Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding
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Date
2016
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
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.
Description
Keywords
Asian seabass, Lates calcarifer, Chromosomes, Fish species, DNA sequencing, Genome sequencing, North-Western India, South-East Asia, Australia, Papua New Guinea
Citation
Vij, S. et al. (2016). Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. PLoS Genetics, 12(4): e1005954