Nội dung được dịch bởi AI, chỉ mang tính chất tham khảo
Phân tích đa khía cạnh cung cấp ít bằng chứng cho việc sao chép toàn bộ genome lặp lại trong quá trình tiến hóa của hexapod
Tóm tắt
Các sự kiện sao chép gen đóng vai trò quan trọng trong sự tiến hóa và thích nghi của các sinh vật. Các gen bị sao chép có thể phát sinh qua nhiều cơ chế khác nhau, bao gồm việc sao chép toàn bộ genome (WGD). Gần đây, WGD được đề xuất là một yếu tố quan trọng thúc đẩy sự tiến hóa, cũng như ở động vật sáu chân. Ở đây, chúng tôi đã phân tích 20 bộ gen hexapod chất lượng cao bằng cách sử dụng các phân phối parenome toàn bộ về khoảng cách đồng nghĩa ước tính (KS), các mẫu đồng tuyến trong genome, và các phương pháp hòa giải cây gene-phân loại cây. Chúng tôi quan sát thấy có sự phong phú của các bản sao gene trong phần lớn các bộ gen hexapod này, nhưng chúng tôi lại phát hiện ít bằng chứng cho WGD. Phần lớn các bản sao gene dường như đã phát sinh từ các quá trình sao chép gene quy mô nhỏ. Chúng tôi đã phát hiện các sao chép đoạn trong sáu bộ gen, nhưng chúng thiếu dấu hiệu đồng tuyến trong genome thường liên quan đến WGD, và tuổi thọ của những sao chép này không trùng với các đỉnh cụ thể trong các phân phối KS. Hơn nữa, việc hòa giải cây gene với cây phân loại không hỗ trợ tất cả trừ một trong những WGD trước đó đã được giả thuyết. Do đó, các phân tích của chúng tôi cung cấp rất ít bằng chứng cho thấy WGD đã đóng vai trò quan trọng trong tiến hóa của hexapod và gợi ý rằng các cơ chế thay thế thúc đẩy các sự kiện sao chép gene trong nhóm động vật này. Ví dụ, chúng tôi đề xuất rằng, cùng với các sự kiện sao chép gene quy mô nhỏ, các giai đoạn tăng cường hoạt động của yếu tố di chuyển có thể là một nguồn quan trọng cho các bản sao gene ở hexapods.
Từ khóa
#sao chép gen #tiến hóa hexapod #genome toàn bộ #đặc điểm di truyền #hoạt động yếu tố di chuyểnTài liệu tham khảo
Ohno S, Wolf U, Atkin NB. Evolution from fish to mammals by gene duplication. Hereditas. 1967;59:169–87. https://doi.org/10.1111/j.1601-5223.1968.tb02169.x.
Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol. 2003;18:292–8. https://doi.org/10.1016/S0169-5347(03)00033-8.
De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y. Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana. Plant Cell. 2017;29:2786–800. https://doi.org/10.1105/TPC.17.00531.
Osborn TC, Chris Pires J, Birchler JA, Auger DL, Jeffery Chen Z, Lee H-S, et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 2003;19:141–7. https://doi.org/10.1016/S0168-9525(03)00015-5.
Crow KD, Wagner GP. What is the role of genome duplication in the evolution of complexity and diversity? Mol Biol Evol. 2006;23:887–92. https://doi.org/10.1093/molbev/msj083.
Yao Y, Carretero-Paulet L, Van de Peer Y. Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy. PLoS One. 2019;14:e0220257. https://doi.org/10.1371/journal.pone.0220257.
Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, Tank DC, et al. Impact of whole-genome duplication events on diversification rates in angiosperms. Am J Bot. 2018;105:348–63. https://doi.org/10.1002/ajb2.1060.
Tank DC, Eastman JM, Pennell MW, Soltis PS, Soltis DE, Hinchliff CE, et al. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. Source New Phytol. 2015;207:454–67. https://doi.org/10.2307/newphytologist.207.2.454.
Schranz ME, Mohammadin S, Edger PP. Ancient whole genome duplications, novelty and diversification: the WGD radiation lag-time model. Curr Opin Plant Biol. 2012;15:147–53. https://doi.org/10.1016/J.PBI.2012.03.011.
Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, et al. Recently formed polyploid plants diversify at lower rates. Science. 2011;333:1257. https://doi.org/10.1126/science.1207205.
