The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

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The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. / Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo; Zhu, Shilin; Shi, Daihu; McDill, Joshua; Yang, Linfeng; Hawkins, Simon; Neutelings, Godfrey; Datla, Raju; Lambert, Georgina; Galbraith, David W.; Grassa, Christopher J.; Geraldes, Armando; Cronk, Quentin C.; Cullis, Christopher; Dash, Prasanta K.; Kumar, Polumetla A.; Cloutier, Sylvie; Sharpe, Andrew G.; Wong, Gane K.-S.; Wang, Jun; Deyholos, Michael K.

I: Plant Journal, Bind 72, Nr. 3, 2012, s. 461-473.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Wang, Z, Hobson, N, Galindo, L, Zhu, S, Shi, D, McDill, J, Yang, L, Hawkins, S, Neutelings, G, Datla, R, Lambert, G, Galbraith, DW, Grassa, CJ, Geraldes, A, Cronk, QC, Cullis, C, Dash, PK, Kumar, PA, Cloutier, S, Sharpe, AG, Wong, GK-S, Wang, J & Deyholos, MK 2012, 'The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads' Plant Journal, bind 72, nr. 3, s. 461-473. https://doi.org/10.1111/j.1365-313X.2012.05093.x

APA

Wang, Z., Hobson, N., Galindo, L., Zhu, S., Shi, D., McDill, J., ... Deyholos, M. K. (2012). The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant Journal, 72(3), 461-473. https://doi.org/10.1111/j.1365-313X.2012.05093.x

Vancouver

Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J o.a. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant Journal. 2012;72(3):461-473. https://doi.org/10.1111/j.1365-313X.2012.05093.x

Author

Wang, Zhiwen ; Hobson, Neil ; Galindo, Leonardo ; Zhu, Shilin ; Shi, Daihu ; McDill, Joshua ; Yang, Linfeng ; Hawkins, Simon ; Neutelings, Godfrey ; Datla, Raju ; Lambert, Georgina ; Galbraith, David W. ; Grassa, Christopher J. ; Geraldes, Armando ; Cronk, Quentin C. ; Cullis, Christopher ; Dash, Prasanta K. ; Kumar, Polumetla A. ; Cloutier, Sylvie ; Sharpe, Andrew G. ; Wong, Gane K.-S. ; Wang, Jun ; Deyholos, Michael K. / The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. I: Plant Journal. 2012 ; Bind 72, Nr. 3. s. 461-473.

Bibtex

@article{c4a244ab33c248eabccd8a3e962a6650,
title = "The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads",
abstract = "Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81{\%} genome coverage. Up to 96{\%} of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93{\%} of published flax ESTs, and 86{\%} of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.",
author = "Zhiwen Wang and Neil Hobson and Leonardo Galindo and Shilin Zhu and Daihu Shi and Joshua McDill and Linfeng Yang and Simon Hawkins and Godfrey Neutelings and Raju Datla and Georgina Lambert and Galbraith, {David W.} and Grassa, {Christopher J.} and Armando Geraldes and Cronk, {Quentin C.} and Christopher Cullis and Dash, {Prasanta K.} and Kumar, {Polumetla A.} and Sylvie Cloutier and Sharpe, {Andrew G.} and Wong, {Gane K.-S.} and Jun Wang and Deyholos, {Michael K.}",
year = "2012",
doi = "10.1111/j.1365-313X.2012.05093.x",
language = "English",
volume = "72",
pages = "461--473",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "3",

}

RIS

TY - JOUR

T1 - The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

AU - Wang, Zhiwen

AU - Hobson, Neil

AU - Galindo, Leonardo

AU - Zhu, Shilin

AU - Shi, Daihu

AU - McDill, Joshua

AU - Yang, Linfeng

AU - Hawkins, Simon

AU - Neutelings, Godfrey

AU - Datla, Raju

AU - Lambert, Georgina

AU - Galbraith, David W.

AU - Grassa, Christopher J.

AU - Geraldes, Armando

AU - Cronk, Quentin C.

AU - Cullis, Christopher

AU - Dash, Prasanta K.

AU - Kumar, Polumetla A.

AU - Cloutier, Sylvie

AU - Sharpe, Andrew G.

AU - Wong, Gane K.-S.

AU - Wang, Jun

AU - Deyholos, Michael K.

PY - 2012

Y1 - 2012

N2 - Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.

AB - Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.

U2 - 10.1111/j.1365-313X.2012.05093.x

DO - 10.1111/j.1365-313X.2012.05093.x

M3 - Journal article

VL - 72

SP - 461

EP - 473

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 3

ER -

ID: 46232924