Assembly, annotation, and comparative analysis of Ipomoea chloroplast genomes provide insights into the parasitic characteristics of Cuscuta species

Abstract

In the Convolvulaceae family, around 1650 species belonging to 60 genera are widely distributed globally, mainly in the tropical and subtropical regions of America and Asia. Although a series of chloroplast genomes in Convolvulaceae were reported and investigated, the evolutionary and genetic relationships among the chloroplast genomes of the Convolvulaceae family have not been extensively elucidated till now. In this study, we first reported the complete chloroplast genome sequence of Ipomoea pes-caprae, a widely distributed coastal plant with medical values. The chloroplast genome of I. pes-caprae is 161667 bp in length, and the GC content is 37.56%. The chloroplastic DNA molecule of I. pes-caprae is a circular structure composed of LSC (large-single-copy), SSC (small-single-copy), and IR (inverted repeat) regions, with the size of the three regions being 88210 bp, 12117 bp, and 30670 bp, respectively. The chloroplast genome of I. pes-caprae contains 141 genes, and 35 SSRs are identified in the chloroplast genome. Our research results provide important genomic information for the molecular phylogeny of I. pes-caprae. The Phylogenetic analysis of 28 Convolvulaceae chloroplast genomes showed that the relationship of I. pes-caprae with I. involucrata or I. obscura was much closer than that with other Convolvulaccae species. Further comparative analyses between the Ipomoea species and Cuscuta species revealed the mechanism underlying the formation of parasitic characteristics of Cuscuta species from the perspective of the chloroplast genome.

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

“…However, we found that, despite the smaller sampling size used, the findings for Refs. 23 and 61 are somewhat congruent with our finding, as well as those of Sun et al 24 , who included complete chloroplast genome sequences of 40 Ipomoea taxa in the sliding window analysis. It is clear that the SSC region contains a significant amount of these highly variable regions in all studies.…”

“…While it is recommended to have at least five to seven closely related chloroplast genome sequences from different species to identify such barcodes 60 , our study has utilized 31 chloroplast genomes derived from 30 different Ipomoea taxa, making the finding highly reliable when compared to other published works (i.e. Park et al 23 , Wang et al 61 ). However, we found that, despite the smaller sampling size used, the findings for Refs.…”