Van de Peer Y, Maere S, Meyer A. The evolutionary significance of ancient genome duplications. Nat Rev Genet. 2009;10:725–32. https://doi.org/10.1038/nrg2600.
Mable BK. ‘Why polyploidy is rarer in animals than in plants’: myths and mechanisms. Biol J Linn Soc. 2004;82:453–66. https://doi.org/10.1111/j.1095-8312.2004.00332.x.
Muller HJ. Why polyploidy is rarer in animals than in plants. Am Nat. 1925;59:346–53. https://doi.org/10.1086/280047.
Orr HA. “Why polyploidy is rarer in animals than in plants”; revisited. Am Nat. 1990;136:759–70. https://doi.org/10.1086/285130.
Hallinan NM, Lindberg DR. Comparative analysis of chromosome counts infers three Paleopolyploidies in the Mollusca. Genome Biol Evol. 2011;3:1150–63. https://doi.org/10.1093/gbe/evr087.
Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, et al. Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity. 2016;116:190–9. https://doi.org/10.1038/hdy.2015.89.
Clarke TH, Garb JE, Hayashi CY, Arensburger P, Ayoub NA. Spider transcriptomes identify ancient large-scale gene duplication event potentially important in silk gland evolution. Genome Biol Evol. 2015;7:1856–70. https://doi.org/10.1093/gbe/evv110.
Li Z, Tiley GP, Galuska SR, Reardon CR, Kidder TI, Rundell RJ, et al. Multiple large-scale gene and genome duplications during the evolution of hexapods. Proc Natl Acad Sci U S A. 2018;115:4713–8. https://doi.org/10.1073/pnas.1710791115.
Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, et al. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol. 2017;15:62. https://doi.org/10.1186/s12915-017-0399-x.
Leite DJ, McGregor AP. Arthropod evolution and development: recent insights from chelicerates and myriapods. Curr Opin Genet Dev. 2016;39:93–100. https://doi.org/10.1016/J.GDE.2016.06.002.
Zwaenepoel A, Li Z, Lohaus R, Van de Peer Y. Finding evidence for whole genome duplications: a reappraisal. Mol Plant. 2019;12:133–6. https://doi.org/10.1016/J.MOLP.2018.12.019.
Zwaenepoel A, Van de Peer Y. Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates. Mol Biol Evol. 2019;36:1384–404. https://doi.org/10.1093/molbev/msz088.
Nakatani Y, McLysaght A. Macrosynteny analysis shows the absence of ancient whole-genome duplication in lepidopteran insects. Proc Natl Acad Sci U S A. 2019;116:1816–8. https://doi.org/10.1073/pnas.1817937116.
Vanneste K, Van de Peer Y, Maere S. Inference of genome duplications from age distributions revisited. Mol Biol Evol. 2013;30:177–90. https://doi.org/10.1093/molbev/mss214.
Tiley GP, Barker MS, Burleigh JG. Assessing the performance of Ks plots for detecting ancient whole genome duplications. Genome Biol Evol. 2018;10:2882–98. https://doi.org/10.1093/gbe/evy200.
Jaillon O, Aury J-M, Brunet F, Petit J-L, Stange-Thomann N, Mauceli E, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431:946–57. https://doi.org/10.1038/nature03025.
Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428:617–24. https://doi.org/10.1038/nature02424.
Nakatani Y, McLysaght A. Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes. Bioinformatics. 2017;33:i369–78. https://doi.org/10.1093/bioinformatics/btx259.
Van de Peer Y. Computational approaches to unveiling ancient genome duplications. Nat Rev Genet. 2004;5:752–63. https://doi.org/10.1038/nrg1449.
Schrader L, Schmitz J. The impact of transposable elements in adaptive evolution. Mol Ecol. 2019;28:1537–49. https://doi.org/10.1111/mec.14794.
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 2011;473:97–100.
Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, et al. Early genome duplications in conifers and other seed plants. Sci Adv. 2015;1:e1501084. https://doi.org/10.1126/sciadv.1501084.
Ruprecht C, Lohaus R, Vanneste K, Mutwil M, Nikoloski Z, Van de Peer Y, et al. Revisiting ancestral polyploidy in plants. Sci Adv. 2017;3:e1603195. https://doi.org/10.1126/sciadv.1603195.
