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Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
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نویسنده
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vij s. ,kuhl h. ,kuznetsova i.s. ,komissarov a. ,yurchenko a.a. ,van heusden p. ,singh s. ,thevasagayam n.m. ,prakki s.r.s. ,purushothaman k. ,saju j.m. ,jiang j. ,mbandi s.k. ,jonas m. ,hin yan tong a. ,mwangi s. ,lau d. ,ngoh s.y. ,liew w.c. ,shen x. ,hon l.s. ,drake j.p. ,boitano m. ,hall r. ,chin c.-s. ,lachumanan r. ,korlach j. ,trifonov v. ,kabilov m. ,tupikin a. ,green d. ,moxon s. ,garvin t. ,sedlazeck f.j. ,vurture g.w. ,gopalapillai g. ,kumar katneni v. ,noble t.h. ,scaria v. ,sivasubbu s. ,jerry d.r. ,o'brien s.j. ,schatz m.c. ,dalmay t. ,turner s.w. ,lok s. ,christoffels a. ,orbán l.
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منبع
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plos genetics - 2016 - دوره : 12 - شماره : 4
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چکیده
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We report here the ~670 mb genome assembly of the asian seabass (lates calcarifer),a tropical marine teleost. we used long-read sequencing augmented by transcriptomics,optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig n50 size over 1 mb and scaffold n50 size over 25 mb that span ~90% of the genome. the population structure of l. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. snp analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the south-east asian population. the quality of the asian seabass genome assembly far exceeds that of any other fish species,and will serve as a new standard for fish genomics. © 2016,public library of science. all rights reserved.
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آدرس
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reproductive genomics group,temasek life sciences laboratory, Singapore, max planck institute for molecular genetics,berlin, Germany, reproductive genomics group,temasek life sciences laboratory,singapore,laboratory of chromosome structure and function,department of cytology and histology,biological faculty,saint petersburg state university,st. petersburg, Russian Federation, theodosius dobzhansky center for genome bioinformatics,saint petersburg state university,st. petersburg, Russian Federation, theodosius dobzhansky center for genome bioinformatics,saint petersburg state university,st. petersburg, Russian Federation, south african mrc bioinformatics unitn national bioinformatics institute,university of the western cape,bellville, South Africa, pacific biosciences,menlo park,ca, United States, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, south african mrc bioinformatics unitn national bioinformatics institute,university of the western cape,bellville, South Africa, south african mrc bioinformatics unitn national bioinformatics institute,university of the western cape,bellville, South Africa, donnelly centre for cellular and biomolecular research,university of toronto,toronto, Canada, south african mrc bioinformatics unitn national bioinformatics institute,university of the western cape,bellville, South Africa, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, reproductive genomics group,temasek life sciences laboratory, Singapore, pacific biosciences,menlo park,ca, United States, pacific biosciences,menlo park,ca, United States, pacific biosciences,menlo park,ca, United States, pacific biosciences,menlo park,ca, United States, pacific biosciences,menlo park,ca, United States, pacific biosciences,menlo park,ca, United States, pacific biosciences,menlo park,ca, United States, institute of molecular and cellular biology,siberian branch of the russian academy of sciences,novosibirsk, Russian Federation, genomics core facility,institute of chemical biology and fundamental medicine,siberian branch of the russian academy of sciences,novosibirsk, Russian Federation, genomics core facility,institute of chemical biology and fundamental medicine,siberian branch of the russian academy of sciences,novosibirsk, Russian Federation, norwich medical school,university of east anglia,norwich research park,norwich, United Kingdom, the genome analysis centre,norwich, United Kingdom, simons center for quantitative biology,cold spring harbor laboratory,one bungtown road,cold spring harbor,ny, United States, simons center for quantitative biology,cold spring harbor laboratory,one bungtown road,cold spring harbor,ny,united states,department of computer science,johns hopkins university,baltimore,md, United States, simons center for quantitative biology,cold spring harbor laboratory,one bungtown road,cold spring harbor,ny, United States, nutrition,genetics & biotechnology division,icar-central institute of brackishwater aquaculturetamil nadu, India, nutrition,genetics & biotechnology division,icar-central institute of brackishwater aquaculturetamil nadu, India, college of marine and environmental sciences,center for sustainable tropical fisheries and aquaculture,james cook university,townsville,qld, Australia, csir-institute of genomics and integrative biology (csir-igib),new delhi, India, csir-institute of genomics and integrative biology (csir-igib),new delhi, India, college of marine and environmental sciences,center for sustainable tropical fisheries and aquaculture,james cook university,townsville,qld, Australia, theodosius dobzhansky center for genome bioinformatics,saint petersburg state university,st. petersburg,russian federation,oceanographic center,nova southeastern university ft. lauderdale,ft. lauderdale,fl, United States, simons center for quantitative biology,cold spring harbor laboratory,one bungtown road,cold spring harbor,ny,united states,department of computer science,johns hopkins university,baltimore,md, United States, school of biological sciences,university of east anglia,norwich research park,norwich, United Kingdom, pacific biosciences,menlo park,ca, United States, the centre for applied genomics,the hospital for sick children,peter gilgan centre for research and learning,toronto,on, Canada, south african mrc bioinformatics unitn national bioinformatics institute,university of the western cape,bellville, South Africa, reproductive genomics group,temasek life sciences laboratory,singapore,department of animal sciences and animal husbandry,georgikon faculty,university of pannonia,keszthely,hungary,centre for comparative genomics,murdoch university,murdoch, Australia
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Authors
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