A systematic comparison of eight new plastome sequences from Ipomoea L

• Published in: PeerJ (San Francisco, CA) Vol. 7; p. e6563
• Main Authors: Sun, Jianying, Dong, Xiaofeng, Cao, Qinghe, Xu, Tao, Zhu, Mingku, Sun, Jian, Dong, Tingting, Ma, Daifu, Han, Yonghua, Li, Zongyun
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 11.03.2019; PeerJ, Inc; PeerJ Inc
• Subjects: Agriculture; Analysis; Bioinformatics; Chloroplast genome; Chloroplasts; Comparative analysis; Conserved sequence; Cytosine; Deoxyribonucleic acid; Divergence hotspot; DNA; DNA sequencing; Evolution; Genes; Genetic research; Genetic resources; Genetics; Genome structure; Genomes; Genomics; Germplasm; Guanine; Inverted repeat; Ipomoea; Molecular biology; Next-generation sequencing; Nucleotide sequence; Nutrition; Phylogenetics; Phylogeny; Plant Science; Plastomes; Potatoes; Purines; Pyrimidines; Repeats; Simple sequence repeats; Software; Species; Taxonomy; Technology; North Carolina; Mexico; United States > US; Peru; China; Genome structure; Repeats; Ipomoea; Divergence hotspot; Chloroplast genome
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.6563

is the largest genus in the family Convolvulaceae. The species in this genus have been widely used in many fields, such as agriculture, nutrition, and medicine. With the development of next-generation sequencing, more than 50 chloroplast genomes of species have been sequenced. However, the repeats and divergence regions in have not been well investigated. In the present study, we sequenced and assembled eight chloroplast genomes from sweet potato's close wild relatives. By combining these with 32 published chloroplast genomes, we conducted a detailed comparative analysis of a broad range of species. Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed. The eight newly sequenced chloroplast genomes ranged from 161,225 to 161,721 bp in length and displayed the typical circular quadripartite structure, consisting of a pair of inverted repeat (IR) regions (30,798-30,910 bp each) separated by a large single copy (LSC) region (87,575-88,004 bp) and a small single copy (SSC) region (12,018-12,051 bp). The average guanine-cytosine (GC) content was approximately 40.5% in the IR region, 36.1% in the LSC region, 32.2% in the SSC regions, and 37.5% in complete sequence for all the generated plastomes. The eight chloroplast genome sequences from this study included 80 protein-coding genes, four rRNAs (rrn23, rrn16, rrn5, and rrn4.5), and 37 tRNAs. The boundaries of single copy regions and IR regions were highly conserved in the eight chloroplast genomes. In , 57-89 pairs of repetitive sequences and 39-64 simple sequence repeats were found. By conducting a sliding window analysis, we found six relatively high variable regions ( intron, - , - , - , - , and ) in the genus, eight ( , - , intron, - , - , - , - , and - ) in the Batatas group, and eight ( intron, - , , and ) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies. The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced species. Our comparative analysis included a broad range of chloroplast genomes, providing valuable information for species identification and enhancing the understanding of genetic resources.