Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research.
Construction of Brassica A and C genome-based ordered pan-transcriptomes for use in rapeseed genomic research.
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DOI：
10.1016/j.dib.2015.06.016
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发表时间：
2015-09
期刊：
影响因子：
1.2
通讯作者：
Bancroft I
中科院分区：
文献类型：
--
作者：
He Z;Cheng F;Li Y;Wang X;Parkin IA;Chalhoub B;Liu S;Bancroft I
本文报道了油菜A、C基因组首个泛转录组资源的建立。这些研究是利用现有的编码DNA序列（CDS）基因模型开发的，这些模型来自现已发表的甘蓝TO1000和甘蓝型油菜（Brassica oleracea TO1000）和甘蓝型油菜（Brassica napus daror -bzh）基因组序列组合，代表了这些物种的染色体，以及来自更新的油菜Chiifu基因组序列组合的初步CDS模型。rapa基因组序列支架需要进行分裂和重新排序，以匹配基于高密度SNP连锁图的预期基因组组织，但甘蓝基因组组装不变。得到的rapa （A基因组）伪分子包含47,656个有序CDS模型，甘蓝（C基因组）伪分子包含54,766个有序CDS模型。对未被同源物代表的甘蓝型油菜CDS模型进行插值，在A和C泛转录组中分别得到52,790和63,308个有序CDS模型，总体上增加了13,676个。将该资源的组织与公开的甘蓝型油菜基因组序列进行比较，结果表明甘蓝型油菜达莫尔-bzh资源具有良好的一致性，而甘蓝型油菜ZS11资源具有更多的共线性。包含泛转录组的CDS数据集可从本文（B. rapa）或公共存储库（B. oleracea和B. napus）获得。
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).