AUTHOR=Park Inkyu , Yang Sungyu , Kim Wook J. , Noh Pureum , Lee Hyun O. , Moon Byeong C. 

TITLE=The Complete Chloroplast Genomes of Six Ipomoea Species and Indel Marker Development for the Discrimination of Authentic Pharbitidis Semen (Seeds of I. nil or I. purpurea)

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.00965

DOI=10.3389/fpls.2018.00965

ISSN=1664-462X

ABSTRACT=<p><italic>Ipomoea</italic> L. is the largest genus within the Convolvulaceae and contains 600–700 species. <italic>Ipomoea</italic> species (morning glories) are economically valuable as horticultural species and scientifically valuable as ecological model plants to investigate mating systems, molecular evolution, and both plant–herbivore and plant–parasite interactions. Furthermore, the dried seeds of <italic>I. nil</italic> or <italic>I. purpurea</italic> are used in Korean traditional herbal medicines. In this study, chloroplast (cp) genomes were sequenced from six <italic>Ipomoea</italic> species, namely, <italic>I. nil</italic> and <italic>I. purpurea</italic> and, for the first time, <italic>I. triloba, I. lacunosa, I. hederacea</italic>, and <italic>I. hederacea</italic> var. <italic>integriuscula</italic>. The cp genomes were 161,354–161,750 bp in length and exhibited conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 transfer RNA genes, and 4 ribosomal RNA genes. The gene order, content, and orientation of the six <italic>Ipomoea</italic> cp genomes were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the six <italic>Ipomoea</italic> cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (<italic>petN-psbM, trnI-CAU-ycf2, ndhH-ndhF, psbC-trnS</italic>, and <italic>ccsA-ndhD</italic>). In addition, the protein-coding genes <italic>accD, cemA</italic>, and <italic>ycf2</italic> exhibited high sequence variability and were under positive selection (Ka/Ks &gt; 1), indicating adaptive evolution to the environment within the <italic>Ipomoea</italic> genus. Phylogenetic analysis of the six <italic>Ipomoea</italic> species revealed that these species clustered according to the APG IV system. In particular, <italic>I. nil</italic> and <italic>I. hederacea</italic> had monophyletic positions, with <italic>I. purpurea</italic> as a sister. <italic>I. triloba</italic> and <italic>I. lacunosa</italic> in the section Batatas and <italic>I. hederacea</italic> and <italic>I. hederacea</italic> var. <italic>integriuscula</italic> in the section Quamoclit were supported in this study with strong bootstrap values and posterior probabilities. We uncovered high-resolution phylogenetic relationships between Ipomoeeae. Finally, indel markers (IPOTY and IPOYCF) were developed for the discrimination of the important herbal medicine species <italic>I. nil</italic> and <italic>I. purpurea</italic>. The cp genomes and analyses in this study provide useful information for taxonomic, phylogenetic, and evolutionary analysis of the <italic>Ipomoea</italic> genome, and the indel markers will be useful for authentication of herbal medicines.</p>