title: Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research.
abstract: This data article reports the establishment of the first pan-transcriptome resources for the Brassica A and C genomes. These were developed using existing coding DNA sequence (CDS) gene models from the now-published Brassica oleracea TO1000 and Brassica napus Darmor-bzh genome sequence assemblies representing the chromosomes of these species, along with preliminary CDS models from an updated Brassica rapa Chiifu genome sequence assembly. The B. rapa genome sequence scaffolds required splitting and re-ordering to match the expected genome organisation based on a high density SNP linkage map, but the B. oleracea assembly was used unchanged. The resulting B. rapa (A genome) pseudomolecules contained 47,656 ordered CDS models and the B. oleracea (C genome) pseudomolecules contained 54,766 ordered CDS models. Interpolation of B. napus CDS models not already represented by orthologues resulted in 52,790 and 63,308 ordered CDS models in the A and C pan-transcriptomes, an increase of 13,676 overall. Comparison of the organisation of this resource with publicly available genome sequences for B. napus showed excellent consistency for the B. napus Darmor-bzh resource, but more breakdown of collinearity for the B. napus ZS11 resource. CDS datasets comprising the pan-transcriptomes are available with this article (B. rapa) or from public repositories (B. oleracea and B. napus).
authors.affiliation: Department of Biology, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Zhesi
authors.initials: Z
authors.lastname: He
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Cheng
authors.affiliation: Department of Biology, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.affiliation: Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Canada S7N0X2.
authors.forename: Isobel A P
authors.initials: IA
authors.lastname: Parkin
authors.affiliation: URGV (Institut National de la Recherche Agronomique, Université Evry Val d'Essonne), Evry, France.
authors.forename: Boulos
authors.initials: B
authors.lastname: Chalhoub
authors.affiliation: Oil Crops Research Institute, CAAS, No. 2 Xudong Second Road, Wuhan, Hubei, China.
authors.forename: Shengyi
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Biology, University of York, Heslington, York YO10 5DD, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft