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

Shubha Vij; Heiner Kuhl; Inna S. Kuznetsova; Aleksey Komissarov; Andrey A. Yurchenko; Peter Van Heusden; Siddharth Singh; Natascha M. Thevasagayam; Sai Rama Sridatta Prakki; Kathiresan Purushothaman; Jolly M. Saju; Junhui Jiang; Stanley Kimbung Mbandi; Mario Jonas; Amy Hin Yan Tong; Sarah Mwangi; Doreen Lau; Si Yan Ngoh; Woei Chang Liew; Xueyan Shen; Lawrence S. Hon; James P. Drake; Matthew Boitano; Richard Hall; Chen Shan Chin; Ramkumar Lachumanan; Jonas Korlach; Vladimir Trifonov; Marsel Kabilov; Alexey Tupikin; Darrell Green; Simon Moxon; Tyler Garvin; Fritz J. Sedlazeck; Gregory W. Vurture; Gopikrishna Gopalapillai; Vinaya Kumar Katneni; Tansyn H. Noble; Vinod Scaria; Sridhar Sivasubbu; Dean R. Jerry; Stephen J. O'Brien; Michael C. Schatz; Tamás Dalmay; Stephen W. Turner; Si Lok; Alan Christoffels; László Orbán

doi:10.1371/journal.pgen.1005954

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

Shubha Vij
, Heiner Kuhl
, Inna S. Kuznetsova
, Aleksey Komissarov
, Andrey A. Yurchenko
, Peter Van Heusden
, Siddharth Singh
, Natascha M. Thevasagayam
, Sai Rama Sridatta Prakki
, Kathiresan Purushothaman
, Jolly M. Saju
, Junhui Jiang
, Stanley Kimbung Mbandi
, Mario Jonas
, Amy Hin Yan Tong
, Sarah Mwangi
, Doreen Lau
, Si Yan Ngoh
, Woei Chang Liew
, Xueyan Shen

Lawrence S. Hon, James P. Drake, Matthew Boitano, Richard Hall, Chen Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, Gopikrishna Gopalapillai, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O'Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Article number	e1005954
Journal	PLoS genetics
Volume	12
Issue number	4
DOIs	https://doi.org/10.1371/journal.pgen.1005954
State	Published - Apr 2016
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Molecular Biology
Genetics
Genetics(clinical)
Cancer Research

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10.1371/journal.pgen.1005954

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Vij, S., Kuhl, H., Kuznetsova, I. S., Komissarov, A., Yurchenko, A. A., Van Heusden, P., Singh, S., Thevasagayam, N. M., Prakki, S. R. S., Purushothaman, K., Saju, J. M., Jiang, J., Mbandi, S. K., Jonas, M., Hin Yan Tong, A., Mwangi, S., Lau, D., Ngoh, S. Y., Liew, W. C., ... Orbán, L. (2016). Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS genetics, 12(4), Article e1005954. https://doi.org/10.1371/journal.pgen.1005954

Vij, S, Kuhl, H, Kuznetsova, IS, Komissarov, A, Yurchenko, AA, Van Heusden, P, Singh, S, Thevasagayam, NM, Prakki, SRS, Purushothaman, K, Saju, JM, Jiang, J, Mbandi, SK, Jonas, M, Hin Yan Tong, A, Mwangi, S, Lau, D, Ngoh, SY, Liew, WC, Shen, X, Hon, LS, Drake, JP, Boitano, M, Hall, R, Chin, CS, Lachumanan, R, Korlach, J, Trifonov, V, Kabilov, M, Tupikin, A, Green, D, Moxon, S, Garvin, T, Sedlazeck, FJ, Vurture, GW, Gopalapillai, G, Kumar Katneni, V, Noble, TH, Scaria, V, Sivasubbu, S, Jerry, DR, O'Brien, SJ, Schatz, MC, Dalmay, T, Turner, SW, Lok, S, Christoffels, A & Orbán, L 2016, 'Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding', PLoS genetics, vol. 12, no. 4, e1005954. https://doi.org/10.1371/journal.pgen.1005954