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000;290:1151–5. https://doi.org/10.1126/science.290.5494.1151.
Faddeeva-Vakhrusheva A, Kraaijeveld K, Derks MFL, Anvar SY, Agamennone V, Suring W, et al. Coping with living in the soil : the genome of the parthenogenetic springtail Folsomia candida. BMC Genomics. 2017;18:493–506. https://doi.org/10.1186/s12864-017-3852-x.
Mahmudi O, Sjöstrand J, Sennblad B, Lagergren J. Genome-wide probabilistic reconciliation analysis across vertebrates. BMC Bioinformatics. 2013;14(Suppl 15):S10. https://doi.org/10.1186/1471-2105-14-S15-S10.
Rabier C-E, Ta T, Ané C. Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. Mol Biol Evol. 2014;31:750–62. https://doi.org/10.1093/molbev/mst263.
Hahn MW, Han MV, Han S-G. Gene family evolution across 12 Drosophila genomes. PLoS Genet. 2007;3:e197. https://doi.org/10.1371/journal.pgen.0030197.
Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet. 2004;38:615–43.
Simillion C, Vandepoele K, Van Montagu MCE, Zabeau M, Van de Peer Y. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2002;99:13627–32. https://doi.org/10.1073/pnas.212522399.
Mandáková T, Lysak MA. Post-polyploid diploidization and diversification through dysploid changes. Curr Opin Plant Biol. 2018;42:55–65. https://doi.org/10.1016/J.PBI.2018.03.001.
Lysak MA, Berr A, Pecinka A, Schmidt R, McBreen K, Schubert I. Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species. Proc Natl Acad Sci U S A. 2006;103:5224–9. https://doi.org/10.1073/pnas.0510791103.
Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinformatics. 2018;19:26. https://doi.org/10.1186/s12859-018-2026-4.
Lyons E, Pedersen B, Kane J, Freeling M. The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. https://doi.org/10.1007/s12042-008-9017-y.
Pace RM, Grbić M, Nagy LM. Composition and genomic organization of arthropod Hox clusters. Evodevo. 2016;7:1–11. https://doi.org/10.1186/s13227-016-0048-4.
Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nat Ecol Evol. 2018;2:557–66. https://doi.org/10.1038/s41559-017-0459-1.
Terrapon N, Li C, Robertson HM, Ji L, Meng X, Booth W, et al. Molecular traces of alternative social organization in a termite genome. Nat Commun. 2014;5:3636. https://doi.org/10.1038/ncomms4636.
Richards S, Gibbs RA, Gerardo NM, Moran N, Nakabachi A, Stern D, et al. Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biol. 2010;8:e1000313. https://doi.org/10.1371/journal.pbio.1000313.
Duboule D. The rise and fall of Hox gene clusters. Development. 2007;134:2549–60.
Fiston-Lavier A-S, Anxolabehere D, Quesneville H. A model of segmental duplication formation in Drosophila melanogaster. Genome Res. 2007;17:1458–70. https://doi.org/10.1101/gr.6208307.
Bailey JA, Liu G, Eichler EE. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet. 2003;73:823–34. https://doi.org/10.1086/378594.
Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, et al. ARTICLE transposable element islands facilitate adaptation to novel environments in an invasive species. Nat Commun. 2014;5 https://doi.org/10.1038/ncomms6495.
Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, et al. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol. 2019;19:11. https://doi.org/10.1186/s12862-018-1324-9.
Le Rouzic A, Payen T, Hua-Van A. Reconstructing the evolutionary history of transposable elements. Genome Biol Evol. 2013;5:77–86. https://doi.org/10.1093/gbe/evs130.
Zwaenepoel A, Van de Peer Y. Wgd—simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics. 2019;35:2153–5. https://doi.org/10.1093/bioinformatics/bty915.
Enright AJ, Van Dongen S, Ouzounis CA. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 2002;30:1575–84. https://doi.org/10.1093/nar/30.7.1575.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. https://doi.org/10.1093/molbev/mst010.
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586–91. https://doi.org/10.1093/molbev/msm088.
Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490. https://doi.org/10.1371/journal.pone.0009490.
Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40:2–14. https://doi.org/10.1093/nar/gkr1293.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45. https://doi.org/10.1101/gr.092759.109.
