title: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
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.
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Shubha
authors.initials: S
authors.lastname: Vij
authors.affiliation: Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Heiner
authors.initials: H
authors.lastname: Kuhl
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.|Laboratory of Chromosome Structure and Function, Department of Cytology and Histology, Biological Faculty, Saint Petersburg State University, St. Petersburg, Russia.
authors.forename: Inna S
authors.initials: IS
authors.lastname: Kuznetsova
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Komissarov
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Yurchenko
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
authors.forename: Peter
authors.initials: P
authors.lastname: Van Heusden
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Siddharth
authors.initials: S
authors.lastname: Singh
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Natascha M
authors.initials: NM
authors.lastname: Thevasagayam
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Sai Rama Sridatta
authors.initials: SR
authors.lastname: Prakki
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Kathiresan
authors.initials: K
authors.lastname: Purushothaman
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Jolly M
authors.initials: JM
authors.lastname: Saju
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Junhui
authors.initials: J
authors.lastname: Jiang
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
authors.forename: Stanley Kimbung
authors.initials: SK
authors.lastname: Mbandi
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
authors.forename: Mario
authors.initials: M
authors.lastname: Jonas
authors.affiliation: Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.
authors.forename: Amy
authors.initials: A
authors.lastname: Hin Yan Tong
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
authors.forename: Sarah
authors.initials: S
authors.lastname: Mwangi
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Doreen
authors.initials: D
authors.lastname: Lau
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Si Yan
authors.initials: SY
authors.lastname: Ngoh
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Woei Chang
authors.initials: WC
authors.lastname: Liew
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.
authors.forename: Xueyan
authors.initials: X
authors.lastname: Shen
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Lawrence S
authors.initials: LS
authors.lastname: Hon
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: James P
authors.initials: JP
authors.lastname: Drake
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Matthew
authors.initials: M
authors.lastname: Boitano
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Hall
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Chen-Shan
authors.initials: CS
authors.lastname: Chin
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Ramkumar
authors.initials: R
authors.lastname: Lachumanan
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Trifonov
authors.affiliation: Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
authors.forename: Marsel
authors.initials: M
authors.lastname: Kabilov
authors.affiliation: Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Tupikin
authors.affiliation: Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
authors.forename: Darrell
authors.initials: D
authors.lastname: Green
authors.affiliation: The Genome Analysis Centre, Norwich, United Kingdom.
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
authors.forename: Tyler
authors.initials: T
authors.lastname: Garvin
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.|Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Fritz J
authors.initials: FJ
authors.lastname: Sedlazeck
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.
authors.forename: Gregory W
authors.initials: GW
authors.lastname: Vurture
authors.affiliation: Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India.
authors.forename: Gopikrishna
authors.initials: G
authors.lastname: Gopalapillai
authors.affiliation: Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India.
authors.forename: Vinaya
authors.initials: V
authors.lastname: Kumar Katneni
authors.affiliation: College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia.
authors.forename: Tansyn H
authors.initials: TH
authors.lastname: Noble
authors.affiliation: CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.affiliation: CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Sivasubbu
authors.affiliation: College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia.
authors.forename: Dean R
authors.initials: DR
authors.lastname: Jerry
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia.|Oceanographic Center, Nova Southeastern University Ft. Lauderdale, Ft. Lauderdale, Florida, United States of America.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America.|Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
authors.affiliation: School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
authors.forename: Tamás
authors.initials: T
authors.lastname: Dalmay
authors.affiliation: Pacific Biosciences, Menlo Park, California, United States of America.
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Turner
authors.affiliation: The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.
authors.forename: Si
authors.initials: S
authors.lastname: Lok
authors.affiliation: South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.
authors.forename: Alan
authors.initials: A
authors.lastname: Christoffels
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore.|Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, Hungary.|Centre for Comparative Genomics, Murdoch University, Murdoch, Australia.
authors.forename: László
authors.initials: L
authors.lastname: Orbán
mesh_terms: D000818:Animals; D001492:Bass / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D016678:Genome; D017404:In Situ Hybridization, Fluorescence; D010802:Phylogeny