Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

Authors

• Shubha Vij, Temasek Life Sciences Laboratory - Singapore
• Heiner Kuhl, Max Planck Institute for Molecular Genetics - Berlin, Germany
• Inna S. Kuznetsova, Temasek Life Sciences Laboratory - Singapore, Saint Petersburg State University - Russia
• Aleksey Komissarov, St. Petersburg State University - Russia
• Andrey A. Yurchenko, St. Petersburg State University - Russia
• Peter Van Heusden, University of the Western Cape - South Africa
• Siddharth Singh, Pacific Biosciences
• Natascha May Thevasagayam, Temasek Life Sciences Laboratory - Singapore
• Sai Rama Sridatta Prakki, Temasek Life Sciences Laboratory - Singapore
• Kathiresan Purushothaman, Temasek Life Sciences Laboratory - Singapore
• Jolly M. Saju, Temasek Life Sciences Laboratory - Singapore
• Junhui Jiang, Temasek Life Sciences Laboratory - Singapore
• Stanley Kimbung Mbandi, University of the Western Cape - South Africa
• Mario Jonas, University of the Western Cape - South Africa
• Amy Hin Yan Tong, University of Toronto - Canada
• Sarah Mwangi, University of the Western Cape - South Africa
• Doreen Lau, Temasek Life Sciences Laboratory - Singapore
• Si Yan Ngoh, Temasek Life Sciences Laboratory - Singapore
• Woei Chang Liew, Temasek Life Sciences Laboratory - Singapore
• Xueyan Shen, Temasek Life Sciences Laboratory - Singapore
• Lawrence S. Hon, Pacific Biosciences
• James P. Drake, Pacific Biosciences
• Matthew Boitano, Pacific Biosciences
• Richard Hall, Pacific Biosciences
• Chen-Shan Chin, Pacific Biosciences
• Ramkumar Lachumanan, Pacific Biosciences
• Jonas Korlach, Pacific Biosciences
• Vladimir Trifonov, Siberian Branch of the Russian Academy of Sciences - Novosibirsk, Russia
• Marsel Kabilov, Siberian Branch of the Russian Academy of Sciences - Novosibirsk, Russia
• Alexey Tupikin, Siberian Branch of the Russian Academy of Sciences - Novosibirsk, Russia
• Darrell Green, University of East Anglia - United Kingdom
• Simon Moxon, The Genome Analysis Centre - United Kingdom
• Tyler Garvin, Cold Spring Harbor Laboratory
• Fritz J. Sedlazeck, Cold Spring Harbor Laboratory; Johns Hopkins University
• Gregory W. Vurture, Cold Spring Harbor Laboratory
• Gopikrishna Gopalapillai, ICAR-Central Institute of Brackishwater Aquaculture - India
• Vinaya Kumar Katneni, ICAR-Central Institute of Brackishwater Aquaculture - India
• Tansyn H. Noble, James Cook University - Australia
• Vinod Scaria, CSIR-Institute of Genomics and Integrative Biology - India
• Sridhar Sivasubbu, CSIR-Institute of Genomics and Integrative Biology - India
• Dean R. Jerry, James Cook University - Australia
• Stephen J. O'Brien, St. Petersburg State University - Russia; Nova Southeastern UniversityFollow
• Michael C. Schatz, Cold Spring Harbor Laboratory; Johns Hopkins University
• Tamas Dalmay, University of East Anglia - United Kingdom
• Stephen W. Turner, Pacific Biosciences
• Si Lok, Peter Gilgan Centre for Research and Learning - Toronto, Canada
• Alan Christoffels, University of the Western Cape - South Africa
• Laszlo Orban, Temasek Life Sciences Laboratory - Singapore; University of Pannonia - Hungary; Murdoch University - Australia

ORCID

0000-0001-7353-8301

ResearcherID

N-1726-2015

Document Type

Article

Publication Title

PLoS Genetics

ISSN

1553-7390

Publication Date

4-15-2016

Abstract

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.

DOI

10.1371/journal.pgen.1005954

Volume

12

Issue

4 e1005954

First Page

1

Last Page

35

Comments

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 public domain dedication.

Additional Comments

GenBank accession #: LLXD00000000; Singapore Competitive Research Program # NRF-CRP7-2010-01; Russian Academy of Sciences grant #: SB RAS no. 137; Russian Ministry of Science megagrant #: 11.G34.31.0068; St. Petersburg State University grant #: IAS 1.37.153.2014; Russian Foundation for Basic Research grant #: RFBR 14-14-00275; National Science Foundation award #s: DBI-1350041, IOS-1237880; National Institute of Health award #: R01-HG006677; Cold Spring Harbor Laboratory training grant #: 5T32GM065094

NSUWorks Citation

Vij, Shubha; Heiner Kuhl; Inna S. Kuznetsova; Aleksey Komissarov; Andrey A. Yurchenko; Peter Van Heusden; Siddharth Singh; Natascha May 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; Tamas Dalmay; Stephen W. Turner; Si Lok; Alan Christoffels; and Laszlo Orban. 2016. "Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding." PLoS Genetics 12, (4 e1005954): 1-35. doi:10.1371/journal.pgen.1005954.