Complete chloroplast genome sequencing and phylogeny of wild Atractylodes lancea from Yuexi, Anhui province

• Published in: Zhongguo zhongyao zazhi Vol. 48; no. 1; p. 52
• Main Authors: Hu, Jian-Peng, Jiang, Lu, Xu, Rui, Wu, Jun-Xian, Guan, Feng-Ya, Yao, Jin-Chen, Liu, Jun-Ling, Zhang, Ya-Zhong, Zha, Liang-Ping
• Format: Journal Article
• Language: Chinese
• Published: China 01.01.2023
• Subjects: Atractylodes - genetics; Genome, Chloroplast; Lamiales; Microsatellite Repeats; Phylogeny; Whole Genome Sequencing; codon bias; phylogenetic analysis; Atractylodes lancea; SSR; chloroplast genome
• ISSN: 1001-5302
• DOI: 10.19540/j.cnki.cjcmm.20221014.102

This study investigated the choroplast genome sequence of wild Atractylodes lancea from Yuexi in Anhui province by high-throughput sequencing, followed by characterization of the genome structure, which laid a foundation for the species identification, analysis of genetic diversity, and resource conservation of A. lancea. To be specific, the total genomic DNA was extracted from the leaves of A. lancea with the improved CTAB method. The chloroplast genome of A. lancea was sequenced by the high-throughput sequencing technology, followed by assembling by metaSPAdes and annotation by CPGAVAS2. Bioiformatics methods were employed for the analysis of simple sequence repeats(SSRs), inverted repeat(IR) border, codon bias, and phylogeny. The results showed that the whole chloroplast genome of A. lancea was 153 178 bp, with an 84 226 bp large single copy(LSC) and a 18 658 bp small single copy(SSC) separated by a pair of IRs(25 147 bp). The genome had the GC content of 37.7% and 124 genes: 87 protein-coding genes, 8 rRN