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Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

Inoue, Jun, Sato, Yukuto, Sinclair, Robert, Tsukamoto, Katsumi, Nishida, Mutsumi·2015·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1507669112
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Abstract

Significance: All genes are duplicated by whole-genome duplication (WGD), reverting in number over time, but the actual timing of genome reshaping through gene loss remains poorly understood. We estimated the spatiotemporal loss/persistence pattern of 6,892 gene lineage pairs after the teleost-specific WGD, using careful orthology assignment and a reliable time-calibrated tree. We found that massive gene loss did occur in the first 60 My, mainly due to events involving the simultaneous loss of multiple redundant genes, and the rate of loss then slowed to an approximately constant level for the subsequent 250 My. Similar genomic gene arrangements within teleosts imply that rapid gene loss led to the reshaping of the teleost genomes before their major divergence.

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  • Ancestral gene order is particularly difficult to reconstruct in teleosts because of an elevated rate of microsyntenic rearrangements and gene copy losses.

    “Because ancestral gene order is particularly difficult to reconstruct in teleosts because of an elevated rate of microsyntenic rearrangements and gene copy losses (Inoue et al. 2015; Nakatani and McLysaght 2017)”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Inoue et al. 2015

    The Discussion reports rapid gene-copy loss and extensive rearrangements in the ancestral teleost genome after whole-genome duplication. It does not establish an elevated rate of specifically microsyntenic rearrangements or state that these changes make ancestral gene order particularly difficult to reconstruct. (LLM, conf=0.85)

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Research works printed but not linked: 46

