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Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order

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Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order. / Bancroft, Ian; Fraser, Fiona; Morgan, Colin; Trick, Martin.

In: Data in Brief, Vol. 3, 06.2015, p. 51-55.

Research output: Contribution to journalArticlepeer-review

Harvard

Bancroft, I, Fraser, F, Morgan, C & Trick, M 2015, 'Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order', Data in Brief, vol. 3, pp. 51-55. https://doi.org/10.1016/j.dib.2015.01.004

APA

Bancroft, I., Fraser, F., Morgan, C., & Trick, M. (2015). Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order. Data in Brief, 3, 51-55. https://doi.org/10.1016/j.dib.2015.01.004

Vancouver

Bancroft I, Fraser F, Morgan C, Trick M. Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order. Data in Brief. 2015 Jun;3:51-55. https://doi.org/10.1016/j.dib.2015.01.004

Author

Bancroft, Ian ; Fraser, Fiona ; Morgan, Colin ; Trick, Martin. / Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order. In: Data in Brief. 2015 ; Vol. 3. pp. 51-55.

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@article{5ca81ae3a2f0488b8057a9d54fd3c3a7,
title = "Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order",
abstract = "This data article includes SNP scoring across lines of the Brassica napus TNDH population based on Illumina sequencing of mRNA, expanded to 75 lines. The 21, 323 mapped markers defined 887 recombination bins, representing an updated genetic linkage map for the species. Based on this new map, 5 genome sequence scaffolds were split and the order and orientation of scaffolds updated to establish a new pseudomolecule specification. The order of unigenes and SNP array probes within these pseudomolecules was determined. Unigenes were assessed for sequence similarity to the A and C genomes. The 57, 246 that mapped to both enabled the collinearity of the A and C genomes to be illustrated graphically. Although the great majority was in collinear positions, some were not. Analyses of 60 such instances are presented, suggesting that the breakdown in collinearity was largely due to either the absence of the homoeologue on one genome (resulting in sequence match to a paralogue) or multiple similar sequences being present. The mRNAseq datasets for the TNDH lines are available from the SRA repository (ERA283648); the remaining datasets are supplied with this article.",
author = "Ian Bancroft and Fiona Fraser and Colin Morgan and Martin Trick",
year = "2015",
month = jun,
doi = "10.1016/j.dib.2015.01.004",
language = "English",
volume = "3",
pages = "51--55",
journal = "Data in Brief",
issn = "2352-3409",
publisher = "Elsevier BV",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order

AU - Bancroft, Ian

AU - Fraser, Fiona

AU - Morgan, Colin

AU - Trick, Martin

PY - 2015/6

Y1 - 2015/6

N2 - This data article includes SNP scoring across lines of the Brassica napus TNDH population based on Illumina sequencing of mRNA, expanded to 75 lines. The 21, 323 mapped markers defined 887 recombination bins, representing an updated genetic linkage map for the species. Based on this new map, 5 genome sequence scaffolds were split and the order and orientation of scaffolds updated to establish a new pseudomolecule specification. The order of unigenes and SNP array probes within these pseudomolecules was determined. Unigenes were assessed for sequence similarity to the A and C genomes. The 57, 246 that mapped to both enabled the collinearity of the A and C genomes to be illustrated graphically. Although the great majority was in collinear positions, some were not. Analyses of 60 such instances are presented, suggesting that the breakdown in collinearity was largely due to either the absence of the homoeologue on one genome (resulting in sequence match to a paralogue) or multiple similar sequences being present. The mRNAseq datasets for the TNDH lines are available from the SRA repository (ERA283648); the remaining datasets are supplied with this article.

AB - This data article includes SNP scoring across lines of the Brassica napus TNDH population based on Illumina sequencing of mRNA, expanded to 75 lines. The 21, 323 mapped markers defined 887 recombination bins, representing an updated genetic linkage map for the species. Based on this new map, 5 genome sequence scaffolds were split and the order and orientation of scaffolds updated to establish a new pseudomolecule specification. The order of unigenes and SNP array probes within these pseudomolecules was determined. Unigenes were assessed for sequence similarity to the A and C genomes. The 57, 246 that mapped to both enabled the collinearity of the A and C genomes to be illustrated graphically. Although the great majority was in collinear positions, some were not. Analyses of 60 such instances are presented, suggesting that the breakdown in collinearity was largely due to either the absence of the homoeologue on one genome (resulting in sequence match to a paralogue) or multiple similar sequences being present. The mRNAseq datasets for the TNDH lines are available from the SRA repository (ERA283648); the remaining datasets are supplied with this article.

U2 - 10.1016/j.dib.2015.01.004

DO - 10.1016/j.dib.2015.01.004

M3 - Article

VL - 3

SP - 51

EP - 55

JO - Data in Brief

JF - Data in Brief

SN - 2352-3409

ER -