Abstract
Chinese cabbage (Brassica rapa ssp. pekinensis) is a major crop that is widely cultivated, especially in Korea, Japan, and China. With the advent of next generation sequencing technology, the cost and time required for sequencing have decreased and the development of genome research accelerated. Genome sequencing of Chinese cabbage was completed in 2011 using the variety Chiifu-401-42, and since then the genome has been continuously updated. In the present study, we conducted whole-genome sequencing of Chinese cabbage inbred line CT001, a line widely used in traditional or molecular breeding, to improve the accuracy of genetic polymorphism analysis. The constructed CT001 pseudomolecule represented 85.4% (219.8 Mb) of the Chiifu reference genome, and a total of 38,567 gene models were annotated using RNA-Seq analysis. In addition, the spontaneous mutation rate of CT001 was estimated by resequencing DNA obtained from individual plants after sexual propagation for six generations to estimate the naturally occurring variations. The CT001 pseudomolecule constructed in this study will provide valuable resources for genomic studies on Chinese cabbage.
Highlights
Brassicaceae is the fifth largest family of flowering plants, comprising 338 genera and approximately 3,700 species [1]
Data for the CT001 pseudomolecule were generated using paired-end reads with an insert size of 150 bp and mate-paired reads with insert size of 3 kb and 5 kb (S1 Table)
The genome assembly had a contig N50 size of 14.1 kb and the gaps between contigs were filled with 100 Ns; the scaffolds were ordered along the 10 chromosomes of B. rapa (S2 Table)
Summary
Brassicaceae is the fifth largest family of flowering plants, comprising 338 genera and approximately 3,700 species [1]. The family is present in various climatic regions and is cultivated worldwide. Brassicaceae crops, including cabbage (Brassica oleracea), rapeseed (Brassica napus), and Chinese cabbage (Brassica rapa), are economically important as they are major vegetable crops in Korea [2,3]. With the recent development of generation sequencing (NGS) technology, it has become possible to produce a considerable volume of information in a short period of time at low cost [4,5]. Advances in algorithms and technologies facilitated the development of genome research [6,7]. NGS technology helps to improve the speed and accuracy of molecular breeding
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