Biology subjects

Zhang, X.-C.

Publications and source records attributed to Zhang, X.-C..

10 recordsLinked to original sources

bioRxiv2024

The earliest allopolyploidization in tracheophytes revealed by phylotranscriptomics and morphology of Selaginellaceae

Selaginellaceae exhibit extraordinary evolutionary history in which they survived and thrived during the Permian-Triassic extinction and did not undergo polyploidization. Here, we reconstructed the phylogenetic relationships of Selaginellaceae by applying large-scale nuclear genes from RNA-seq, and found that each group showed phylogenetic incongruences among single-gene trees with different frequencies. In particular, three different phylogenetic positions of the sanguinolenta group were recovered by different nuclear gene sets. We evaluated the factors that might lead to the phylogenetic incongruence of the sanguinolenta group and concluded that hybridization between each ancestor of two superclades is the most likely cause. We presented the supporting evidence from gene flow test, species network inference, and plastome-based phylogeny. Furthermore, morphological characters and chromosomal evidence also lend support to the hybrid origin of this group. The divergence time estimations, using two gene sets respectively, indicated the splits between the sanguinolenta group and each related superclade happened around the same period, implying that the hybridization event probably occurred during the Early Triassic. This study reveals an ancient allopolyploidization with integrative evidence and robust analyses, which sheds new light on the recalcitrant phylogenetic problem of the sanguinolenta group and reports the polyploidization in the basal vascular plants, Selaginellaceae.

genomics↗

bioRxiv2023

Plastome-based Phylogenomic analyses provide insights into the germplasm resource diversity of Cibotium in China

Germplasm resource is the source of herbal medicine production. Cultivation of superior germplasm resources helps to resolve the serious conflict between long-term population persistence and growing market demand by producing materials with high quality consistently. Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness of lower extremity. Long-history use of Cibotium has rendered wild populations of this species declined seriously in China. Without sufficient understanding of species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone selecting high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic difference distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense, a cryptic species endemic to NW Yunnan and adjacent region of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed in the east and west side of a classic phylogeographic boundary that probably shaped by monsoons and landforms in China. We also evaluated the resolution of nine traditional barcode loci, and designed five new DNA barcodes based on the plastome data which can discriminate all these species and lineages of Chinese Cibotium accurately. These novel findings integrated genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit germplasm resources of Cibotium in China.

evolutionary biology↗

bioRxiv2022

The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation

Lycophytes and euphyllophytes (ferns and seed plants) are the two surviving lineages of vascular plants. The modern lycophytes (clubmosses) are herbaceous found either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). The contrasting genome size between homosporous and heterosporous plants has long been an attractive topic. Most clubmosses are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimers disease, but the evolutionary trajectory of which in land plants is unexplored. To better understand these fundamental questions, the genome data of a homosporous lycophyte is urgently required. We generated the Lycopodium clavatum L. genome by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is LTR. Two whole genome duplications (WGDs) are rigorously detected. The content of LTR-RTs was more than ten times higher in homosporous lycophytes than heterosporous ones, although most appeared within one Mya. Then, we find that the LTR-RTs birth-death mode (a much greater birth and extremely slower death) contributes the accumulation of LTR-RTs resulting homosporous lycophyte genome expansion, while in heterosporous lycophytes, the mode is exactly the opposite. Furthermore, the five necessary enzymes of the HupA biosynthetic pathway were identified in the L. clavatum genome, but absent in the other land plants. This decoded genome data will be a key cornerstone to elucidating the fundamental aspects of lycophyte biology and land plant evolution.

genomics↗

bioRxiv2021

A screen for mutants deficient in coronatine-mediated suppression of root immunity identifies Arabidopsis SDA1 as a novel integrator of immunity and phytohormone signaling

Despite the importance of the root immune system in the interaction with rhizosphere microbes, the majority of genetic screens for immunity regulators have been performed in leaves. A previous screen identified 27 hsm (hormone-mediated suppression of MAMP-triggered immunity) mutants that are impaired in jasmonic acid (JA)-mediated suppression of pattern-triggered immunity (PTI) in roots. Here we characterized 16 of the hsm mutants that retain JA sensitivity and are potential negative regulators of root immunity. We found that the majority of hsm mutants show enhanced resistance to Fusarium, a root fungal pathogen; however, only a subset are more resistant to a foliar pathogen. Surprisingly, 12 of 16 hsm mutants are also impaired in abscisic acid (ABA)-mediated suppression of PTI, suggesting a largely shared pathway between JA- and ABA-mediated immune suppression in roots. Although all hsm mutants are insensitive to JA-mediated suppression of root immunity, hsm4 shows hypersensitivity to JA-mediated root growth inhibition and JA-induced gene expression. Consistently, hsm4 is more resistant to leaf pathogens, suggesting that HSM4 is a negative regulator of both root and leaf immunity. Hsm4 was mapped to a mutation in a conserved ARM-repeat protein homologous to yeast SDA1, which has been reported to regulate 60S ribosome biogenesis. As translational reprogramming is a critical layer of immune regulation, this work suggests that AtSDA1 is a novel negative translational regulator of immunity. Additionally, a comprehensive characterization of all 16 hsm mutants provides a genetic toolkit to identify novel mechanisms that regulate root immunity.