  1. M Lynch The Origins of Genome Architecture (Sinauer Associates, Sunderland, MA, 2007).
  2. Y Jiao, AH Paterson, Polyploidy-associated genome modifications during land plant evolution. Philos Trans R Soc Lond B Biol Sci 369, 20130355 (2014). · DOI
  3. AM Selmecki, , Polyploidy can drive rapid adaptation in yeast. Nature 519, 349–352 (2015). · DOI
  4. M Kellis, BW Birren, ES Lander, Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617–624 (2004). · DOI
  5. DR Scannell, KP Byrne, JL Gordon, S Wong, KH Wolfe, Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440, 341–345 (2006). · DOI
  6. T Makino, A McLysaght, Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci USA 107, 9270–9274 (2010). · DOI
  7. M Schartl, , The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits. Nat Genet 45, 567–572 (2013). · DOI
  8. K Trachana, , Orthology prediction methods: A quality assessment using curated protein families. BioEssays 33, 769–780 (2011). · DOI · Paper page
  9. Y Sato, M Nishida, Teleost fish with specific genome duplication as unique models of vertebrate evolution. Environ Biol Fishes 88, 169–188 (2010). · DOI · Paper page
  10. RE Broughton, R Betancur-R, C Li, G Arratia, G Ortí, Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Curr 5, 5 (2013).
  11. AJ Vilella, , EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19, 327–335 (2009). · DOI · Paper page
  12. Y Sato, Y Hashiguchi, M Nishida, Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol 9, 127 (2009). · DOI
  13. M Nei, A Roychoudhury, Probability of fixation of nonfunctional genes at duplicate loci. Am Nat 107, 362–372 (1973). · DOI
  14. S Kuraku, A Meyer, The evolution and maintenance of Hox gene clusters in vertebrates and the teleost-specific genome duplication. Int J Dev Biol 53, 765–773 (2009). · DOI
  15. RJA Buggs, , Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Curr Biol 22, 248–252 (2012). · DOI
  16. C Berthelot, , The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun 5, 3657 (2014). · DOI
  17. P Xu, , Genome sequence and genetic diversity of the common carp, Cyprinus carpio. Nat Genet 46, 1212–1219 (2014). · DOI
  18. I Braasch, J Postlethwait, Polyploidy in fish and the teleost genome duplication. Polyploidy and Genome Evolution, eds PS Soltis, DE Soltis (Springer, Berlin), pp. 341–383 (2012). · DOI
  19. I Braasch, , A new model army: Emerging fish models to study the genomics of vertebrate Evo-Devo. J Exp Zool B Mol Dev Evol 324, 316–341 (2014). · DOI · Paper page
  20. PV Lovell, , Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol 15, 565 (2014). · DOI
  21. A Force, , Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999). · DOI · Paper page
  22. JF Gout, M Lynch, Maintenance and loss of duplicated genes by dosage subfunctionalization. Mol Biol Evol 32, 2141–2148 (2015). · DOI
  23. KS Kassahn, VT Dang, SJ Wilkins, AC Perkins, MA Ragan, Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates. Genome Res 19, 1404–1418 (2009). · DOI
  24. WP Yu, , Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster. Proc Natl Acad Sci USA 105, 3819–3824 (2008). · DOI
  25. JS Nelson Fishes of the World (Wiley, 4th Ed, Hoboken, NJ, 2006).
  26. M Miya, M Nishida, The mitogenomic contributions to molecular phylogenetics and evolution of fishes: A 15-year retrospect. Ichthyol Res 62, 29–71 (2015). · DOI
  27. TJ Near, , Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci USA 109, 13698–13703 (2012). · DOI · Paper page
  28. BC Faircloth, L Sorenson, F Santini, ME Alfaro, A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 8, e65923 (2013). · DOI
  29. KJ Martin, PWH Holland, Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication. Mol Biol Evol 31, 2592–2611 (2014). · DOI · Paper page
  30. SF Altschul, , Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402 (1997). · DOI · Paper page
  31. K Katoh, K Kuma, H Toh, T Miyata, MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33, 511–518 (2005). · DOI
  32. S Capella-Gutiérrez, JM Silla-Martínez, T Gabaldón, trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009). · DOI
  33. M Suyama, D Torrents, P Bork, PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34, W609–W612 (2006). · DOI
  34. K Tamura, M Nei, Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10, 512–526 (1993).
  35. Z Yang, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39, 306–314 (1994). · DOI · Paper page
  36. K Chen, D Durand, M Farach-Colton, NOTUNG: A program for dating gene duplications and optimizing gene family trees. J Comput Biol 7, 429–447 (2000). · DOI
  37. GF Berriz, JE Beaver, C Cenik, M Tasan, FP Roth, Next generation software for functional trend analysis. Bioinformatics 25, 3043–3044 (2009). · DOI
  38. GD Edgecombe, , Higher-level metazoan relationships: Recent progress and remaining questions. Org Divers Evol 11, 151–172 (2011). · DOI
  39. Y Azuma, Y Kumazawa, M Miya, K Mabuchi, M Nishida, Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol Biol 8, 215 (2008). · DOI
  40. M Kasahara, , The medaka draft genome and insights into vertebrate genome evolution. Nature 447, 714–719 (2007). · DOI · Paper page
  41. CV Henkel, , Primitive duplicate Hox clusters in the European eel’s genome. PLoS One 7, e32231 (2012). · DOI
  42. DM Hillis, Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47, 3–8 (1998). · DOI
  43. EM Lemmon, AR Lemmon, High-throughput genomic data in systematics and phylogenetics. Annu Rev Ecol Evol Syst 44, 99–121 (2013). · DOI
  44. P Stankiewicz, , Genomic disorders: Genome architecture results in susceptibility to DNA rearrangements causing common human traits. Cold Spring Harb Symp Quant Biol 68, 445–454 (2003). · DOI
  45. AL Hufton, G Panopoulou, Polyploidy and genome restructuring: A variety of outcomes. Curr Opin Genet Dev 19, 600–606 (2009). · DOI
  46. JM Smith, J Haigh, The hitch-hiking effect of a favourable gene. Genet Res 23, 23–35 (1974). · DOI · Paper page

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Metadata

Authors
Inoue, J., Sato, Y., Sinclair, R., Tsukamoto, K., & Nishida, M.
Affiliations
  • Mathematical Biology Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan;
  • Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan;
  • Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan;
ORCID
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2015-11-17
Volume
112
Issue
48
Pages
14918-14923
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.1507669112
Cited by
210
References
3
Language
en
Licence
www.pnas.org/site/misc/userlicense.xhtml (vor)
Funders
Japan Society for the Promotion of Science (24770070, 21228005)

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