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

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

Author information

1
Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
2
Max Planck Institute for Molecular Genetics, Berlin, Germany.
3
Laboratory of Chromosome Structure and Function, Department of Cytology and Histology, Biological Faculty, Saint Petersburg State University, St. Petersburg, Russia.
4
Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.
5
South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
6
Pacific Biosciences, Menlo Park, California, United States of America.
7
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
8
Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.
9
Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
10
Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
11
The Genome Analysis Centre, Norwich, United Kingdom.
12
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
13
Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America.
14
Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India.
15
College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia.
16
CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.
17
Oceanographic Center, Nova Southeastern University Ft. Lauderdale, Ft. Lauderdale, Florida, United States of America.
18
School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
19
The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.
20
Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, Hungary.
21
Centre for Comparative Genomics, Murdoch University, Murdoch, Australia.

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.

PMID:
27082250
PMCID:
PMC4833346
DOI:
10.1371/journal.pgen.1005954
[Indexed for MEDLINE]
Free PMC Article

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