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; Tamas 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 (Lead Author), 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 ShenLawrence 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, Tamas Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán

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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
Article number	e1005954
Journal	PLoS Genetics
Volume	12
Issue number	4
DOIs	https://doi.org/10.1371/journal.pgen.1005954
Publication status	Published - 15 Apr 2016

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2016 Vij et al. Chromosomal-levelFinal published version, 3.82 MBLicence: CC BY

Tamas Dalmay
- T.Dalmayuea.acuk
- School of Biological Sciences - Professor of RNA Biology
- Plant Sciences - Member
Person: Research Group Member, Academic, Teaching & Research
Darrell Green
- D.Greenuea.acuk
- Norwich Medical School - Lecturer in RNA Biology
- Metabolic Health - Member
Person: Research Centre Member, Academic, Teaching & Research
Simon Moxon
- S.Moxonuea.acuk
- School of Biological Sciences - Associate Professor in Bioinformatics
Person: Academic, Teaching & Research

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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., Kimbung Mbandi, S., Jonas, M., Tong, A. H. Y., 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), [e1005954]. https://doi.org/10.1371/journal.pgen.1005954

Vij, Shubha ; Kuhl, Heiner ; Kuznetsova, Inna S. ; Komissarov, Aleksey ; Yurchenko, Andrey A. ; Van Heusden, Peter ; Singh, Siddharth ; Thevasagayam, Natascha M. ; Prakki, Sai Rama Sridatta ; Purushothaman, Kathiresan ; Saju, Jolly M. ; Jiang, Junhui ; Kimbung Mbandi, Stanley ; Jonas, Mario ; Tong, Amy Hin Yan ; Mwangi, Sarah ; Lau, Doreen ; Ngoh, Si Yan ; Liew, Woei Chang ; Shen, Xueyan ; Hon, Lawrence S. ; Drake, James P. ; Boitano, Matthew ; Hall, Richard ; Chin, Chen-Shan ; Lachumanan, Ramkumar ; Korlach, Jonas ; Trifonov, Vladimir ; Kabilov, Marsel ; Tupikin, Alexey ; Green, Darrell ; Moxon, Simon ; Garvin, Tyler ; Sedlazeck, Fritz J. ; Vurture, Gregory W. ; Gopalapillai, Gopikrishna ; Katneni, Vinaya Kumar ; Noble, Tansyn H. ; Scaria, Vinod ; Sivasubbu, Sridhar ; Jerry, Dean R. ; O'Brien, Stephen J. ; Schatz, Michael C. ; Dalmay, Tamas ; Turner, Stephen W. ; Lok, Si ; Christoffels, Alan ; Orbán, László. / Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding. In: PLoS Genetics. 2016 ; Vol. 12, No. 4.

@article{85bebf3399144da4821a92f24934f439,

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.",

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 {Kimbung Mbandi}, Stanley and Mario Jonas and Tong, {Amy Hin Yan} 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 Chen-Shan Chin 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 Katneni, {Vinaya Kumar} and Noble, {Tansyn H.} and Vinod Scaria and Sridhar Sivasubbu and Jerry, {Dean R.} and O'Brien, {Stephen J.} and Schatz, {Michael C.} and Tamas Dalmay and Turner, {Stephen W.} and Si Lok and Alan Christoffels and L{\'a}szl{\'o} Orb{\'a}n",

note = "This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.",

year = "2016",

month = apr,

day = "15",

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

language = "English",

volume = "12",

journal = "PLoS Genetics",

issn = "1553-7390",

publisher = "Public Library of Science",

number = "4",

}

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, Kimbung Mbandi, S, Jonas, M, Tong, AHY, Mwangi, S, Lau, D, Ngoh, SY, Liew, WC, Shen, X, Hon, LS, Drake, JP, Boitano, M, Hall, R, Chin, C-S, Lachumanan, R, Korlach, J, Trifonov, V, Kabilov, M, Tupikin, A, Green, D , Moxon, S, Garvin, T, Sedlazeck, FJ, Vurture, GW, Gopalapillai, G, Katneni, VK, 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

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

In: PLoS Genetics, Vol. 12, No. 4, e1005954, 15.04.2016.

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

TY - JOUR

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 - Kimbung Mbandi, Stanley

AU - Jonas, Mario

AU - Tong, Amy Hin Yan

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 - Katneni, Vinaya Kumar

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, Tamas

AU - Turner, Stephen W.

AU - Lok, Si

AU - Christoffels, Alan

AU - Orbán, László

N1 - This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

PY - 2016/4/15

Y1 - 2016/4/15

N2 - 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.

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.

U2 - 10.1371/journal.pgen.1005954

DO - 10.1371/journal.pgen.1005954

M3 - Article

VL - 12

JO - PLoS Genetics

JF - PLoS Genetics

SN - 1553-7390

IS - 4

M1 - e1005954

ER -

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

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Tamas Dalmay

Darrell Green

Simon Moxon

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