Kumar S, Stecher G, Suleski M, Hedges SB. TimeTree: a resource for timelines, timetrees, and divergence times. Mol Biol Evol. 2017;34:1812–9.
Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157. https://doi.org/10.1186/s13059-015-0721-2.
Whelan S, Irisarri I, Burki F. PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences. Bioinformatics. 2018; https://doi.org/10.1093/bioinformatics/bty448.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539–42. https://doi.org/10.1093/sysbio/sys029.
Szöllősi GJ, Rosikiewicz W, Boussau B, Tannier E, Daubin V. Efficient exploration of the space of reconciled gene trees. Syst Biol. 2013;62:901–12. https://doi.org/10.1093/sysbio/syt054.
Manni M, Simao FA, Robertson HM, Gabaglio MA, Waterhouse RM, Misof B, et al. The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations. Preprint at https://www.biorxiv.org/content/10.1101/585695v3. https://doi.org/10.1101/585695.
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017;356:92–5.
Evans JD, Mckenna D, Scully E, Cook SC, Dainat B, Egekwu N, et al. Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory. Giga Sci. 2018;7:1–16. https://doi.org/10.1093/gigascience/giy138.
Weinstock GM, Robinson GE, Gibbs RA, Worley KC, Evans JD, Maleszka R, et al. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006;443:931–49.
Mine S, Sumitani M, Aoki F, Hatakeyama M, Suzuki MG. Identification and functional characterization of the sex-determining gene doublesex in the sawfly, Athalia rosae (Hymenoptera: Tenthredinidae). Appl Entomol Zool. 2017;52:497–509.
Chen W, Hasegawa DK, Kaur N, Kliot A, Pinheiro PV, Luan J, et al. The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance. BMC Biol. 2016;14:110. https://doi.org/10.1186/s12915-016-0321-y.
Xia Q, Wang J, Zhou Z, Li R, Fan W, Cheng D, et al. The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol. 2008;38:1036–45.
Driscoll TP, Verhoeve VI, Gillespie JJ, Johnston JS, Guillotte ML, Rennoll-Bankert KE, et al. Cat fleas in flux: rampant gene duplication, genome size plasticity, and paradoxical Wolbachia infection. Preprint at https://www.biorxiv.org/content/10.1101/2020.04.14.038018v1. https://doi.org/10.1101/2020.04.14.038018.
Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, et al. The release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015;25:445–58.
Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, et al. Genome-enabled insights into the biology of thrips as crop pests. Preprint at https://www.biorxiv.org/content/10.1101/2020.02.12.941716v1.full. https://doi.org/10.1101/2020.02.12.941716.
Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, et al. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. BMC Genomics. 2017;18:1–19. https://doi.org/10.1186/s12864-017-4197-1.
Brand P, Lin W, Johnson BR. The draft genome of the invasive walking stick, Medauroidea extradendata, reveals extensive lineage-specific gene family expansions of cell wall degrading enzymes in Phasmatodea. G3 genes, genomes. Genet. 2018;8:1403–8.
Faddeeva-Vakhrusheva A, Derks MFL, Anvar SY, Agamennone V, Suring W, Smit S, et al. Gene family evolution reflects adaptation to soil environmental stressors in the genome of the collembolan Orchesella cincta. Genome Biol Evol. 2016;8:2106–17. https://doi.org/10.1093/gbe/evw134.
Johnston JS, Yoon KS, Strycharz JP, Pittendrigh BR, Clark JM. Body lice and head lice (Anoplura: Pediculidae) have the smallest genomes of any hemimetabolous insect reported to date. J Med Entomol. 2007;44:1009–12. https://doi.org/10.1093/jmedent/44.6.1009.
Grishin NV, Shen J, Cong Q, Kinch LN, Borek D, Otwinowski Z. Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. F1000Research. 2016;5:2631. https://doi.org/10.12688/f1000research.9765.1.
Kim HS, Murphy T, Xia J, Caragea D, Park Y, Beeman RW, et al. BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Res. 2009;38:D437–42. https://doi.org/10.1093/nar/gkp807.
Battelle B-A, Ryan JF, Kempler KE, Saraf SR, Marten CE, Warren WC, et al. Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata). Genome Biol Evol. 2016;8:1571–89. https://doi.org/10.1093/gbe/evw100.