Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua
Autoři:
Foyez Shams aff001; Fiona Dyer aff001; Ross Thompson aff001; Richard P. Duncan aff001; Jason D. Thiem aff003; Andrzej Kilian aff001; Tariq Ezaz aff001
Působiště autorů:
Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
aff001; Centre for Applied Water Science, University of Canberra, Canberra, Australian Capital Territory, Australia
aff002; Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
aff003; Diversity Arrays Technology, Bruce, Australian Capital Territory, Australia
aff004
Vyšlo v časopise:
PLoS ONE 14(12)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0226365
Souhrn
Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1–0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable.
Klíčová slova:
Comparative genomics – DNA sequence analysis – Evolutionary genetics – Genome analysis – Genome evolution – Multiple alignment calculation – Sequence alignment – Sticklebacks
Zdroje
1. Ezaz T, Azad B, O’Meally D, Young MJ, Matsubara K, Edwards MJ, et al. Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1. BMC genomics. 2013;14(1):899.
2. Shetty S, Griffin DK, Graves JAM. Comparative Painting Reveals Strong Chromosome Homology Over 80 Million Years of Bird Evolution. Chromosome Research. 1999;7(4):289–95. doi: 10.1023/a:1009278914829 10461874
3. Taylor JS, Van de Peer Y, Braasch I, Meyer A. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences. 2001;356(1414):1661–79. doi: 10.1098/rstb.2001.0975 11604130
4. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics. 2011;12(7):499–510. doi: 10.1038/nrg3012 21681211
5. Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, et al. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics. 2011;12:53. Epub 2011/01/25. doi: 10.1186/1471-2164-12-53 21255432.
6. Sturm RA, Duffy DL, Zhao ZZ, Leite FP, Stark MS, Hayward NK, et al. A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. The American Journal of Human Genetics. 2008;82(2):424–31. doi: 10.1016/j.ajhg.2007.11.005 18252222
7. Vignal A, Milan D, SanCristobal M, Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution. 2002;34(3):275–306.
8. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, et al. Diversity arrays technology: a generic genome profiling technology on open platforms. Data Production and Analysis in Population Genomics: Methods and Protocols. 2012:67–89.
9. Baloch FS, Alsaleh A, Shahid MQ, Çiftçi VE. Sáenz de Miera L, Aasim M, et al. A Whole Genome DArTseq and SNP Analysis for Genetic Diversity Assessment in Durum Wheat from Central Fertile Crescent. PloS one. 2017;12(1):e0167821. doi: 10.1371/journal.pone.0167821 28099442
10. Romanov MN, Dementyeva NV, Plemyashov KV, Terletsky VP, Stanishevskaya OI, Kudinov AA, et al. Applying SNP array technology to assess genetic diversity in Russian gene pool of chickens. 2017.
11. Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, et al. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature. 2000;407(6803):513–6. doi: 10.1038/35035083 11029002
12. Couch AJ, Unmack PJ, Dyer FJ, Lintermans M. Who’s your mama? Riverine hybridisation of threatened freshwater Trout Cod and Murray Cod. PeerJ. 2016;4:e2593. Epub 2016/11/05. doi: 10.7717/peerj.2593 27812407.
13. Melville J, Haines ML, Boysen K, Hodkinson L, Kilian A, Date KLS, et al. Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates. Royal Society open science. 2017;4(7):161061. doi: 10.1098/rsos.161061 28791133
14. Wells SJ, Dale J. Contrasting gene flow at different spatial scales revealed by genotyping-by-sequencing in Isocladus armatus, a massively colour polymorphic New Zealand marine isopod. PeerJ. 2018;6:e5462. doi: 10.7717/peerj.5462 30155361
15. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9. doi: 10.1093/bioinformatics/bts199 22543367
16. Kohany O, Gentles AJ, Hankus L, Jurka J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC bioinformatics. 2006;7:474. Epub 2006/10/27. doi: 10.1186/1471-2105-7-474 17064419.
17. Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, et al. Ensembl 2016. Nucleic acids research. 2016;44(D1):D710–6. doi: 10.1093/nar/gkv1157 26687719
18. Louis A, Muffato M, Roest Crollius H. Genomicus: five genome browsers for comparative genomics in eukaryota. Nucleic acids research. 2012;41(D1):D700–D5.
19. Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, et al. Phylogenetic classification of bony fishes. BMC evolutionary biology. 2017;17(1):162. doi: 10.1186/s12862-017-0958-3 28683774
20. Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, et al. De novo genome assembly and annotation of Australia’s largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. GigaScience. 2017;6(8):1–6.
21. Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nature Reviews Genetics. 2007;8(4):272. doi: 10.1038/nrg2072 17363976
22. Consortium IHGS. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860. doi: 10.1038/35057062 11237011
23. Girard L, Freeling M. Regulatory changes as a consequence of transposon insertion. Developmental genetics. 1999;25(4):291–6. doi: 10.1002/(SICI)1520-6408(1999)25:4<291::AID-DVG2>3.0.CO;2-5 10570460
24. Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, et al. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nature communications. 2016;7:11396. doi: 10.1038/ncomms11396 27097561
25. Gamble T, Coryell J, Ezaz T, Lynch J, Scantlebury DP, Zarkower D. Restriction site-associated DNA sequencing (RAD-seq) reveals an extraordinary number of transitions among gecko sex-determining systems. Molecular Biology and Evolution. 2015;32(5):1296–309. doi: 10.1093/molbev/msv023 25657328
26. Manousaki T, Tsakogiannis A, Taggart JB, Palaiokostas C, Tsaparis D, Lagnel J, et al. Exploring a nonmodel teleost genome through rad sequencing—linkage mapping in Common Pandora, Pagellus erythrinus and comparative genomic analysis. G3: Genes, genomes, genetics. 2016;6(3):509–19.
27. Shao C, Niu Y, Rastas P, Liu Y, Xie Z, Li H, et al. Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA research. 2015;22(2):161–70. doi: 10.1093/dnares/dsv001 25762582
Článek vyšel v časopise
PLOS One
2019 Číslo 12
- Jak a kdy u celiakie začíná reakce na lepek? Možnou odpověď poodkryla čerstvá kanadská studie
- Pomůže v budoucnu s triáží na pohotovostech umělá inteligence?
- Spermie, vajíčka a mozky – „jednohubky“ z výzkumu 2024/38
- Infekce se v Americe po příjezdu Kolumba šířily nesrovnatelně déle, než se traduje
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
Nejčtenější v tomto čísle
- Methylsulfonylmethane increases osteogenesis and regulates the mineralization of the matrix by transglutaminase 2 in SHED cells
- Oregano powder reduces Streptococcus and increases SCFA concentration in a mixed bacterial culture assay
- The characteristic of patulous eustachian tube patients diagnosed by the JOS diagnostic criteria
- Parametric CAD modeling for open source scientific hardware: Comparing OpenSCAD and FreeCAD Python scripts
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy