Welcome to Chinese Journal of Tropical Crops,

Chinese Journal of Tropical Crops ›› 2023, Vol. 44 ›› Issue (5): 880-893.DOI: 10.3969/j.issn.1000-2561.2023.05.002

• Omics & Biotechnology • Previous Articles     Next Articles

Comparative Analysis and Sequencing of Chloroplast Genome of Colocasia esculenta var. Redbud and Colocasia esculenta var. Lipu

JIA Xinbi, PAN Rao, XIAO Yao, LUO Sha, SHAN Nan, SUN Jingyu, WANG Shenglin, ZHOU Qinghong, HUANG Yingjin, ZHU Qianglong*()   

  1. Jiangxi Province Key Laboratory of Root and Tuber Crops Biology / Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
  • Received:2022-06-07 Revised:2022-07-24 Online:2023-05-25 Published:2023-06-07
  • Contact: *ZHU Qianglong,E-mail:longzhu2011@126.com


To confirm the characteristics and difference of the chloroplast (cp) genome of Colocasia esculenta var. Redbud and Colocasia esculenta var. Lipu, the two taros were taken as experimental materials in the study, their genomic DNA were first extracted form fresh leaves using an improved CTAB method and the two complete cp genomes were obtained using high-throughput sequencing technology and bioinformatics analysis, simple sequence repeat (SSR) identification, multiple sequence alignment, sliding window analysis on DNA polymorphism and phylogenetic tree analysis were then conducted on two complete cp genomes. The results showed that the length of the complete cp genomes of Redbud and Lipu was 162 478 bp and 162 453 bp, respectively, exhibiting the typical cyclic quadripartite structure. A total of 131 genes were annotated both in the two, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes, of which 18 genes had two copies and 23 genes had introns. A total of 130 and 124 SSR sites were identified in Redbud and Lipu respectively, the content of A/T in the SSR repeats was 63.08% and 61.29% respectively. 15 SSR polymorphic primers were identified. A total of 236 cp single nucleotide polymorphism (SNP) sites were detected between Redbud and Lipu, of which 26.7% were in the gene coding region, which leading to 25 missense variant genes, the variation of the genes may promote the difference between the two varieties. Compared with the representative species from 13 genus of Aroideae showed that the structure, types, and numbers of gene were relatively conservative. The trnS-trnG and ndhF-rpl32 were the highest variation sites in SSC and LSC region, respectively. The phylogenetics analysis using maximum likelihood method (ML) showed that the genus Colocasia had the closest relationship with the genus Steudnera, but the farthest relationship with the genus Sauromatum in the Ariodeae. The results would provide a theoretical basis for the germplasm resource exploitation,genetic diversity evaluation and phylogenetic analysis of C. esculenta.

Key words: Colocasia esculenta var. Redbud, Colocasia esculenta var. Lipu, chloroplast genome, SSR, SNP, phylogenetic analysis

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