PLoS Genetics (Apr 2016)

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

  • 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

DOI
https://doi.org/10.1371/journal.pgen.1005954
Journal volume & issue
Vol. 12, no. 4
p. e1005954

Abstract

Read online

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.