Biology subjects

Zhang, H.-R.

Publications and source records attributed to Zhang, H.-R..

3 recordsLinked to original sources

bioRxiv2019

Phylogenomics of Selaginellaceae with special reference to the enigmatic sanguinolenta group

Selaginellaceae has been repeatedly proved as monophyly by previous studies with only one genus being recognized. However, the subgeneric classification has been debated during the recent decades. Furthermore, phylogenetic position of the newly identified sanguinolenta group has not been resolved, varying depending on the datasets and analysis methods. We carried out the phylogenomic analyses of twenty-six species from Selaginellaceae with ten species being newly sequenced and three species representing the sanguinolenta group. Four of the ten newly sequenced plastomes are assembled into the complete molecules, whereas the other six species are only assembled into five to sixteen contigs owing to high numbers of repeats. The phylogenetic framework from our study is basically congruent with the subgeneric classification of Weststrand and Korall (2016b). The position of sanguinolenta group was resolved as the basal clade in subg. Stachygynandrum, which support the position {beta} proposed by Weststrand and Korall (2016a), also supported by the morphological characters of dimorphic vegetative leaves, monomorphic sporophylls and intermixed sporangial arrangements. Both values of dS, dN and GC content in Selaginellaceae plastomes were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). The correlation analysis showed that the elevated synonymous substitution rate was significantly correlated with the high GC content in Selaginellaceae. Besides, the values of dS and dN differs significantly between branches in the phylogenetic tree of Selaginellaceae. We propose that both high GC content and the extensive RNA editing sites contributed to the elevated substitution rate in Selaginellaceae, and all of these three factors could influence the stability of phylogenetic topology of Selaginellaceae.

evolutionary biology↗

bioRxiv2018

Direct Repeats Co-occur with Few Short Dispersed Repeats in Plastid Genome of A Spikemoss, Selaginella vardei (Selaginellaceae, Lycophyta)

BackgroundIt is hypothesized that the highly conserved inverted repeat (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organizations, whereas the mechanism of the occurrence and stability maintenance of the newly reported direct repeats (DR) structure was yet awaiting further exploration. Here we introduced the DR structure of plastome in Selaginella vardei (Selaginellaceae, Lycophyta), trying to elucidate the mechanism of DR occurrence and stability maintenance.\n\nResultsThe plastome of S. vardei is 121,254 bp in length and encodes 76 different genes, of which 62 encode proteins, 10 encode tRNAs and four encode rRNAs. Unexpectedly, the two identical rRNA gene regions (13,893 bp) are arranged into DR, and a ca. 50-kb trnN-trnF inversion spanning one DR copy exists in S. vardei, comparing to the typical IR organization of Isoetes flaccida (Isoetaceae, Lycophyta). We find extremely rare short dispersed repeats (SDRs) in plastome of S. vardei and is confirmed in its closely related species S. indica. The occurrence time of DR in Selaginellaceae is estimated at late Triassic (ca. 215 Ma) based on the phylogenetic framework of land plants.\n\nConclusionsWe propose that the unconventional DR structure, co-occurred with extremely few SDRs, plays key role in maintaining the stability of plastome, and reflects a relic of the environmental upheaval during extinction event. We suggest that the ca. 50-kb inversion resulted in the DR structure, and recombination between DR regions is confirmed to generate multipartite subgenomes and diverse multimers, which shed lights on the diverse structures in plastome of land plants.

genomics↗

bioRxiv2018

The Unique Evolutionary Trajectory and Dynamic Conformations of DR and IR/DR-coexisting Plastomes of the Early Vascular Plant Selaginellaceae (Lycophyte)

Both direct repeats (DR) and inverted repeats (IR) are documented in the published plastomes of four Selaginella species indicating the unusual and diverse plastome structure in the family Selaginellaceae. In this study, we newly sequenced complete plastomes of seven species from five main lineages of Selaginellaceae and also re-sequenced three species (S. tamariscina, S. uncinata and S. moellendorffii) to explore the evolutionary trajectory of Selaginellaceae plastomes. Our results showed that the plastomes of Selaginellaceae vary remarkably in size, gene contents, gene order and GC contents. Notably, both DR and IR structure existed in the plastomes of Selaginellaceae with DR structure being an early diverged character. The occurrence of DR structure was right after the Permian-Triassic (P-T) extinction (ca. 246 Ma) and remained in most subgenera of Selaginellaceae, whereas IR structure only reoccurred in the most derived subg. Heterostachys (ca. 23 Ma). The presence of a pair of large repeats psbK-trnQ, together with DR/IR region in S. bisulcata, S. pennata, S. uncinata, and S. hainanensis, could frequently mediate diverse homologous recombination and create approximately equal stoichiometric isomers (IR/DR-coexisting) and subgenomes. High proportion of repeats is presumably responsible for the dynamic IR/DR-coexisting plastomes, which possess a lower synonymous substitution rate (dS) compared with DR-possessing plastomes. We propose that the occurrence of DR structure, together with few repeats, is possibly selected to adapt to the environmental upheaval during the P-T crisis and the IR/DR-coexisting plastomes also reached an equilibrium in plastome organization through highly efficient homologous recombination to maintain stability.\n\nData depositionAll the plastomes were deposited in GenBank under accession numbers MG272483-MG272484, MH598531-MH598537 and MK156800.

genomics↗