Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis

Rami A. Dalloul; Julie A. Long; Aleksey V. Zimin; Luqman Aslam; Kathryn Beal; Le Ann Blomberg; Pascal Bouffard; David W. Burt; Oswald Crasta; Richard P.M.A. Crooijmans; Kristal Cooper; Roger A. Coulombe; Supriyo De; Mary E. Delany; Jerry B. Dodgson; Jennifer J. Dong; Clive Evans; Karin M. Frederickson; Paul Flicek; Liliana Florea; Otto Folkerts; Martien A.M. Groenen; Tim T. Harkins; Javier Herrero; Steve Hoffmann; Hendrik Jan Megens; Andrew Jiang; Pieter de Jong; Pete Kaiser; Heebal Kim; Kyu Won Kim; Sungwon Kim; David Langenberger; Mi Kyung Lee; Taeheon Lee; Shrinivasrao Mane; Guillaume Marcais; Manja Marz; Audrey P. McElroy; Thero Modise; Mikhail Nefedov; Cédric Notredame; Ian R. Paton; William S. Payne; Geo Pertea; Dennis Prickett; Daniela Puiu; Dan Qioa; Emanuele Raineri; Magali Ruffier; Steven L. Salzberg; Michael C. Schatz; Chantel Scheuring; Carl J. Schmidt; Steven Schroeder; Stephen M.J. Searle; Edward J. Smith; Jacqueline Smith; Tad S. Sonstegard; Peter F. Stadler; Hakim Tafer; Zhijian Tu; Curtis P. van Tassell; Albert J. Vilella; Kelly P. Williams; James A. Yorke; Liqing Zhang; Hong Bin Zhang; Xiaojun Zhang; Yang Zhang; Kent M. Reed

doi:10.1371/journal.pbio.1000475

Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis

Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin, Luqman Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W. Burt, Oswald Crasta, Richard P.M.A. Crooijmans, Kristal Cooper, Roger A. Coulombe, Supriyo De, Mary E. Delany, Jerry B. Dodgson, Jennifer J. Dong, Clive Evans, Karin M. Frederickson, Paul Flicek, Liliana FloreaOtto Folkerts, Martien A.M. Groenen, Tim T. Harkins, Javier Herrero, Steve Hoffmann, Hendrik Jan Megens, Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu Won Kim, Sungwon Kim, David Langenberger, Mi Kyung Lee, Taeheon Lee, Shrinivasrao Mane, Guillaume Marcais, Manja Marz, Audrey P. McElroy, Thero Modise, Mikhail Nefedov, Cédric Notredame, Ian R. Paton, William S. Payne, Geo Pertea, Dennis Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L. Salzberg, Michael C. Schatz, Chantel Scheuring, Carl J. Schmidt, Steven Schroeder, Stephen M.J. Searle, Edward J. Smith, Jacqueline Smith, Tad S. Sonstegard, Peter F. Stadler, Hakim Tafer, Zhijian Tu, Curtis P. van Tassell, Albert J. Vilella, Kelly P. Williams, James A. Yorke, Liqing Zhang, Hong Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M. Reed

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

293 Scopus citations

Abstract

A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

Original language	English (US)
Article number	e1000475
Journal	PLoS biology
Volume	8
Issue number	9
DOIs	https://doi.org/10.1371/journal.pbio.1000475
State	Published - Sep 2010
Externally published	Yes

ASJC Scopus subject areas

General Neuroscience
General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology
General Agricultural and Biological Sciences

Access to Document

10.1371/journal.pbio.1000475

Cite this

Dalloul, R. A., Long, J. A., Zimin, A. V., Aslam, L., Beal, K., Blomberg, L. A., Bouffard, P., Burt, D. W., Crasta, O., Crooijmans, R. P. M. A., Cooper, K., Coulombe, R. A., De, S., Delany, M. E., Dodgson, J. B., Dong, J. J., Evans, C., Frederickson, K. M., Flicek, P., ... Reed, K. M. (2010). Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis. PLoS biology, 8(9), Article e1000475. https://doi.org/10.1371/journal.pbio.1000475

Dalloul, RA, Long, JA, Zimin, AV, Aslam, L, Beal, K, Blomberg, LA, Bouffard, P, Burt, DW, Crasta, O, Crooijmans, RPMA, Cooper, K, Coulombe, RA, De, S, Delany, ME, Dodgson, JB, Dong, JJ, Evans, C, Frederickson, KM, Flicek, P, Florea, L, Folkerts, O, Groenen, MAM, Harkins, TT, Herrero, J, Hoffmann, S, Megens, HJ, Jiang, A, de Jong, P, Kaiser, P, Kim, H, Kim, KW, Kim, S, Langenberger, D, Lee, MK, Lee, T, Mane, S, Marcais, G, Marz, M, McElroy, AP, Modise, T, Nefedov, M, Notredame, C, Paton, IR, Payne, WS, Pertea, G, Prickett, D, Puiu, D, Qioa, D, Raineri, E, Ruffier, M, Salzberg, SL , Schatz, MC, Scheuring, C, Schmidt, CJ, Schroeder, S, Searle, SMJ, Smith, EJ, Smith, J, Sonstegard, TS, Stadler, PF, Tafer, H, Tu, Z, van Tassell, CP, Vilella, AJ, Williams, KP, Yorke, JA, Zhang, L, Zhang, HB, Zhang, X, Zhang, Y & Reed, KM 2010, 'Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis', PLoS biology, vol. 8, no. 9, e1000475. https://doi.org/10.1371/journal.pbio.1000475

