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

Abstract

Background Fagopyrum (Polygonaceae) is a small plant lineage comprised of more than fifteen economically and medicinally important species. However, the phylogenetic relationships of the genus are not well explored, and the characteristics of Fagopyrum chloroplast genomes (plastomes) remain poorly understood so far. It restricts the comprehension of species diversity in Fagopyrum. Therefore, a comparative plastome analysis and comprehensive phylogenomic analyses are required to reveal the taxonomic relationship among species of Fagopyrum. Results In the current study, 12 plastomes were sequenced and assembled from eight species and two varieties of Fagopyrum. In the comparative analysis and phylogenetic analysis, eight previously published plastomes of Fagopyrum were also included. A total of 49 plastomes of other genera in Polygonaceae were retrieved from GenBank and used for comparative analysis with Fagopyrum. The variation of the Fagopyrum plastomes is mainly reflected in the size and boundaries of inverted repeat/single copy (IR/SC) regions. Fagopyrum is a relatively basal taxon in the phylogenomic framework of Polygonaceae comprising a relatively smaller plastome size (158,768–159,985 bp) than another genus of Polygonaceae (158,851–170,232 bp). A few genera of Polygonaceae have nested distribution of the IR/SC boundary variations. Although most species of Fagopyrum show the same IRb/SC boundary with species of Polygonaceae, only a few species show different IRa/SC boundaries. The phylogenomic analyses of Fagopyrum supported the cymosum and urophyllum groups and resolved the systematic position of subclades within the urophyllum group. Moreover, the repeat sequence types and numbers were found different between groups of Fagopyrum. The plastome sequence identity showed significant differences between intra-group and inter-group. Conclusions The deletions of intergenic regions cause a short length of Fagopyrum plastomes, which may be the main reason for plastome size diversity in Polygonaceae species. The phylogenomic reconstruction combined with the characteristics comparison of plastomes supports grouping within Fagopyrum. The outcome of these genome resources may facilitate the taxonomy, germplasm resources identification as well as plant breeding of Fagopyrum.

Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization

“…Zhang et al [ 55 ] adopted plastid phylogenomics to reveal the deep phylogenetic relationships and diversification history of Rosaceae. Li et al [ 56 ] also reported that phylogenomic analyses of Fagopyrum supported the division of the cymosum and urophyllum groups, and resolved the systematic position of subclades within the urophyllum group. However, it should be noted that plastid genomes could enhance species discrimination and reveal phylogeny, but they are still not powerful enough to resolve all species in complicated genera and recently diverged lineages, such as Paris , Berberis , and Rhododendron [ 26 , 57 , 58 ].…”

The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

“…Fan et al [ 1 ] compared the plastomes of eight Fagopyrum species to determine sequence differentiation, repeat content, and the phylogeny of these species. Further building on previous studies Li et al [ 6 ] analyzed 12 plastomes of Fagopyrum and 49 plastomes from other genera in Polygonaceae demonstrating the utility of this type of data in resolving relationships at multiple taxonomic levels. In addition to these studies in Fagopyrum , several studies have shown that using a pan-genome approach to analyze plastome DNA sequences can provide useful insights into the origin and diversity of domesticated crops at the population level [ 29 ].…”

“…The cultivation of buckwheat can be traced back to about 4000 years ago [ 2 , 5 ]. The Fagopyrum genus contains about 15 to 28 species [ 6 ] of which only three are cultivated. The cultivated species are Fagopyrum esculentum (common buckwheat or sweet buckwheat) which is widely cultivated in Asia, Europe, and the Americas, while F. tataricum (Tartary buckwheat) and F. dibotrys (golden buckwheat) are mainly cultivated in China [ 1 ].…”

“…The cultivated species are Fagopyrum esculentum (common buckwheat or sweet buckwheat) which is widely cultivated in Asia, Europe, and the Americas, while F. tataricum (Tartary buckwheat) and F. dibotrys (golden buckwheat) are mainly cultivated in China [ 1 ]. The demand for flour made from F. esculentum as a replacement for wheat-based flour is growing given the lack of gluten in the seeds [ 6 , 7 ]. The seeds of F. tataricum are used as an important functional food [ 6 , 8 ], and F. dibotrys is a famous traditional Chinese herbal medicine whose the edible seeds and leaves are eaten to improve health [ 9 – 11 ].…”

“…The demand for flour made from F. esculentum as a replacement for wheat-based flour is growing given the lack of gluten in the seeds [ 6 , 7 ]. The seeds of F. tataricum are used as an important functional food [ 6 , 8 ], and F. dibotrys is a famous traditional Chinese herbal medicine whose the edible seeds and leaves are eaten to improve health [ 9 – 11 ]. Increasingly, Fagopyrum species are being used as an important part in people’s diet, however, characterization of the existing germplasm resources lags behind the need.…”