Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation

English version

Autoři: Jee-Soo Park ^aff001; Ji-Hyun Park ^aff001; Young-Doo Park ^aff001
Působiště autorů: Department of Horticultural Biotechnology, Kyung Hee University, Yongin, Korea ^aff001
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pone.0222283

Souhrn

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.

Klíčová slova:

Biology and life sciences – Genetics – Genomics – Plant genomics – Genome analysis – Plant genetics – Bioengineering – Biotechnology – Plant biotechnology – Plant science – Organisms – Eukaryota – Plants – Computational biology – Engineering and technology – Research and analysis methods – Animal studies – Experimental organism systems – Molecular biology – Sequence assembly tools – Database and informatics methods – Bioinformatics – Sequence analysis – Sequence alignment – Molecular biology techniques – Mutation – DNA construction – DNA library construction – Genomic library construction – Artificial gene amplification and extension – Polymerase chain reaction – Substitution mutation – Brassica – Inbred strains

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Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation

Souhrn

Klíčová slova:

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