Phylogenomic and comparative analyses of Rheum (Polygonaceae, Polygonoideae)

Abstract

Species of Rheum have high medicinal value, with the center of diversity in the Qinghai-Tibet Plateau (QTP) and adjacent regions. However, phylogenetic relationships of Rheum are still unclear due to fragment markers providing insufficient informative loci. Here, we sequenced and annotated plastomes of nine Rheum species, and compared the genome structure among the novel nine species along with three published species. Comparative analyses revealed that plastomes of Rheum share a relatively conserved structure. Five highly divergent regions (accD, ccsA, matK, ndhF, and ndhH) can be used as valuable molecular markers for further species delimitation and population genetic studies. Twenty-two accessions representing 17 species were used for phylogenetic analysis, which generated a robust phylogenetic tree and revealed two major clades within Rheum. Phylogenetic results showed that glasshouse structures and cushions of Rheum are results of parallel evolution during adaptation to similar environments. Inconsistent tree topology between concatenated and coalescent methods was detected, implying that incomplete lineage sorting and hybridization may have occurred in the evolutionary history of Rheum. Divergence time estimation based on two fossil calibrations and three secondary calibrations revealed a Miocene to middle Oligocene origin of Rheum. Our study provides valuable genomic resources for the medicinally important genus Rheum, while gaining helpful insights into its systematics and evolution.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae)

“…In Persicarieae, mononucleotide repeats predominated, followed by dinucleotide and trinucleotide repeats ( Table S4 ). Most of the Persicarieae species SSRs were-composed solely of A or T as in plastomes of other Polygonaceae ( Fan et al., 2021 ; Zhang et al., 2021 ). The plastomes of the Persicarieae species are rich in SSRs and could be good resources to develop SSRs markers for further studies.…”

“…A total of 1000 ML bootstrap trees with branch lengths were generated by RAxML and used to estimate the minimum and maximum ages of the internal nodes. According to previous studies ( Manchester and O’Leary, 2010 ; Sun et al., 2012 ; Schuster et al., 2013 ; Zhang et al., 2014b ; Yao et al., 2019 ; Zhang et al., 2021 ), two fossil calibrations and three secondary calibrations were used. The crown age of Polygonaceae was set to an age range of 72.1-66 Ma implemented via a lognormal prior distribution.…”

“…Polygonaceae is composed of annual or perennial herbs or vines, mainly distributed in the northern temperate and tropical regions ( Sanchez et al., 2009 ; Schuster et al., 2011a ; Schuster et al., 2011b ). Many Polygonaceae species are economically important, such as those used in traditional Chinese medicine (e.g., Fallopia ), as horticultural ornamentals (e.g., Reynoutria ), and in the development of the ecological environment (e.g., Calligonum and Persicaria ) ( Sun et al., 2014a ; Olaru et al., 2015 ; Choi et al., 2019 ; Fan et al., 2021 ; Zhang et al., 2021 ). Due to the high diversity of Polygonaceae, large‐scale phylogenies have been used to address questions on taxonomy and ancestral states ( Frye and Kron, 2003 ; Sanchez et al., 2009 ; Sanchez et al., 2011 ; Schuster et al., 2015 ).…”

A tribute to Professor Wen‐Tsai Wang (1926–2022)

“…In September 1990 he visited the herbarium of Uppsala University (UPS) (Li, 2001) to check specimens collected by Dr. Harry Smith (1889–1971), who collected more than 10,000 specimens from China (Herner, 1988), and the following year he visited the herbaria of the Royal Botanic Gardens at Kew (K) and Edinburgh (E), the Berlin Botanical Garden and Botanical Museum (B), and the Muséum National d'Histoire Naturelle in Paris (P). During this journey abroad, he checked specimens of Ranunculaceae, Boraginaceae, Urticaceae and Gesneriaceae, and wrote several taxonomic treatments and an important paper on distribution patterns and migration routes in the Eastern Asiatic Region (Wang, 1992, 1993) that inspired many studies on eastern Asian biogeography (Wen & al., 2014; Nie & al., 2016; Liu & al., 2021; Mao & al., 2021; Zhang & al., 2022).…”

Plastome phylogenomics and biogeography of the subfam. Polygonoideae (Polygonaceae)

“…Whole plastome sequencing is a cost-effective method that has been widely applied to resolve phylogenetic relationships at different taxonomic levels ( Dong et al., 2020 ; Jung et al., 2021 ; Wen et al., 2021 ). Recently, such approaches have been applied to investigate the phylogenetic relationships of genera within Polygonaceae ( Song et al., 2020 ; Zhou et al., 2020 ; Yang et al., 2021 ; Zhang et al., 2021 ). However, a comprehensive analysis, including plastome structure, phylogenomics and biogeography of Polygonoideae is lacking.…”