10.1104/pp.113.231696.
Article
CAS
PubMed
PubMed Central
Google Scholar
Semon M, Wolfe KH. Consequences of genome duplication. Current Opinion in Genetics & Development. 2007;17(6):505–12. https://doi.org/10.1016/j.gde.2007.09.007.
Article
CAS
Google Scholar
Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nature Reviews Genetics. 2010;11(2):97–108. https://doi.org/10.1038/nrg2689.
Article
CAS
PubMed
Google Scholar
Arguello JR, Chen Y, Yang S, Wang W, Long M. Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. PLoS Genet. 2006;2(5):e77. https://doi.org/10.1371/journal.pgen.0020077.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bennetzen JL. Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev. 2005;15(6):621–7. https://doi.org/10.1016/j.gde.2005.09.010.
Article
CAS
PubMed
Google Scholar
Jiang N, Bao ZR, Zhang XY, Eddy SR, Wessler SR. Pack-MULE transposable elements mediate gene evolution in plants. Nature. 2004;431(7008):569–73. https://doi.org/10.1038/nature02953.
Article
CAS
PubMed
Google Scholar
Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet. 2005;37(9):997–1002. https://doi.org/10.1038/ng1615.
Article
CAS
PubMed
Google Scholar
Buljan M, Frankish A, Bateman A. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol. 2010;11(7):R74. https://doi.org/10.1186/gb-2010-11-7-r74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Williford A, Betrán E: Gene fusion. In eLS. John Wiley & Sons, Ltd; 2013, Gene Fusion
Yang SA, Arguello JR, Li X, Ding Y, Zhou Q, Chen Y, et al. Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. Plos Genet. 2008;4(1):e3. https://doi.org/10.1371/journal.pgen.0040003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang Y, Chen J, Dong C, Sosa D, Xia S, Ouyang Y, et al. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. Plant Cell. 2021;34(2):802–17. https://doi.org/10.1093/plcell/koab291.
Article
PubMed Central
Google Scholar
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–11. https://doi.org/10.1093/bioinformatics/btp120.
Article
CAS
PubMed
PubMed Central
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511–U174. https://doi.org/10.1038/nbt.1621.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, et al. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010;463(7282):763–8. https://doi.org/10.1038/nature08747.
Article
CAS
Google Scholar
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR: The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 2007, 35:D883-D887, Database, DOI: https://doi.org/10.1093/nar/gkl976.
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 2013;6(1). https://doi.org/10.1186/1939-8433-6-4.
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang C, Iwamoto M, Abe T, et al: Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol 2013, 54:E6-+.
Gao ZY, Zhao SC, He WM, Guo LB, Peng YL, Wang JJ, et al. Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Proc Natl Acad Sci U S A. 2013;110(35):14492–7. https://doi.org/10.1073/pnas.1306579110.
Article
PubMed
PubMed Central
Google Scholar
Lamesch P, Berardini TZ, Li DH, Swarbreck D, Wilks C, Sasidharan R, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40(D1):D1202–10. https://doi.org/10.1093/nar/gkr1090.
Article
CAS
PubMed
Google Scholar
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457(7229):551–6. https://doi.org/10.1038/nature07723.
Article
CAS
PubMed
Google Scholar
Schnable PS. The B73 maize genome: complexity, diversity, and dynamics (November, pg 1112, 2009). Science. 2012;337:1040.
CAS
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. https://doi.org/10.1101/gr.107524.110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang L, Xie WB, Chen Y, Tang WJ, Yang JY, Ye RJ, et al. A dynamic gene expression atlas covering the entire life cycle of rice. Plant J. 2010;61(5):752–66. https://doi.org/10.1111/j.1365-313X.2009.04100.x.
Article
CAS
PubMed
Google Scholar
Jain M. Genome-wide identification of novel internal control genes for normalization of gene expression during various stages of development in rice. Plant Sci. 2009;176(5):702–6. https://doi.org/10.1016/j.plantsci.2009.02.001.
Article
CAS
Google Scholar
Zhang C. Gene fusion as an important mechanism to generate new genes in the genus Oryza (GriffinDetector). Github. 2022; https://github.com/zhangcj2022/GriffinDetector.git.
Zhang C. Gene fusion as an important mechanism to generate new genes in the genus Oryza (GriffinDetector). Zenodo. 2022. https://doi.org/10.5281/zenodo.6480086.