De novo assembly of chloroplast genomes of Corchorus capsularis and C. olitorius yields species-specific InDel markers

Shusheng Fang; Liemei Zhang; Jianmin Qi; Liwu Zhang

Crop Journal (Feb 2021)

De novo assembly of chloroplast genomes of Corchorus capsularis and C. olitorius yields species-specific InDel markers

Shusheng Fang,
Liemei Zhang,
Jianmin Qi,
Liwu Zhang

Affiliations

Shusheng Fang: Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Experiment Station of Agriculture and Rural Affairs of Ministry for Jute and Kenaf in Southeast China/Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
Liemei Zhang: Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Experiment Station of Agriculture and Rural Affairs of Ministry for Jute and Kenaf in Southeast China/Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
Jianmin Qi: Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Experiment Station of Agriculture and Rural Affairs of Ministry for Jute and Kenaf in Southeast China/Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
Liwu Zhang: Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops/Fujian Provincial Key Laboratory of Crop Breeding by Design, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Experiment Station of Agriculture and Rural Affairs of Ministry for Jute and Kenaf in Southeast China/Fujian Public Platform for Germplasm Resources of Bast Fiber Crops/Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China; Corresponding author.

Journal volume & issue: Vol. 9, no. 1
pp. 216 – 226

Abstract

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Jute (Corchorus spp.) is a member of the Malvaceae family, which comprises more than 100 species. The systematic positions of jute species have remained unsettled. Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies. In the present study, the chloroplast genomes of Corchorus capsularis and C. olitorius were assembled, with sizes of respectively 161,088 and 161,766 bp. Both genomes contained 112 unique genes (78 protein-coding, four rRNA, and 30 tRNA genes). Four regions with high variation between the two species were located in single-copy rather than inverted-repeat regions. A total of 66 simple sequence repeats (SSRs) were identified in the C. capsularis chloroplast genome and 56 in that of C. olitorius. Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites, of which one marker (cpInDel 205) could discriminate the two jute species. Comparison of the C. capsularis and C. olitorius chloroplast genomes with those of other species in the Malvaceae revealed breakpoints in the accD locus, which is involved in fatty acid synthesis, in C. capsularis and C. olitorius. This finding suggests that genes from the chloroplast genome might have been transferred to the nuclear genome in some Corchorus species. This hypothesis was supported by synteny analysis of the accD region among the nuclear, chloroplast, and mitochondrial genomes. To our knowledge, this is the first report of the assembled chloroplast genome sequences of C. capsularis and C. olitorius. C. capsularis and C. olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera. These results will expand our understanding of the systematics of species in the Malvaceae.

Published in Crop Journal

ISSN: 2095-5421 (Print); 2214-5141 (Online)
Publisher: KeAi Communications Co., Ltd.
Country of publisher: China
LCC subjects: Agriculture: Agriculture (General)
Website: https://www.keaipublishing.com/en/journals/the-crop-journal/

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