AUTHOR=Fan Yu , Jin Ya’nan , Ding Mengqi , Tang Yu , Cheng Jianping , Zhang Kaixuan , Zhou Meiliang 

TITLE=The Complete Chloroplast Genome Sequences of Eight Fagopyrum Species: Insights Into Genome Evolution and Phylogenetic Relationships

JOURNAL=Frontiers in Plant Science

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.799904

DOI=10.3389/fpls.2021.799904

ISSN=1664-462X

ABSTRACT=<p>Buckwheat (<italic>Fagopyrum</italic> genus, Polygonaceae), is an annual or perennial, herbaceous or semi-shrub dicotyledonous plant. There are mainly three cultivated buckwheat species, common buckwheat (<italic>Fagopyrum esculentum)</italic> is widely cultivated in Asia, Europe, and America, while Tartary buckwheat (<italic>F. tataricum</italic>) and <italic>F. cymosum</italic> (also known as <italic>F. dibotrys</italic>) are mainly cultivated in China. The genus <italic>Fagopyrum</italic> is taxonomically confusing due to the complex phenotypes of different <italic>Fagopyrum</italic> species. In this study, the chloroplast (cp) genomes of three <italic>Fagopyrum</italic> species, <italic>F. longistylum</italic>, <italic>F. leptopodum</italic>, <italic>F. urophyllum</italic>, were sequenced, and five published cp genomes of <italic>Fagopyrum</italic> were retrieved for comparative analyses. We determined the sequence differentiation, repeated sequences of the cp genomes, and the phylogeny of <italic>Fagopyrum</italic> species. The eight cp genomes ranged, gene number, gene order, and GC content were presented. Most of variations of <italic>Fagopyrum</italic> species cp genomes existed in the LSC and SSC regions. Among eight <italic>Fagopyrum</italic> chloroplast genomes, six variable regions (<italic>ndhF</italic>-<italic>rpl32</italic>, <italic>trnS-trnG</italic>, <italic>trnC</italic>, <italic>trnE-trnT</italic>, <italic>psbD</italic>, and <italic>trnV</italic>) were detected as promising DNA barcodes. In addition, a total of 66 different SSR (simple sequence repeats) types were found in the eight <italic>Fagopyrum</italic> species, ranging from 8 to 16 bp. Interestingly, many SSRs showed significant differences especially in some photosystem genes, which provided valuable information for understanding the differences in light adaptation among different <italic>Fagopyrum</italic> species. Genus <italic>Fagopyrum</italic> has shown a typical branch that is distinguished from the <italic>Rumex</italic>, <italic>Rheum</italic>, and <italic>Reynoutria</italic>, which supports the unique taxonomic status in <italic>Fagopyrum</italic> among the Polygonaceae. In addition, phylogenetic analysis based on the cp genomes strongly supported the division of eight <italic>Fagopyrum</italic> species into two independent evolutionary directions, suggesting that the separation of cymosum group and urophyllum group may be earlier than the flower type differentiation in <italic>Fagopyrum</italic> plants. The results of the chloroplast-based phylogenetic tree were further supported by the <italic>matK</italic> and Internal Transcribed Spacer (ITS) sequences of 17 <italic>Fagopyrum</italic> species, which may help to further anchor the taxonomic status of other members in the urophyllum group in <italic>Fagopyrum</italic>. This study provides valuable information and high-quality cp genomes for identifying species and evolutionary analysis for future <italic>Fagopyrum</italic> research.</p>