A systematic comparison of eight new plastome sequences from <i>Ipomoea</i> L



Sun, Jianying, Dong, Xiaofeng, Cao, Qinghe, Xu, Tao, Zhu, Mingku, Sun, Jian, Dong, Tingting, Ma, Daifu, Han, Yonghua and Li, Zongyun
(2019) A systematic comparison of eight new plastome sequences from <i>Ipomoea</i> L. PeerJ, 7. e6563 - e6563.

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Abstract

<jats:sec> <jats:title>Background</jats:title> <jats:p><jats:italic>Ipomoea</jats:italic> 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 <jats:italic>Ipomoea</jats:italic> species have been sequenced. However, the repeats and divergence regions in <jats:italic>Ipomoea</jats:italic> 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 <jats:italic>Ipomoea</jats:italic> species.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>Eight chloroplast genomes were assembled using short DNA sequences generated by next-generation sequencing technology. By combining these chloroplast genomes with 32 other published <jats:italic>Ipomoea</jats:italic> chloroplast genomes downloaded from GenBank and the Oxford Research Archive, we conducted a comparative analysis of the repeat sequences and divergence regions across the <jats:italic>Ipomoea</jats:italic> genus. In addition, separate analyses of the Batatas group and Quamoclit group were also performed.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>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 <jats:italic>Ipomoea</jats:italic>, 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 (<jats:italic>ndhA</jats:italic> intron, <jats:italic>ndhH</jats:italic>-<jats:italic>ndhF</jats:italic>, <jats:italic>ndhF</jats:italic>-<jats:italic>rpl32</jats:italic>, <jats:italic>rpl32</jats:italic>-<jats:italic>trnL</jats:italic>, <jats:italic>rps16</jats:italic>-<jats:italic>trnQ</jats:italic>, and <jats:italic>ndhF</jats:italic>) in the <jats:italic>Ipomoea</jats:italic> genus, eight (<jats:italic>trnG</jats:italic>, <jats:italic>rpl32</jats:italic>-<jats:italic>trnL</jats:italic>, <jats:italic>ndhA</jats:italic> intron, <jats:italic>ndhF</jats:italic>-<jats:italic>rpl32</jats:italic>, <jats:italic>ndhH</jats:italic>-<jats:italic>ndhF</jats:italic>, <jats:italic>ccsA</jats:italic>-<jats:italic>ndhD</jats:italic>, <jats:italic>trnG</jats:italic>-<jats:italic>trnR</jats:italic>, and <jats:italic>pasA</jats:italic>-<jats:italic>ycf3</jats:italic>) in the Batatas group, and eight (<jats:italic>ndhA</jats:italic> intron, <jats:italic>petN</jats:italic>-<jats:italic>psbM</jats:italic>, <jats:italic>rpl32-trnL</jats:italic>, <jats:italic>trnG-trnR, trnK-rps16, ndhC-trnV, rps16-trnQ,</jats:italic> and <jats:italic>trnG</jats:italic>) in the Quamoclit group. Our maximum-likelihood tree based on whole chloroplast genomes confirmed the phylogenetic topology reported in previous studies.</jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>The chloroplast genome sequence and structure were highly conserved in the eight newly-sequenced <jats:italic>Ipomoea</jats:italic> species. Our comparative analysis included a broad range of <jats:italic>Ipomoea</jats:italic> chloroplast genomes, providing valuable information for <jats:italic>Ipomoea</jats:italic> species identification and enhancing the understanding of <jats:italic>Ipomoea</jats:italic> genetic resources.</jats:p> </jats:sec>

Item Type: Article
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 14 May 2021 09:11
Last Modified: 04 Apr 2022 18:19
DOI: 10.7717/peerj.6563
Open Access URL: https://peerj.com/articles/6563/
URI: https://livrepository.liverpool.ac.uk/id/eprint/3122676