Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

Abstract

The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum ( Fagopyrum ) tibeticum . Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum ( Fagopyrum ) tibeticum , Atraphaxis bracteata and Calligonum ebinuricum . Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum ( Fagopyrum ) tibeticum , A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum . Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum , which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum .

Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa

“…S 2 , Table 2 , S 3 ). These results were found similar to previous studies that explored a few species of Fagopyrum [ 36 , 40 ]. Different from previous studies, a detailed plastome characteristics comparison between Fagopyrum with other Polygonaceae genera was performed in this study.…”

Phylogenetic estimation and morphological evolution of Alsineae (Caryophyllaceae) shed new insight into the taxonomic status of the genus Pseudocerastium

“…A monotypic genus nested within a large morphologically diverse genus might be a common phenomenon in angiosperms, and the different morphological features of the monotypic genus might indicate that it may have undergone different evolutionary history compared with its close relatives, such as those reported in the monotypic genera Guihaiothamnus Lo ( Xie et al., 2014 ) and Parapteropyrum A.J. Li ( Tian et al., 2011 ; Yang et al., 2020 ). Thus, the specific name Stellaria aquatic (L.) Scop [ = Myosoton aquaticum (L.).…”

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

“…DNA barcoding is widely used in species identification, germplasm management, genetic diversity analysis, phylogeny, and evolution (Gregory, 2005;Liu et al, 2019). In previous studies, the phylogeny of structural Fagopyrum plants was mainly based on SSR markers (Ma et al, 2009;Yang et al, 2020), single-copy nuclear gene (Ohnishi and Matsuoka, 1996;Ohsako and Ohnishi, 1998). The taxonomic analysis and genetic identification of Fagopyrum species are hampered by the lack of genomic information.…”