Biology subjects

Jiao, W.-B.

Publications and source records attributed to Jiao, W.-B..

11 recordsLinked to original sources

bioRxiv2026

PlantRegMoD: An integrative and AI-driven multi-omics database for plant regeneration research

Plant regeneration underpins plant developmental plasticity, tissue culture, genetic transformation and crop improvement. Although numerous related omics datasets have been generated, specialized multi-omics databases for this field are still scarce. Here, we constructed PlantRegMoD, an AI-powered integrated database dedicated to plant regeneration. This platform hosts 20.54 TB standardized multi-omics data from 147 projects across 32 plant species and 2,593 samples. We established a unified hierarchical classification system covering five major categories and nine regeneration models, and curated 236 regeneration genes as well as their 28,190 homologs across 58 representative plant species. It contains extensive transcriptomic resources across all regeneration models, together with 196,423 single cells and over 8.81 million epigenetic peaks to dissect cellular heterogeneity and multi-layered epigenetic regulation. Equipped with nine online omics-related tools and a RAG-based intelligent Q&A system, PlantRegMoD greatly reduces bioinformatic barriers and serves as a robust resource for mechanistic, functional and evolutionary studies of plant regeneration.

plant biology↗

bioRxiv2025

The mutational dynamics of the Arabidopsis centromeres

Centromeres are specialized chromosomal regions essential for sister chromatid cohesion and spindle attachment during cell division. Although many centromeres consist of highly variable tandem repeat arrays, the mutational processes driving this variability remain poorly understood. Here, using replicated genome assemblies of Arabidopsis thaliana mutation accumulation (MA) lines, we define the centromeric mutation spectrum. We find that point mutations occur at an almost tenfold higher rates than in chromosome arms, largely driven by non-allelic gene conversion between closely linked repeat units. Large kilobase-scale indels are also frequent and consistently preserve the tandem repeat array by adding or removing only complete repeat units. Analysis of MA lines deficient in the helicase RTEL1 supports the involvement of homology-directed DNA repair in these mutational processes. Moreover, simulations of sequence turnover using the centromere-specific mutation spectrum recapitulate the emergence of homogenized repeat blocks characteristic of natural centromeres. Together, our results show that centromere evolution is driven by a distinct mutational spectrum shaped by homology-directed DNA repair, providing a quantitative framework for how local mutational processes generate and maintain the large-scale architecture of centromeric DNA.

genomics↗

bioRxiv2025

Varigraph: an accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes

Graph pangenome references can address single-reference bias, thereby enhancing the accuracy of variant genotyping and empowering downstream applications in population genetics and quantitative genetics. However, existing pangenome-based genotyping methods struggle with large or complex pangenome graphs, particularly in polyploid genomes. Here, we introduce Varigraph, an algorithm that leverages the comparison of unique and repetitive k-mers between variant sites and short reads for genotyping both small and large variants. Varigraph outperforms current state-of-the-art linear and graph-based genotypers across non-human genomes while maintaining comparable accuracy in human genomes. By employing an efficient data structure, Varigraph achieves higher accuracy in repetitive regions while managing computational costs for large datasets. Notably, Varigraph is the first tool capable of effectively utilizing pangenome graphs for genotyping autopolyploids, enabling precise determination of allele dosage. This work provides a robust and accurate solution for genotyping non-human genomes and will facilitate genomic studies of polyploid crops.

genomics↗

bioRxiv2024

Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm

Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals--tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-- both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.

plant biology↗

bioRxiv2023

A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline

BackgroundAlthough sequencing technologies have boosted the measurement of the sequencing diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods have been developed to address this issue and tested for human genomes, however, their performance in plant genomes remains largely elusive. Furthermore, pipelines integrating the advantages of current genotyping methods might be required, considering the different complexity of plant genomes. ResultsHere we comprehensively evaluate eight such genotypers in different scenarios in terms of variant type and size, sequencing parameters, genomic context, and complexity, as well as graph size, using both simulated and read data sets from representative plant genomes. Our evaluation reveals that there are still great challenges to applying existing methods to plants, such as excessive repeats and variants or high resource consumption. Therefore, we propose a pipeline called Ensemble Variant Genotyper (EVG) that can achieve better genotype concordances without increasing resource consumption. EVG can achieve comparably higher genotyping recall and precision even using 5x reads. Furthermore, we demonstrate that EVG is more robust with an increasing number of variants, especially for insertion and deletion. ConclusionsOur study will provide new insights into the development and application of graph-based genotyping algorithms. We conclude that EVG provides an accurate, unbiased, and cost-effective way for genotyping both small and large variations and will be potentially used in population-scale genotyping for large, repetitive, and heterozygous plant genomes.

