한국어류학회지 (Korean Journal of Ichthyology)

  • 제33권4호
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  • Pages.205-216
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  • 2021
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  • 1225-8598(pISSN)
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  • 2288-3371(eISSN)
한국어류학회 (The Ichthyological Society of Korea)
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엑손 포획 - 원리와 어류의 계통유전체학 및 집단유전체학으로의 응용

Exon Capture - Principle and Applications to Phylogenomics and Population Genomics of Fishes

  • Li, Chenhong (Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University)
  • 투고 : 2021.10.25
  • 심사 : 2021.11.29
  • 발행 : 2021.12.31
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⟨ 이전 논문 다음 논문 ⟩

초록

한 유전좌위 또는 소수의 유전좌위에 기반한 계통발생학적 재구성은 분자 계통수/종 계통수의 불일치로 인해 오해를 불러일으킬 수 있다. 종의 구분과 종내 연구에서도 적은 유전좌위를 사용할 때 통계력 부족으로 해상도가 낮은 경우가 많이 발생한다. 엑손 포획법은 게놈 규모의 데이터를 수집하는 가장 효율적인 방법 중 하나로, 종내 및 상위 수준에서 생물의 패턴과 역사를 구명하는 연구에 크게 이바지할 수 있다. 이 논문에서는 단일 유전자 방법에서 게놈 접근으로의 전환의 진보와 게놈 기술에 비해 엑손 포획법의 적용 이점을 설명하였다. 또한 엑손 포획법의 원리를 설명하고 이 방법의 적용을 위한 상세한 제언을 기술하였다. 최종적으로, 두 가지 적용을 활용한 엑손 포획법을 설명하고 이 기술에 대한 미래 전망을 논의하였다.

Phylogenetic reconstruction based on one locus or a few loci can be misleading due to gene-tree/species-tree discordance. Species delimitation and intraspecific studies also often suffered from low resolution because of insufficient statistic power when few loci were used. Exon capture method is one of the most efficient way to collect genome-scale data, which can significantly augment studies that aimed to investigate patterns and histories of organisms at both intraspecific and high level. Here, I showed the advancement of shifting from single-gene method to genomic approach and the benefit of applying exon capture method comparing to alternative genomic techniques. Then, I explained the principle of exon capture method as well as providing detailed recommendations for applying this method. Finally, I demonstrated exon capture method using two applications and discussed future perspectives of this technology.

키워드

과제정보

CL was supported by the Science and Technology Commission of Shanghai Municipality (19050501900, 19410740500).

참고문헌

  1. Ai, Q., L. Sang, H. Tan, X. Huang, B. Bao and C. Li. 2021. Genetic and morphological differences between yellowtail kingfish (Seriola lalandi) from the Bohai Sea, China and the Southern Ocean, Australia. Aquac. Fish., 6: 260-266. https://doi.org/10.1016/j.aaf.2020.03.004.
  2. Arcila, D., L.C. Hughes, B. Melendez-Vazquez, C.C. Baldwin, W.T. White, K.E. Carpenter, J.T. Williams, M.D. Santos, J.J. Pogonoski, M. Miya, G. Orti and R.R. Betancur. 2021. Testing the Utility of alternative metrics of branch support to address the ancient evolutionary radiation of Tunas, Stromateoids, and Allies(Teleostei: Pelagiaria). Syst. Biol., 70: 1123-1144. https://doi.org/10.1093/sysbio/syab018.
  3. Atta, C.J., H. Yuan, C. Li, D. Arcila, R.R. Betancur, L.C. Hughes, G. Orti and L. Tornabene. 2021. Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Mol. Phylogenet. Evol., 166: 107315. https://doi.org/10.1016/j.ympev.2021.107315.
  4. Baird, N.A., P.D. Etter, T.S. Atwood, M.C. Currey, A.L. Shiver, Z.A. Lewis, E.U. Selker, W.A. Cresko and E.A. Johnson. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE, 3: e3376. https://doi.org/10.1371/journal.pone.0003376.
  5. Betancur, R.R., D. Arcila, R.P. Vari, L.C. Hughes, C. Oliveira, M.H. Sabaj and G. Orti. 2019. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution, 73: 329-345. https://doi.org/10.1111/evo.13666.
  6. Bi, K., D. Vanderpool, S. Singhal, T. Linderoth, C. Moritz and J.M. Good. 2012. Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genom., 13: 403. https://doi.org/10.1186/1471-2164-13-403.
  7. Campana, M.G. 2018. BaitsTools: Software for hybridization capture bait design. Mol. Ecol. Resour., 8: 356-361. https://doi.org/10.1111/1755-0998.12721.
  8. Campbell, M.A., T.J. Buser, M.E. Alfaro and J.A. Lopez. 2020. Addressing incomplete lineage sorting and paralogy in the inference of uncertain salmonid phylogenetic relationships. PeerJ, 8: e9389. https://doi.org/10.7717/peerj.9389.
  9. Chen, L., Q. Qiu, Y. Jiang, K. Wang, Z. Lin, Z. Li, F. Bibi, Y. Yang, J. Wang, W. Nie, W. Su, G. Liu, Q. Li, W. Fu, X. Pan, C. Liu, J. Yang, C. Zhang, Y. Yin, Y. Wang, Y. Zhao, C. Zhang, Z. Wang, Y. Qin, W. Liu, B. Wang, Y. Ren, R. Zhang, Y. Zeng, R.R. da Fonseca, B. Wei, R. Li, W. Wan, R. Zhao, W. Zhu, Y. Wang, S. Duan, Y. Gao, Y.E. Zhang, C. Chen, C. Hvilsom, C.W. Epps, L.G. Chemnick, Y. Dong, S. Mirarab, H.R. Siegismund, O.A. Ryder, M.T.P. Gilbert, H.A. Lewin, G. Zhang, R. Heller and W. Wang. 2019. Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science, 364: eaav6202. https://doi.org/10.1126/science.aav6202.
  10. Cheng, F., Q. Wang, D.P. Maisano and C. Li. 2019. Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River. Ecol. Evol., 9, 12202-12215. https://doi.org/10.1002/ece3.5708.
  11. Collins, R.A. and T. Hrbek. 2015. An in silico comparison of reducedrepresentation and sequence-capture protocols for phylogenomics. BioRxiv, 032565. https://doi.org/10.1101/032565.
  12. Collins, T.M., O. Fedrigo and G.J. Naylor. 2005. Choosing the best genes for the job: the case for stationary genes in genomescale phylogenetics. Syst. Biol., 54: 493-500. https://doi.org/10.1080/10635150590947339.
  13. Corrigan, S., D.P. Maisano, C. Eddy, C. Duffy, L. Yang, C. Li, A.L. Bazinet, S. Mona and G.J.P. Naylor. 2017. Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks. Mol. Phylogenet. Evol., 110: 122-126. https://doi.org/10.1016/j.ympev.2017.03.011.
  14. Davey, J.W. and M.L. Blaxter. 2010. RADSeq: next-generation population genetics. Brief Funct Genomics, 9: 416-423. https://doi.org/10.1093/bfgp/elq031.