plant biology↗

bioRxiv2020

Loss of a plant receptor kinase recruits beneficial rhizosphere-associated Pseudomonas

Maintaining microbiome structure is critical for the health of both plants1 and animals2. In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress3,4. However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without general dysbiosis have remained elusive. Here we show that through regulation of NADPH oxidase, FERONIA kinase negatively regulates beneficial Pseudomonas fluorescens in the Arabidopsis rhizosphere microbiome. By rescreening a collection of Arabidopsis mutants that affect root immunity under gnotobiotic conditions, followed by microbiome sequencing in natural soil, we identified a FERONIA mutant (fer-8) with a rhizosphere microbiome enriched in P. fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial and promoted plant growth. The effect of FER on rhizosphere Pseudomonads was independent of its immune coreceptor function, role in development, and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere Pseudomonad levels. Overexpression of the ROP2 gene (encoding a client of FER and positive regulator of NADPH oxidase5) in fer-8 plants suppressed Pseudomonad overgrowth. This work shows that FER-mediated ROS production regulates levels of beneficial Pseudomonads in the rhizosphere microbiome.

plant biology↗

bioRxiv2020

SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis

Tea is the oldest and most popular nonalcoholic beverage consumed in the world. It provides abundant secondary metabolites that account for its diverse flavors and health benefits. Here we present the first high-quality chromosome-length reference genome of C. sinensis var. sinensis using long read single-molecule real time (SMRT) sequencing and Hi-C technologies to anchor the [~]2.85-Gb genome assembly into 15 pseudo-chromosomes with a scaffold N50 length of [~]195.68 Mb. We annotated at least 2.17 Gb ([~]74.13%) of repetitive sequences and high-confidence prediction of 40,812 protein-coding genes in the [~]2.92-Gb genome assembly. This accurately assembled genome allows us to comprehensively annotate functionally important gene families such as those involved in the biosynthesis of catechins, theanine and caffeine. The contiguous genome assembly provides the first view of the repetitive landscape allowing us to accurately characterize retrotransposon diversity. The large tea tree genome is dominated by a handful of Ty3-gypsy long terminal repeat (LTR) retrotransposon families that recently expanded to high copy numbers. We uncover the latest bursts of numerous non-autonomous LTR retrotransposons that may interfere with the propagation of autonomous retroelements. This reference genome sequence will largely facilitate the improvement of agronomically important traits relevant to the tea quality and production.

genomics↗

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↗

bioRxiv2018

Polyploidy and elevation contribute to opposing latitudinal gradients in diversification and species richness in lady ferns (Athyriaceae)

O_LIIn ferns, the temperate-tropical sister clades Athyrium and Diplazium present an opportunity to study a latitudinal contrast in diversification dynamics.\nC_LIO_LIWe generated a taxonomically expanded molecular chronogram and used macroevolutionary models to analyze how diversification rates have changed through time, across lineages, and in concert with changes in elevation and ploidy. We tested a novel model of cladogenetic state-change in which polyploidy can arise as an infraspecific polymorphism, with diversification parameters distinct from those of pure diploids and polyploids.\nC_LIO_LIBoth Athyrium and Diplazium accelerated their diversification near the Oligocene-Miocene transition. In Diplazium, the rate shift is older, with subsequent net diversification somewhat slower and suggestive of diversity-dependence. In Athyrium, diversification is faster and associated with higher elevations. In both clades, polyploids have the highest rate of net accumulation but lowest (negative) net diversification, while the converse is true for polymorphic species; diploids have low rates of both net accumulation and diversification.\nC_LIO_LIDiversification in Athyrium may have responded to ecological opportunities in expanding temperate habitats during the Neogene, especially in mountains, while the pattern in Diplazium suggests saturation in the tropics. Neopolyploids are generated rapidly, primarily through accelerated cladogenesis in polymorphic species, but are evolutionary dead ends.\nC_LI

plant biology↗