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

abstract = "We report here the \textasciitilde{}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 \textasciitilde{}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{\textquoteright} 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.",

author = "Shubha Vij and Heiner Kuhl and Kuznetsova, \{Inna S.\} and Aleksey Komissarov and Yurchenko, \{Andrey A.\} and \{Van Heusden\}, Peter and Siddharth Singh and Thevasagayam, \{Natascha M.\} and Prakki, \{Sai Rama Sridatta\} and Kathiresan Purushothaman and Saju, \{Jolly M.\} and Junhui Jiang and Mbandi, \{Stanley Kimbung\} and Mario Jonas and \{Hin Yan Tong\}, Amy and Sarah Mwangi and Doreen Lau and Ngoh, \{Si Yan\} and Liew, \{Woei Chang\} and Xueyan Shen and Hon, \{Lawrence S.\} and Drake, \{James P.\} and Matthew Boitano and Richard Hall and Chin, \{Chen Shan\} and Ramkumar Lachumanan and Jonas Korlach and Vladimir Trifonov and Marsel Kabilov and Alexey Tupikin and Darrell Green and Simon Moxon and Tyler Garvin and Sedlazeck, \{Fritz J.\} and Vurture, \{Gregory W.\} and Gopikrishna Gopalapillai and \{Kumar Katneni\}, Vinaya and Noble, \{Tansyn H.\} and Vinod Scaria and Sridhar Sivasubbu and Jerry, \{Dean R.\} and O'Brien, \{Stephen J.\} and Schatz, \{Michael C.\} and Tam{\'a}s Dalmay and Turner, \{Stephen W.\} and Si Lok and Alan Christoffels and L{\'a}szl{\'o} Orb{\'a}n",

year = "2016",

month = apr,

doi = "10.1371/journal.pgen.1005954",

language = "English (US)",

volume = "12",

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T1 - Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

AU - Vij, Shubha

AU - Kuhl, Heiner

AU - Kuznetsova, Inna S.

AU - Komissarov, Aleksey

AU - Yurchenko, Andrey A.

AU - Van Heusden, Peter

AU - Singh, Siddharth

AU - Thevasagayam, Natascha M.

AU - Prakki, Sai Rama Sridatta

AU - Purushothaman, Kathiresan

AU - Saju, Jolly M.

AU - Jiang, Junhui

AU - Mbandi, Stanley Kimbung

AU - Jonas, Mario

AU - Hin Yan Tong, Amy

AU - Mwangi, Sarah

AU - Lau, Doreen

AU - Ngoh, Si Yan

AU - Liew, Woei Chang

AU - Shen, Xueyan

AU - Hon, Lawrence S.

AU - Drake, James P.

AU - Boitano, Matthew

AU - Hall, Richard

AU - Chin, Chen Shan

AU - Lachumanan, Ramkumar

AU - Korlach, Jonas

AU - Trifonov, Vladimir

AU - Kabilov, Marsel

AU - Tupikin, Alexey

AU - Green, Darrell

AU - Moxon, Simon

AU - Garvin, Tyler

AU - Sedlazeck, Fritz J.

AU - Vurture, Gregory W.

AU - Gopalapillai, Gopikrishna

AU - Kumar Katneni, Vinaya

AU - Noble, Tansyn H.

AU - Scaria, Vinod

AU - Sivasubbu, Sridhar

AU - Jerry, Dean R.

AU - O'Brien, Stephen J.

AU - Schatz, Michael C.

AU - Dalmay, Tamás

AU - Turner, Stephen W.

AU - Lok, Si

AU - Christoffels, Alan

AU - Orbán, László

PY - 2016/4

Y1 - 2016/4

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AB - 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.

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DO - 10.1371/journal.pgen.1005954

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AN - SCOPUS:84964854635

SN - 1553-7390

VL - 12

JO - PLoS genetics

JF - PLoS genetics

IS - 4

M1 - e1005954

ER -

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

Abstract

ASJC Scopus subject areas

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