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

PLoS Genet. 2016 Apr 15;12(4):e1005954. doi: 10.1371/journal.pgen.1005954. eCollection 2016 Apr.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bass / classification
  • Bass / genetics*
  • Chromosome Mapping*
  • Genome
  • In Situ Hybridization, Fluorescence
  • Phylogeny