Biotechnology Bulletin ›› 2023, Vol. 39 ›› Issue (6): 233-247.doi: 10.13560/j.cnki.biotech.bull.1985.2022-1369

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Chloroplast Genomic Characterization and Phylogenetic Analysis of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan

YIN Ming-hua1,2,3,4(), YU Huan-yuan1, XIAO Xin-yi1, WANG Yu-ting1   

  1. 1. College of Life Sciences, Shangrao Normal University, Shangrao 334001
    2. Shangrao Agricultural Technology Innovation Research Institute, Shangrao 334001
    3. Key Laboratory of Protection and Utilization of Medicinal and Edible Plant Resources in Shangrao City, Shangrao 334001
    4. Shangrao Key Laboratory of Germplasm Conservation and Utilization of Potato and Taro Crops, Shangrao 334001
  • Received:2022-11-07 Online:2023-06-26 Published:2023-07-07
  • Contact: YIN Ming-hua E-mail:yinminghua04@163.com

Abstract:

In order to analyze the structure and composition of the chloroplast genome of Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, its evolutionary position in Colocasia genus and its difference from the chloroplast genome of the same genus were determined, which may provide relevant basis for species identification, genetic diversity analysis and resource protection of Colocasia genus. The Illumina NovaSeq 6000 sequencing platform was used to sequence the genome of the chloroplast of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan. Bioinformatics analysis methods were to conduct sequence assembly, annotation and feature analysis, and bioinformatics software such as Geneious, MISA, MAFF, FASTREE, CUSP, Chips and Codon W were used to analyze the genome structure and number, codon preference, sequence duplication, SSR sites and phylogeny. The results showed that the chloroplast genome size of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan was 162 544 bp, showing a tetrad structure. It contained 130 genes, including 84 protein coding genes, 37 tRNA genes, 8 ribosomal rRNA genes and 1 pseudogene. By codon preference analysis, the average number of effective codons was 45.60, and 39 genes with ENC value < 45, indicating strong codon preference. Through SSR analysis, 101 SSR sites were detected, of which single nucleotide repeats were the most(about 83.17%), and single nucleotide was mainly A/T type. Compared with related species, the chloroplast genome sequence was highly conserved, especially the protein coding sequence was highly similar. In addition, the phylogenetic analysis showed that C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan was clustered into one branch with Colocasia genus and Remusatia genus. This study obtained the basic information of chloroplast genome and phylogenetic location of C. esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, and provided a preliminary study for its species identification, genetic diversity of natural population and functional genomics.

Key words: Colocasia esculenta L. Schoot var. cormosus cv. ‘Hongyayu’ from Jiangxi Yanshan, chloroplast genome characterization, phylogenetic analysis, SSR analysis, IR boundary analysis, codon preference