  15. Delsuc, F., H. Brinkmann and H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet., 6: 361-375. https://doi.org/10.1038/nrg1603.
  16. Emerson, K.J., C.R. Merz, J.M. Catchen, P.A. Hohenlohe, W.A. Cresko, W.E. Bradshaw and C.M. Holzapfel. 2010. Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. U.S.A., 107: 16196-16200. https://doi.org/10.1073/pnas.1006538107.
  17. Faircloth, B.C., J.E. McCormack, N.G. Crawford, M.G. Harvey, R.T. Brumfield and T.C. Glenn. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol., 61: 717-726. https://doi.org/10.1093/sysbio/sys004.
  18. Funk, D.J. and K.E. Omland. 2003. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst., 34: 397-423. https://doi.org/10.1146/annurev.ecolsys.34.011802.132421.
  19. Hebert, F.O., S. Renaut and L. Bernatchez. 2013. Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair(Coregonus clupeaformis). Mol. Ecol., 22: 4896-4914. https://doi.org/10.1111/mec.12447.
  20. Hedtke, S.M., M.J. Morgan, D.C. Cannatella and D.M. Hillis. 2013. Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time. PLoS ONE, 8: e67908. https://doi.org/10.1371/journal.pone.0067908.
  21. Huang, J.M., H. Yuan and C.H. Li. 2021. Protocol for cross-species target-gene enrichment. Bio-101: e1010606. https://doi.org/10.21769/BioProtoc.1010606.
  22. Hugall, A.F., T.D. O'Hara, S. Hunjan, R. Nilsen and A. Moussalli. 2016. An exon-capture system for the entire class Ophiuroidea. Mol. Biol. Evol., 33: 281-294. https://doi.org/10.1093/molbev/msv216.
  23. Hughes, L.C., G. Orti, Y. Huang, Y. Sun, C.C. Baldwin, A.W. Thompson, D. Arcila, R.R. Betancur, C. Li, L. Becker, N. Bellora, X. Zhao, X. Li, M. Wang, C. Fang, B. Xie, Z. Zhou, H. Huang, S. Chen, B. Venkatesh and Q. Shi. 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc. Natl. Acad. Sci. U.S.A., 115: 6249-6254. https://doi.org/10.1073/pnas.1719358115.
  24. Hughes, L.C., G. Orti, H. Saad, C. Li, W.T. White, C.C. Baldwin, K.A. Crandall, D. Arcila and R.R. Betancur. 2021. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol. Ecol. Resour., 21: 816-833. https://doi.org/10.1111/1755-0998.13287.
  25. Ilves, K.L. and H. Lopez-Fernandez. 2014. A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics. Mol. Ecol. Resour., 14: 802-811. https://doi.org/10.1111/1755-0998.12222.
  26. Ilves, K.L., D. Torti and H. Lopez-Fernandez. 2018. Exon-based phylogenomics strengthens the phylogeny of Neotropical cichlids and identifies remaining conflicting clades(Cichliformes: Cichlidae: Cichlinae). Mol. Phylogenet. Evol., 118: 232-243. https://doi.org/10.1016/j.ympev.2017.10.008.
  27. Jarvis, E.D., S. Mirarab, A.J. Aberer, B. Li, P. Houde, C. Li, S.Y. Ho, B.C. Faircloth, B. Nabholz, J.T. Howard, A. Suh, C.C. Weber, R.R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, M.S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W.C. Warren, D. Ray, R.E. Green, M.W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E.P. Derryberry, M.F. Bertelsen, F.H. Sheldon, R.T. Brumfield, C.V. Mello, P.V. Lovell, M. Wirthlin, M.P. Schneider, F. Prosdocimi, J.A. Samaniego, A.M. Vargas Velazquez, A. Alfaro-Nunez, P.F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D.M. Lambert, Q. Zhou, P. Perelman, A.C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F.E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F.K. Barker, K.A. Jonsson, W. Johnson, K.P. Koepfli, S. O'Brien, D. Haussler, O.A. Ryder, C. Rahbek, E. Willerslev, G.R. Graves, T.C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S.V. Edwards, A. Stamatakis, D.P. Mindell, J. Cracraft, E.L. Braun, T. Warnow, W. Jun, M.T. Gilbert and G. Zhang. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346: 1320-1331. https://doi.org/10.1126/science.1253451.
