Biology Faculty Articles

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

Document Type

Article

Publication Date

4-15-2016

Publication Title

PLoS Genetics

ISSN

1553-7390

Volume

12

Issue/No.

4 e1005954

First Page

1

Last Page

35

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.

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

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

DOI

10.1371/journal.pgen.1005954

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