AUTHOR=Zoclanclounon Yedomon Ange Bovys , Thamilarasan Senthil Kumar , Mo Youngjun , Ahn Byoung-Ohg , Kim Jeong-Gu , Lee Keunpyo 

TITLE=Insights into chloroplast genome structure and phylogenetic relationships within the Sesamum species complex (Pedaliaceae)

JOURNAL=Frontiers in Genetics

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1207306

DOI=10.3389/fgene.2023.1207306

ISSN=1664-8021

ABSTRACT=<p><bold>Background:</bold> In the <italic>Sesamum</italic> species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships.</p><p><bold>Results:</bold> In the present study, we generated complete chloroplast genomes of six wild relatives (<italic>Sesamum alatum</italic>, <italic>Sesamum angolense</italic>, <italic>Sesamum pedaloides</italic>, <italic>Ceratotheca sesamoides</italic> (syn. <italic>Sesamum sesamoides</italic>), <italic>Ceratotheca triloba</italic> (syn. <italic>Sesamum trilobum</italic>), and <italic>Sesamum radiatum</italic>) and a Korean cultivar, <italic>Sesamum indicum</italic> cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863–153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including <italic>ndhA</italic>, <italic>ndhE</italic>, <italic>ndhF</italic>, <italic>ycf1</italic>, and <italic>psaC–ndhD</italic>. Concordant tree topologies suggest <italic>ndhF</italic> as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that <italic>S. radiatum</italic> (2n = 64) occurred concomitantly with the sister species <italic>C. sesamoides</italic> (2n = 32) approximately 0.05 million years ago (Mya). In addition, <italic>S. alatum</italic> was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others.</p><p><bold>Conclusion:</bold> Altogether, we propose to rename <italic>C. sesamoides</italic> and <italic>C. triloba</italic> as <italic>S. sesamoides</italic> and <italic>S. trilobum</italic>, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the <italic>Sesamum</italic> species complex.</p>