Biology subjects

Zhang, R.-G.

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

7 recordsLinked to original sources

bioRxiv2026

Orthologous synteny provides robust structural evidence for the ancestral angiosperm ε-WGD

The ancestral angiosperm whole-genome duplication ({varepsilon}-WGD) is a pivotal yet contentious event that has long been debated. A recent study refuted its occurrence based on deviations from expected retention patterns of dosage-sensitive genes. Here, we provide both structural (orthologous synteny) and phylogenetic (subgenome-aware) evidence to revisit this debate. With improved annotation of the Ginkgo genome, we uncover a clear 1:2 orthologous synteny ratio between Ginkgo and early-diverging angiosperms (Amborella and Aristolochia), which lack lineage-specific WGDs. Subgenome-aware phylogenomic analyses further demonstrate that the Amborella/Aristolochia subgenomes diverged after the gymnosperm-angiosperm split but before the radiation of extant angiosperms. Together, these findings provide direct structural evidence for an ancestral angiosperm tetraploidization in the early Jurassic, following divergence from gymnosperms. We argue that the recent refutation of the {varepsilon}-WGD relies on restrictive assumptions regarding ploidy level and duplicate retention that may not hold for deep-time polyploidy events. Our results provide a robust resolution to this long-standing debate and reaffirm the {varepsilon}-WGD as a shared synapomorphy of extant angiosperms.

evolutionary biology↗

bioRxiv2024

A novel downstream factor in willows replaces the ancestral sex determining gene

Sex chromosome turnover has occurred in many groups, and is mediated by the translocation or duplication of apical sex-determining genes, or the replacement of original sex determination genes by new ones. In dioecious plants, the former frequently occurs, while the latter is rarely reported. Here, we assembled four haplotype-resolved chromosome-level genomes from four lineages of the Salix polyclona complex, including three diploids (E, E-TS, and W1) and one autotetraploid (W2). Our analyses reveal that diploids have a ZW/ZZ system, while autotetraploid has a ZZZW/ZZZZ system on chromosome 15. The apical sex-determining genes of Salicaceae, ARR17-like duplicates on chromosomes 15 and 19, which can indirectly turn-on/off the expression of PISTILLATA (PI) gene and determine sex, appears to have lost the function of sex determination in the S. polyclona complex. We found a novel sex determining factor on the 15W of the complex, namely partial PI-like duplicates, which has taken over the function from the ARR17-like duplicates. In conclusion, a new dominant sex-determining gene was recruited in the S. polyclona complex, replacing the ancestral apical sex-determining ARR17-like duplicates. The newly identified partial PI-like duplicates exhibit a direct influence on the downstream intact PI-like duplications, providing valuable insights into the evolutionary trajectory of the top-down sex determination pathway.

evolutionary biology↗

bioRxiv2024

Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes

With the explosive growth of whole-genome datasets, the accurate detection of orthologous synteny has become crucial for the reconstruction of evolutionary history. However, the currently available methods for the identification of orthologous synteny have great limitations: the methods are difficult to scale with varying polyploidy histories, and the accurate removal of out-paralogy is challenging. In this study, we developed a scalable and robust approach, the Orthology Index (OI), to identify orthologous synteny. Our evaluation of a large-scale dataset with diverse polyploidization events demonstrated that the technique is highly reliable. This discovery highlights OI as a potentially unified criterion for the identification of orthologous synteny, and this is further validated using simulation-based benchmarks. In addition, we explore its broad applications in reconstructing the evolutionary histories of plant genomes, including inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, significantly enhancing our analytical prowess in plant evolutionary genomics.

genomics↗

bioRxiv2024

Nearly complete genome assembly of a critically endangered pine illuminates evolution and conservation of conifers

Population genetic theory predicts that severe bottlenecks and extremely small effective population sizes (Ne) should reduce the ability of natural selection to eliminate harmful mutations. Under this framework, deleterious alleles are expected to accumulate and even fix, eroding fitness, constraining evolutionary rescue, and potentially precipitating mutational meltdown. Yet, empirical tests of these predictions in species at the extreme lower bound of Ne remain rare. We address this gap using Pinus squamata, one of the rarest tree species on Earth, with only 35 wild individuals remaining. We generated a near-complete reference genome (29.2 Gb) for this species and performed population genomic analyses across nearly all of its extant individuals, together with two closely related species. P. squamata exhibits extraordinarily low nucleotide diversity ({pi} = 3.35 x 10-), the lowest reported for any plant. Demographic inference reveals a recent and severe bottleneck ([~]20 generations ago) that reduced Ne to [~]2.7 and resulted in intense inbreeding. Contrary to theoretical expectations, we uncover evidence for highly efficient purifying selection: strongly deleterious mutations are markedly depleted, indicating substantial purging despite the extremely small Ne. Genome-wide patterns further implicate selection at linked sites--including background selection and pseudo-overdominance--as dominant forces shaping genomic variation in the species. These results challenge the prevailing view that drift overwhelms selection in extremely small populations. Instead, they suggest that, under certain genomic and demographic conditions, purifying selection can remain unexpectedly effective, potentially mitigating the risk of mutational meltdown in the rarest species.

genomics↗

bioRxiv2023

Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes and reversion to autosomes

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid Salix dunnii using Hi-C and PacBio HiFi reads. We use phylogenomics of nuclear and plastid genomes to show that weeping willow arose from crosses between female ancestor from the Salix clade, having XY sex chromosomes on chromosome 7, with a male ancestor from the Vetrix clade, having ancestral XY sex chromosomes on chromosome 15. Our analysis reveals that weeping willow has one pair sex chromosomes, ZW on chromosome 15, that derive from the ancestral XY sex chromosomes in the Vetrix-clade male ancestor, and the X chromosomes on chromosome 7 from the Salix-clade female ancestor has reverted to an autosome. Taken together, our results point to rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow. Significance StatementWe assembled haplotype-resolved genomes and obtained gap-free sex chromosomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid Salix dunnii. The weeping willow arose from two dioecious ancestors, that have XY sex chromosomes on chromosome 7 and 15, respectively. The one pair sex chromosomes 15W and 15Z in weeping willow derived from ancestral 15X and 15Y, respectively. Inversions contributed to the evolutions of sex-linked regions (SLRs) of diploid and polyploid willows.

evolutionary biology↗

bioRxiv2020

Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii X-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for studying sex chromosome evolution in Salicaceae family.

genomics↗

bioRxiv2019

TEsorter: lineage-level classification of transposable elements using conserved protein domains

SummaryTransposable elements (TEs) constitute an import part in eukaryotic genomes, but their classification, especially in the lineage or clade level, is still challenging. For this purpose, we propose TEsorter, which is based on conserved protein domains of TEs. It is easy-to-use, fast with multiprocessing, sensitive and precise to classify TEs especially LTR retrotransposons (LTR-RTs). Its results can also directly reflect phylogenetic relationships and diversities of the classified LTR-RTs.\n\nAvailabilityThe code in Python is freely available at https://github.com/zhangrengang/TEsorter.

bioinformatics↗