@article{d277b9c5d8e14ba7b69f35825e3c3cbb,

title = "Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis",

abstract = "A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.",

author = "Dalloul, {Rami A.} and Long, {Julie A.} and Zimin, {Aleksey V.} and Luqman Aslam and Kathryn Beal and Blomberg, {Le Ann} and Pascal Bouffard and Burt, {David W.} and Oswald Crasta and Crooijmans, {Richard P.M.A.} and Kristal Cooper and Coulombe, {Roger A.} and Supriyo De and Delany, {Mary E.} and Dodgson, {Jerry B.} and Dong, {Jennifer J.} and Clive Evans and Frederickson, {Karin M.} and Paul Flicek and Liliana Florea and Otto Folkerts and Groenen, {Martien A.M.} and Harkins, {Tim T.} and Javier Herrero and Steve Hoffmann and Megens, {Hendrik Jan} and Andrew Jiang and {de Jong}, Pieter and Pete Kaiser and Heebal Kim and Kim, {Kyu Won} and Sungwon Kim and David Langenberger and Lee, {Mi Kyung} and Taeheon Lee and Shrinivasrao Mane and Guillaume Marcais and Manja Marz and McElroy, {Audrey P.} and Thero Modise and Mikhail Nefedov and C{\'e}dric Notredame and Paton, {Ian R.} and Payne, {William S.} and Geo Pertea and Dennis Prickett and Daniela Puiu and Dan Qioa and Emanuele Raineri and Magali Ruffier and Salzberg, {Steven L.} and Schatz, {Michael C.} and Chantel Scheuring and Schmidt, {Carl J.} and Steven Schroeder and Searle, {Stephen M.J.} and Smith, {Edward J.} and Jacqueline Smith and Sonstegard, {Tad S.} and Stadler, {Peter F.} and Hakim Tafer and Zhijian Tu and {van Tassell}, {Curtis P.} and Vilella, {Albert J.} and Williams, {Kelly P.} and Yorke, {James A.} and Liqing Zhang and Zhang, {Hong Bin} and Xiaojun Zhang and Yang Zhang and Reed, {Kent M.}",

year = "2010",

month = sep,

doi = "10.1371/journal.pbio.1000475",

language = "English (US)",

volume = "8",

journal = "PLoS biology",

issn = "1544-9173",

publisher = "Public Library of Science",

number = "9",

}

TY - JOUR

T1 - Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo)

T2 - Genome assembly and analysis

AU - Dalloul, Rami A.

AU - Long, Julie A.

AU - Zimin, Aleksey V.

AU - Aslam, Luqman

AU - Beal, Kathryn

AU - Blomberg, Le Ann

AU - Bouffard, Pascal

AU - Burt, David W.

AU - Crasta, Oswald

AU - Crooijmans, Richard P.M.A.

AU - Cooper, Kristal

AU - Coulombe, Roger A.

AU - De, Supriyo

AU - Delany, Mary E.

AU - Dodgson, Jerry B.

AU - Dong, Jennifer J.

AU - Evans, Clive

AU - Frederickson, Karin M.

AU - Flicek, Paul

AU - Florea, Liliana

AU - Folkerts, Otto

AU - Groenen, Martien A.M.

AU - Harkins, Tim T.

AU - Herrero, Javier

AU - Hoffmann, Steve

AU - Megens, Hendrik Jan

AU - Jiang, Andrew

AU - de Jong, Pieter

AU - Kaiser, Pete

AU - Kim, Heebal

AU - Kim, Kyu Won

AU - Kim, Sungwon

AU - Langenberger, David

AU - Lee, Mi Kyung

AU - Lee, Taeheon

AU - Mane, Shrinivasrao

AU - Marcais, Guillaume

AU - Marz, Manja

AU - McElroy, Audrey P.

AU - Modise, Thero

AU - Nefedov, Mikhail

AU - Notredame, Cédric

AU - Paton, Ian R.

AU - Payne, William S.

AU - Pertea, Geo

AU - Prickett, Dennis

AU - Puiu, Daniela

AU - Qioa, Dan

AU - Raineri, Emanuele

AU - Ruffier, Magali

AU - Salzberg, Steven L.

AU - Schatz, Michael C.

AU - Scheuring, Chantel

AU - Schmidt, Carl J.

AU - Schroeder, Steven

AU - Searle, Stephen M.J.

AU - Smith, Edward J.

AU - Smith, Jacqueline

AU - Sonstegard, Tad S.

AU - Stadler, Peter F.

AU - Tafer, Hakim

AU - Tu, Zhijian

AU - van Tassell, Curtis P.

AU - Vilella, Albert J.

AU - Williams, Kelly P.

AU - Yorke, James A.

AU - Zhang, Liqing

AU - Zhang, Hong Bin

AU - Zhang, Xiaojun

AU - Zhang, Yang

AU - Reed, Kent M.

PY - 2010/9

Y1 - 2010/9

N2 - A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

AB - A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

UR - http://www.scopus.com/inward/record.url?scp=77957903598&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77957903598&partnerID=8YFLogxK

U2 - 10.1371/journal.pbio.1000475

DO - 10.1371/journal.pbio.1000475

M3 - Article

C2 - 20838655

AN - SCOPUS:77957903598

SN - 1544-9173

VL - 8

JO - PLoS biology

JF - PLoS biology

IS - 9

M1 - e1000475

ER -

Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this