  28. Jensen, M.R., E.E. Sigsgaard, S. Liu, A. Manica, S.S. Bach, M.M. Hansen, P.R. Moller and P.F. Thomsen. 2021. Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples. Mol. Ecol. Resour., 21: 690-702. https://doi.org/10.1111/1755-0998.13293.
  29. Jiang, J., H. Yuan, X. Zheng, Q. Wang, T. Kuang, J. Li, J. Liu, S. Song, W. Wang, F. Cheng, H. Li, J. Huang and C. Li. 2019. Gene markers for exon capture and phylogenomics in ray-finned fishes. Ecol. Evol., 9: 3973-3983. https://doi.org/10.1002/ece3.5026.
  30. Kolmann, M.A., L.C. Hughes, L.P. Hernandez, D. Arcila, R.R. Betancur, M.H. Sabaj, H. Lopez-Fernandez and G. Orti. 2021. Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy. Syst. Biol., 70: 576-592. https://doi.org/10.1093/sysbio/syaa104.
  31. Kuang, T., L. Tornabene, J. Li, J. Jiang, P. Chakrabarty, J.S. Sparks, G.J.P. Naylor and C. Li. 2018. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Mol. Phylogenet. Evol., 128: 192-202. https://doi.org/10.1016/j.ympev.2018.07.018.
  32. Kurland, C.G., B. Canback and O.G. Berg. 2003. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. U.S.A., 100: 9658-9662. https://doi.org/10.1073/pnas.1632870100.
  33. Lappin, F.M., R.L. Shaw and D.J. Macqueen. 2016. Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish: Proof of concept for key components of the insulin-like growth factor axis. Mar. Genomics, 30: 15-26. https://doi.org/10.1016/j.margen.2016.003.
  34. Lemmon, A.R., S.A. Emme and E.M. Lemmon. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Syst. Biol., 61: 727-744. https://doi.org/10.1093/sysbio/sys049.
  35. Li, C. 2007. A genome-scale approach to phylogeny of ray-finned fish (Actinopterygii) and molecular systematics of Clupeiformes. School of Biological Sciences. Doctoral Thesis, University of Nebraska, Lincoln, Nebraska, U.S.A., 118pp.
  36. Li, C., S. Corrigan, L. Yang, N. Straube, M. Harris, M. Hofreiter, W.T. White and G.J. Naylor. 2015. DNA capture reveals transoceanic gene flow in endangered river sharks. Proc. Natl. Acad. Sci. U.S.A., 112: 13302-13307. https://doi.org/10.1073/pnas.1508735112.
  37. Li, C., M. Hofreiter, N. Straube, S. Corrigan and G. Naylor. 2013. Capturing protein-coding genes across highly divergent species. BioTechniques, 54: 321-326. https://doi.org/10.2144/000114039.
  38. Li, C., K.A. Matthes-Rosana, M. Garcia and G.J. Naylor. 2012. Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups. Mol. Phylogenet. Evol., 63: 365-373. https://doi.org/10.1016/j.ympev.2012.01.013.
  39. Li, H., Y. He, J. Jiang, Z. Liu and C. Li. 2018. Molecular systematics and phylogenetic analysis of the Asian endemic freshwater sleepers (Gobiiformes: Odontobutidae). Mol. Phylogenet. Evol., 121: 1-11. https://doi.org/10.1016/j.ympev.2017.12.026.
  40. Liu, J., J. Jiang, S. Song, L. Tornabene, R. Chabarria, G.J. Naylor and C. Li. 2017. Multilocus DNA barcoding-species identification with multilocus data. Sci. Rep., 7: 1-12. https://doi.org/10.1038/s41598-017-16920-2.
  41. Luikart, G., P.R. England, D. Tallmon, S. Jordan and P. Taberlet. 2003. The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet., 4: 981-994. https://doi.org/10.1038/nrg1226.
  42. Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol., 46: 523-536. https://doi.org/10.1093/sysbio/46.3.523.
  43. Maddison, W.P. and L.L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol., 55: 21-30. https://doi.org/10.1080/10635150500354928.
