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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...

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Autores principales: Vij, Shubha, Kuhl, Heiner, Kuznetsova, Inna S., Komissarov, Aleksey, Yurchenko, Andrey A., Van Heusden, Peter, Singh, Siddharth, Thevasagayam, Natascha M., Prakki, Sai Rama Sridatta, Purushothaman, Kathiresan, Saju, Jolly M., Jiang, Junhui, Mbandi, Stanley Kimbung, Jonas, Mario, Hin Yan Tong, Amy, Mwangi, Sarah, Lau, Doreen, Ngoh, Si Yan, Liew, Woei Chang, Shen, Xueyan, Hon, Lawrence S., Drake, James P., Boitano, Matthew, Hall, Richard, Chin, Chen-Shan, Lachumanan, Ramkumar, Korlach, Jonas, Trifonov, Vladimir, Kabilov, Marsel, Tupikin, Alexey, Green, Darrell, Moxon, Simon, Garvin, Tyler, Sedlazeck, Fritz J., Vurture, Gregory W., Gopalapillai, Gopikrishna, Kumar Katneni, Vinaya, Noble, Tansyn H., Scaria, Vinod, Sivasubbu, Sridhar, Jerry, Dean R., O'Brien, Stephen J., Schatz, Michael C., Dalmay, Tamás, Turner, Stephen W., Lok, Si, Christoffels, Alan, Orbán, László
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833346/
https://www.ncbi.nlm.nih.gov/pubmed/27082250
http://dx.doi.org/10.1371/journal.pgen.1005954
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author Vij, Shubha
Kuhl, Heiner
Kuznetsova, Inna S.
Komissarov, Aleksey
Yurchenko, Andrey A.
Van Heusden, Peter
Singh, Siddharth
Thevasagayam, Natascha M.
Prakki, Sai Rama Sridatta
Purushothaman, Kathiresan
Saju, Jolly M.
Jiang, Junhui
Mbandi, Stanley Kimbung
Jonas, Mario
Hin Yan Tong, Amy
Mwangi, Sarah
Lau, Doreen
Ngoh, Si Yan
Liew, Woei Chang
Shen, Xueyan
Hon, Lawrence S.
Drake, James P.
Boitano, Matthew
Hall, Richard
Chin, Chen-Shan
Lachumanan, Ramkumar
Korlach, Jonas
Trifonov, Vladimir
Kabilov, Marsel
Tupikin, Alexey
Green, Darrell
Moxon, Simon
Garvin, Tyler
Sedlazeck, Fritz J.
Vurture, Gregory W.
Gopalapillai, Gopikrishna
Kumar Katneni, Vinaya
Noble, Tansyn H.
Scaria, Vinod
Sivasubbu, Sridhar
Jerry, Dean R.
O'Brien, Stephen J.
Schatz, Michael C.
Dalmay, Tamás
Turner, Stephen W.
Lok, Si
Christoffels, Alan
Orbán, László
author_facet Vij, Shubha
Kuhl, Heiner
Kuznetsova, Inna S.
Komissarov, Aleksey
Yurchenko, Andrey A.
Van Heusden, Peter
Singh, Siddharth
Thevasagayam, Natascha M.
Prakki, Sai Rama Sridatta
Purushothaman, Kathiresan
Saju, Jolly M.
Jiang, Junhui
Mbandi, Stanley Kimbung
Jonas, Mario
Hin Yan Tong, Amy
Mwangi, Sarah
Lau, Doreen
Ngoh, Si Yan
Liew, Woei Chang
Shen, Xueyan
Hon, Lawrence S.
Drake, James P.
Boitano, Matthew
Hall, Richard
Chin, Chen-Shan
Lachumanan, Ramkumar
Korlach, Jonas
Trifonov, Vladimir
Kabilov, Marsel
Tupikin, Alexey
Green, Darrell
Moxon, Simon
Garvin, Tyler
Sedlazeck, Fritz J.
Vurture, Gregory W.
Gopalapillai, Gopikrishna
Kumar Katneni, Vinaya
Noble, Tansyn H.
Scaria, Vinod
Sivasubbu, Sridhar
Jerry, Dean R.
O'Brien, Stephen J.
Schatz, Michael C.
Dalmay, Tamás
Turner, Stephen W.
Lok, Si
Christoffels, Alan
Orbán, László
author_sort Vij, Shubha
collection PubMed
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.
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spelling pubmed-48333462016-04-22 Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding Vij, Shubha Kuhl, Heiner Kuznetsova, Inna S. Komissarov, Aleksey Yurchenko, Andrey A. Van Heusden, Peter Singh, Siddharth Thevasagayam, Natascha M. Prakki, Sai Rama Sridatta Purushothaman, Kathiresan Saju, Jolly M. Jiang, Junhui Mbandi, Stanley Kimbung Jonas, Mario Hin Yan Tong, Amy Mwangi, Sarah Lau, Doreen Ngoh, Si Yan Liew, Woei Chang Shen, Xueyan Hon, Lawrence S. Drake, James P. Boitano, Matthew Hall, Richard Chin, Chen-Shan Lachumanan, Ramkumar Korlach, Jonas Trifonov, Vladimir Kabilov, Marsel Tupikin, Alexey Green, Darrell Moxon, Simon Garvin, Tyler Sedlazeck, Fritz J. Vurture, Gregory W. Gopalapillai, Gopikrishna Kumar Katneni, Vinaya Noble, Tansyn H. Scaria, Vinod Sivasubbu, Sridhar Jerry, Dean R. O'Brien, Stephen J. Schatz, Michael C. Dalmay, Tamás Turner, Stephen W. Lok, Si Christoffels, Alan Orbán, László PLoS Genet Research Article 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. Public Library of Science 2016-04-15 /pmc/articles/PMC4833346/ /pubmed/27082250 http://dx.doi.org/10.1371/journal.pgen.1005954 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Research Article
Vij, Shubha
Kuhl, Heiner
Kuznetsova, Inna S.
Komissarov, Aleksey
Yurchenko, Andrey A.
Van Heusden, Peter
Singh, Siddharth
Thevasagayam, Natascha M.
Prakki, Sai Rama Sridatta
Purushothaman, Kathiresan
Saju, Jolly M.
Jiang, Junhui
Mbandi, Stanley Kimbung
Jonas, Mario
Hin Yan Tong, Amy
Mwangi, Sarah
Lau, Doreen
Ngoh, Si Yan
Liew, Woei Chang
Shen, Xueyan
Hon, Lawrence S.
Drake, James P.
Boitano, Matthew
Hall, Richard
Chin, Chen-Shan
Lachumanan, Ramkumar
Korlach, Jonas
Trifonov, Vladimir
Kabilov, Marsel
Tupikin, Alexey
Green, Darrell
Moxon, Simon
Garvin, Tyler
Sedlazeck, Fritz J.
Vurture, Gregory W.
Gopalapillai, Gopikrishna
Kumar Katneni, Vinaya
Noble, Tansyn H.
Scaria, Vinod
Sivasubbu, Sridhar
Jerry, Dean R.
O'Brien, Stephen J.
Schatz, Michael C.
Dalmay, Tamás
Turner, Stephen W.
Lok, Si
Christoffels, Alan
Orbán, László
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833346/
https://www.ncbi.nlm.nih.gov/pubmed/27082250
http://dx.doi.org/10.1371/journal.pgen.1005954
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