A systematic comparison of eight new plastome sequences from Ipomoea L

Abstract

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

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

“…The conservation of plastome features has been recorded in several Angiosperm groups ( Cai et al, 2015 ; Reginato et al, 2016 ; Sun et al, 2019 ; Yan et al, 2019 ) and our results corroborate that plastomes are highly conserved in Asteraceae, even at the generic or subtribal level, in size, GC content, number of genes and gene order ( Wang et al, 2015 ; Salih et al, 2017 ; Shen et al, 2020 ).…”

Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

“…The chloroplast genome sequences of 11 wild species of Ipomoea ( Ipomoea trifida , Ipomoea tabascana , Ipomoea triloba , Ipomoea cordatotriloba , Ipomoea cynanchifolia , Ipomoea splendor-Sylvae , Ipomoea ramosissima , Ipomoea leucantha , Ipomoea lacunosa , Ipomoea nil , Ipomoea purpurea ) [ 48 ] and cultivar Xushu18 [ 49 ] were downloaded from the NCBI [ 50 ]. The GeneBank files of the 11 wild species and 107 cultivars were imported to the software CGView Comparison Tool [ 51 ], and the script “build_blast_atlas.sh” was used to automatically create maps for nucleotide (blastn) comparison.…”

New plastomes of eight Ipomoea species and four putative hybrids from Eastern Amazon

“…marabaensis in rpoC1 was previously observed [ 5 ]. We could not find any reference for the ycf1 H-disp repeat in the repeats databases, but the ycf1 gene is considered a genomic marker [ 27 , 71 ] and variable sites were also identified by different studies [ 26 , 27 , 29 , 72 ]. The H-disp region found between ndhH and rps15 was also observed in all plastomes, and already adopted as marker region for species discrimination in some studies [ 73 , 74 ].…”