Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding

Journal Publication ResearchOnline@JCU
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
Dean Jerry
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.

Journal

PLoS Genetics

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12

ISBN/ISSN

1553-7404

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4

Pages Count

35

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Publisher

Public Library of Science

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DOI

10.1371/journal.pgen.1005954