genomics↗

bioRxiv2023

The identification and analysis of meristematic mutations within the apple tree that developed the RubyMac sport mutation

Understanding the molecular basis of sport mutations in fruit trees can accelerate breeding of novel cultivars. For this, we analyzed the DNA of the apple tree that evolved the RubyMac phenotype through a sport mutation that introduced changes in fruit coloration in upper branches of the tree. Unexpectedly, we not only found 46 de novo mutations, but also 54 somatic gene conversions (i.e., loss-of-heterozygosity mutations) distinguishing the mutant and wild-type branches of the tree. Approximately 30% of the de novo mutations and 80% of the gene conversions were observed only in specific cells layers suggesting that they occurred in the corresponding meristematic layers. Interestingly, the de novo mutations were enriched for GC=>AT transitions, while the gene conversions showed the opposite bias for AT=>GC transitions suggesting that GC-biased gene conversions have the potential to counteract the AT-bias of de novo mutations. By comparing the gene expression patterns in fruit skins from mutant and wild-type branches, we found 56 differentially expressed genes including 18 that were involved in anthocyanin biosynthesis. While none of the differently expressed genes harbored a mutation, we found that some of the mutations affected the integrity of candidate genes in regions of the genome that were recently associated with natural variation in fruit coloration.

genomics↗

bioRxiv2021

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Potato is the most important tuber crop in the world. However, separate reconstruction of the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar Otava using high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, almost 50% of the genome were found to be identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving around 20% of the genome. Among 38,214 genes, only 54% were present in four haplotypes with an average of 3.2 copies per gene. Analyzing the leaf transcriptome as example, we found that 11% of the genes featured differently expressed alleles in at least one of the haplotypes, of which 25% are likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding.

genomics↗

bioRxiv2020

The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana

Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudo-functionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. While such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions which included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently co-exist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

evolutionary biology↗

bioRxiv2019

Chromosome-level assemblies of multiple Arabidopsis thaliana accessions reveal hotspots of genomic rearrangements

We report chromosome-level, reference-quality assemblies of seven Arabidopsis thaliana accessions selected across the global range of this predominately ruderal plant. Each genome revealed between 13-17 Mb rearranged and 5-6 Mb novel sequence introducing copy-number changes in [~]5,000 genes, including [~]1,900 genes which are not part of the current reference annotation. Analyzing the collinearity between the genomes revealed [~]350 regions (4.1% of the euchromatin) where accession-specific tandem duplications destroyed the syntenic gene order between the genomes. These hotspots of rearrangements were characterized by the loss of meiotic recombination in hybrids within these regions and the enrichment of genes implicated in biotic stress response. Together this suggests that hotspots of rearrangements are governed by altered evolutionary dynamics as compared to the rest of the genome, which are based on new mutations and not on the recombination of existing variation, and thereby enable a quick response to the ever-evolving challenges of biotic stress.

genetics↗

bioRxiv2019

SyRI: identification of syntenic and rearranged regions from whole-genome assemblies

Here, we present SyRI, an efficient tool for genome-wide structural rearrangement identification from genome graphs, which are build up from pair-wise whole-genome alignments. Instead of searching for differences, SyRI starts by finding all co-linear regions between the genomes. As all remaining regions are SRs by definition, they just have to be classified as inversions, translocations, or duplications based on their positions in convoluted networks of repetitive alignments. Finally, SyRI reports local variations like SNPs and indels within syntenic and rearranged regions. We show SyRIs broad applicability to multiple species and genetically validate the presence of ~100 translocations identified in Arabidopsis.

bioinformatics↗

bioRxiv2018

Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in two floodplain Arabis species

Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil flood-plain and compared it to sites restored by hay-transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious flood-plain species Arabis nemorensis is co-occurring in pristine and restored sites with its relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay-transfer maintains genetic diversity for both species. In addition, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer also maintained diversity, but did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay-transfer on genetic diversity also depend on the genetic makeup of each species in the donor communities, especially when material is mixed. Our results demonstrate the efficiency of hay-transfer for habitat restoration and emphasize the importance of pre-restoration characterization of micro-geographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, i.e. maximize the adaptive potential of the entire restored plant community. Overseeing these patterns may differentially alter the adaptive potential of species present, thereby altering the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo and reference-based RAD-seq pipelines show that the genomic impact of restoration can be reliably monitored on species lacking prior genomic knowledge.

ecology↗