  44. Maisano Delser, P., S. Corrigan, M. Hale, C. Li, M. Veuille, S. Planes, G. Naylor and S. Mona. 2016. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Sci. Rep., 6: 33753. https://doi.org/10.1038/srep33753.
  45. Meyer, M. and M. Kircher. 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc., 2010: pdb.prot5448. https://doi.org/10.1101/pdb.prot5448.
  46. Nielsen, E.E., J.A.T. Morgan, S.L. Maher, J. Edson, M. Gauthier, J. Pepperell, B.J. Holmes, M.B. Bennett and J.R. Ovenden. 2017. Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material. Mol. Ecol. Resour., 17: 431-442. https://doi.org/10.1111/1755-0998.12580.
  47. Peterson, B.K., J.N. Weber, E.H. Kay, H.S. Fisher and H.E. Hoekstra. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7: e37135. https://doi.org/10.1371/journal.pone.0037135.
  48. Rincon-Sandoval, M., R.R. Betancur and J.A. Maldonado-Ocampo. 2019. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. Mol. Ecol., 28: 1096-1115. https://doi.org/10.1111/mec.15036.
  49. Roa-Varon, A., R.B. Dikow, G. Carnevale, L. Tornabene, C.C. Baldwin, C. Li and E.J. Hilton. 2021. Confronting sources of systematic error to resolve historically contentious relationships: a case study using Gadiform fishes(Teleostei, Paracanthopterygii, Gadiformes). Syst. Biol., 70: 739-755. https://doi.org/10.1093/sysbio/syaa095.
  50. Sarker, A., J. Jiang, H. Naher, J. Huang, K.K. Sarker, G. Yin, M.A. Baki and C. Li. 2021. Cross-species gene enrichment revealed a single population of Hilsa shad (Tenualosa ilisha) with low genetic variation in Bangladesh waters. Sci. Rep., 11: 11560. https://doi.org/10.1038/s41598-021-90864-6.
  51. Sarker, A., H. Naher, J. Huang, K.K. Sarker, M.A. Baki and C. Li. 2020. Genetic diversity of Hilsa kelee collected from the Bay of Bengal and the Arabian Sea. Mar. Biodivers., 50: 94. https://doi.org/10.1007/s12526-020-01114-3.
  52. Song, S., J. Zhao and C. Li. 2017. Species delimitation and phylogenetic reconstruction of the sinipercids(Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences. Mol. Phylogenet. Evol., 111: 44-55. https://doi.org/10.1016/j.ympev.2017.03.014.
  53. Straube, N., C. Li, J.M. Claes, S. Corrigan and G.J. Naylor. 2015. Molecular phylogeny of Squaliformes and first occurrence of bioluminescence in sharks. BMC Evol. Biol., 15: 162. https://doi.org/10.1186/s12862-015-0446-6.
  54. Straube, N., C. Li, M. Mertzen, H. Yuan and T. Moritz. 2018. A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies. BMC Evol. Biol., 18: 158. https://doi.org/10.1186/s12862-018-1267-1.
  55. Therkildsen, N.O. and S.R. Palumbi. 2017. Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species. Mol. Ecol. Resour., 17: 194-208. https://doi.org/10.1111/1755-0998.12593.
  56. White, W.T., S. Corrigan, L. Yang, A.C. Henderson, A.L. Bazinet, D.L. Swofford and G.J.P. Naylor. 2018. Phylogeny of the manta and devilrays(Chondrichthyes: Mobulidae), with an updated taxonomic arrangement for the family. Zool. J. Linn. Soc., 182: 50-75. https://doi.org/10.1093/zoolinnean/zlx018.
  57. Yin, G., Y. Pan, A. Sarker, M.A. Baki, J.K. Kim, H. Wu and C. Li. 2019. Molecular systematics of Pampus (Perciformes: Stromateidae) based on thousands of nuclear loci using target-gene enrichment. Mol. Phylogenet. Evol., 140: 106595. https://doi.org/10.1016/j.ympev.2019.106595.
  58. Zong, C., S. Lu, A.R. Chapman and X.S. Xie. 2012. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338: 1622-1626. https://doi.org/10.1126/science.1229164.