Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species

作者：Lifang Li, Min Yang, Ying Qi, Penghua Gao, Shaowu Yang, Yongteng Zhao, Jianwei Guo, Huanyu Wei, Jiani Liu, Jianrong Zhao, Feiyan Huang, Lei Yu · 发表于：BMC Genomics · 年份：2024 · DOI：10.1186/s12864-024-11053-z · 被引用次数：12 · 研究领域：Genomics and Phylogenetic Studies、Polysaccharides Composition and Applications、Bioinformatics and Genomic Networks

BACKGROUND: The genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences. RESULTS: The Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 - 98,561 bp), a small single copy (SSC, 14,172 - 21,575 bp), and a pair of inverted repeats (IRs, 26,225 - 35,204 bp). The genomes contain 108 - 113 unique genes, including 76 - 79 protein-coding genes, 28 - 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps...