Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2016-04-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC4833346?pdf=render |
| _version_ | 1828869439222710272 |
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| author | Shubha Vij Heiner Kuhl Inna S Kuznetsova Aleksey Komissarov Andrey A Yurchenko Peter Van Heusden Siddharth Singh Natascha M Thevasagayam Sai Rama Sridatta Prakki Kathiresan Purushothaman Jolly M Saju Junhui Jiang Stanley Kimbung Mbandi Mario Jonas Amy Hin Yan Tong Sarah Mwangi Doreen Lau Si Yan Ngoh Woei Chang Liew Xueyan Shen Lawrence S Hon James P Drake Matthew Boitano Richard Hall Chen-Shan Chin Ramkumar Lachumanan Jonas Korlach Vladimir Trifonov Marsel Kabilov Alexey Tupikin Darrell Green Simon Moxon Tyler Garvin Fritz J Sedlazeck Gregory W Vurture Gopikrishna Gopalapillai Vinaya Kumar Katneni Tansyn H Noble Vinod Scaria Sridhar Sivasubbu Dean R Jerry Stephen J O'Brien Michael C Schatz Tamás Dalmay Stephen W Turner Si Lok Alan Christoffels László Orbán |
| author_facet | Shubha Vij Heiner Kuhl Inna S Kuznetsova Aleksey Komissarov Andrey A Yurchenko Peter Van Heusden Siddharth Singh Natascha M Thevasagayam Sai Rama Sridatta Prakki Kathiresan Purushothaman Jolly M Saju Junhui Jiang Stanley Kimbung Mbandi Mario Jonas Amy Hin Yan Tong Sarah Mwangi Doreen Lau Si Yan Ngoh Woei Chang Liew Xueyan Shen Lawrence S Hon James P Drake Matthew Boitano Richard Hall Chen-Shan Chin Ramkumar Lachumanan Jonas Korlach Vladimir Trifonov Marsel Kabilov Alexey Tupikin Darrell Green Simon Moxon Tyler Garvin Fritz J Sedlazeck Gregory W Vurture Gopikrishna Gopalapillai Vinaya Kumar Katneni Tansyn H Noble Vinod Scaria Sridhar Sivasubbu Dean R Jerry Stephen J O'Brien Michael C Schatz Tamás Dalmay Stephen W Turner Si Lok Alan Christoffels László Orbán |
| author_sort | Shubha Vij |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T05:50:18Z |
| format | Article |
| id | doaj.art-26b1610fd0f643e5bcd947608d08dcc3 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-13T05:50:18Z |
| publishDate | 2016-04-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-26b1610fd0f643e5bcd947608d08dcc32022-12-21T23:57:33ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042016-04-01124e100595410.1371/journal.pgen.1005954Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.Shubha VijHeiner KuhlInna S KuznetsovaAleksey KomissarovAndrey A YurchenkoPeter Van HeusdenSiddharth SinghNatascha M ThevasagayamSai Rama Sridatta PrakkiKathiresan PurushothamanJolly M SajuJunhui JiangStanley Kimbung MbandiMario JonasAmy Hin Yan TongSarah MwangiDoreen LauSi Yan NgohWoei Chang LiewXueyan ShenLawrence S HonJames P DrakeMatthew BoitanoRichard HallChen-Shan ChinRamkumar LachumananJonas KorlachVladimir TrifonovMarsel KabilovAlexey TupikinDarrell GreenSimon MoxonTyler GarvinFritz J SedlazeckGregory W VurtureGopikrishna GopalapillaiVinaya Kumar KatneniTansyn H NobleVinod ScariaSridhar SivasubbuDean R JerryStephen J O'BrienMichael C SchatzTamás DalmayStephen W TurnerSi LokAlan ChristoffelsLászló OrbánWe 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.http://europepmc.org/articles/PMC4833346?pdf=render |
| spellingShingle | Shubha Vij Heiner Kuhl Inna S Kuznetsova Aleksey Komissarov Andrey A Yurchenko Peter Van Heusden Siddharth Singh Natascha M Thevasagayam Sai Rama Sridatta Prakki Kathiresan Purushothaman Jolly M Saju Junhui Jiang Stanley Kimbung Mbandi Mario Jonas Amy Hin Yan Tong Sarah Mwangi Doreen Lau Si Yan Ngoh Woei Chang Liew Xueyan Shen Lawrence S Hon James P Drake Matthew Boitano Richard Hall Chen-Shan Chin Ramkumar Lachumanan Jonas Korlach Vladimir Trifonov Marsel Kabilov Alexey Tupikin Darrell Green Simon Moxon Tyler Garvin Fritz J Sedlazeck Gregory W Vurture Gopikrishna Gopalapillai Vinaya Kumar Katneni Tansyn H Noble Vinod Scaria Sridhar Sivasubbu Dean R Jerry Stephen J O'Brien Michael C Schatz Tamás Dalmay Stephen W Turner Si Lok Alan Christoffels László Orbán Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genetics |
| title | Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. |
| title_full | Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. |
| title_fullStr | Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. |
| title_full_unstemmed | Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. |
| title_short | Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. |
| title_sort | chromosomal level assembly of the asian seabass genome using long sequence reads and multi layered scaffolding |
| url | http://europepmc.org/articles/PMC4833346?pdf=render |
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