ArticlePLoS genetics2016
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
Erratum issuedOpen access · goldAbstract read
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Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 86 papers.
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86citing papers in PubMed
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86 citing papers in PubMed, 218 citations in OpenAlex.
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- Correlation between DNA methylation and transcriptomic changes in golden Asian sea bass (Lates calcarifer): An integrated approach.Journal of fish biology · 2026Article
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- A telomere-to-telomere gap-free genome assembly of the protandrous hermaphrodite Asian seabass (Lates calcarifer).Scientific data · 2025Article
- Mapping of Growth-Associated SNP Markers in Asian Seabass (Latest calcarifer) Using the Marey Map Approach.Marine biotechnology (New York, N.Y.) · 2025Article
- Chromosome-level genome assembly with telomeric repeats at scaffold ends for Rhabdosargus sarba.Scientific data · 2025Article
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- Bioinformatics in Russia: history and present-day landscape.Briefings in bioinformatics · 2024Review
- Genomic structural variation in Barramundi Perch Lates calcarifer and potential roles in speciation and adaptation.G3 (Bethesda, Md.) · 2024Article
- Draft Genome of Akame (Lates Japonicus) Reveals Possible Genetic Mechanisms for Long-Term Persistence and Adaptive Evolution with Low Genetic Diversity.Genome biology and evolution · 2024Article
- Comparative Nutritional and Histological Analysis of Malabar Red Snapper (Animals : an open access journal from MDPI · 2024Article
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
48 authors at 17 institutions in 10 countries.
Shubha VijReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Heiner KuhlMax Planck Institute for Molecular Genetics, Berlin, Germany.
Inna S KuznetsovaReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Aleksey KomissarovTheodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.
Andrey A YurchenkoTheodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.
Peter Van HeusdenSouth African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
Siddharth SinghPacific Biosciences, Menlo Park, California, United States of America.
Natascha M ThevasagayamReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Sai Rama Sridatta PrakkiReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Kathiresan PurushothamanReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Jolly M SajuReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Junhui JiangReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Stanley Kimbung MbandiSouth African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
Mario JonasSouth African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
Amy Hin Yan TongDonnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
Sarah MwangiSouth African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
Doreen LauReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Si Yan NgohReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Woei Chang LiewReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Xueyan ShenReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Lawrence S HonPacific Biosciences, Menlo Park, California, United States of America.
James P DrakePacific Biosciences, Menlo Park, California, United States of America.
Matthew BoitanoPacific Biosciences, Menlo Park, California, United States of America.
Richard HallPacific Biosciences, Menlo Park, California, United States of America.
Chen-Shan ChinPacific Biosciences, Menlo Park, California, United States of America.
Ramkumar LachumananPacific Biosciences, Menlo Park, California, United States of America.
Jonas KorlachPacific Biosciences, Menlo Park, California, United States of America.
Vladimir TrifonovInstitute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.
Marsel KabilovGenomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Alexey TupikinGenomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
Darrell GreenNorwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
Simon MoxonThe Genome Analysis Centre, Norwich, United Kingdom.
Tyler GarvinSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
Fritz J SedlazeckSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
Gregory W VurtureSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
Gopikrishna GopalapillaiNutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India.
Vinaya Kumar KatneniNutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India.
Tansyn H NobleCollege of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia.
Vinod ScariaCSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.
Sridhar SivasubbuCSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.
Dean R JerryCollege of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia.
Stephen J O'BrienTheodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.
Michael C SchatzSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
Tamás DalmaySchool of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
Stephen W TurnerPacific Biosciences, Menlo Park, California, United States of America.
Si LokThe Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.
Alan ChristoffelsSouth African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
László OrbánReproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
Temasek Life Sciences Laboratory · SGPacific Biosciences (United States) · USUniversity of the Western Cape · ZACold Spring Harbor Laboratory · USSiberian Branch of the Russian Academy of Sciences · RUSt Petersburg University · RUCentral Institute of Brackishwater Aquaculture · INInstitute of Genomics and Integrative Biology · INJames Cook University · AUEarlham Institute · GBJohns Hopkins University · USMax Planck Institute for Molecular Genetics · DEMurdoch University · AUNorwich Research Park · GBSickKids Foundation · CAUniversity of East Anglia · GBUniversity of Toronto · CA
Funding
Computational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7MCSHL Watson School of Biological SciencesT32GM065094 · NIGMS · COLD SPRING HARBOR LABORATORY · PI GANN, ALEXANDER · 2002 to 2021
$4.8MNHGRI NIH HHS R01 HG006677NIGMS NIH HHS T32 GM065094
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.
Indexed as
Chromosome MappingAnimalsBassGenomeIn Situ Hybridization, FluorescencePhylogeny
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