Wenxiu Ye

PlantOmicsGWAS provides a reproducible framework for plant GWAS and genomic prediction, supporting both linear and pan-genome references to improve analysis of structural variations.

The paper evaluates reference genomes and cell-type annotation frameworks for snRNA-seq in apple, finding that GDDH13 provides the best mapping and annotation performance, and that combining marker genes with cross-species frameworks improves cell-type identification.

This study investigates the origin and evolution of grapevines through phylogenomic analysis of 29 genome assemblies, revealing evolutionary relationships and genomic features contributing to their adaptation.

This paper presents haplotype-resolved T2T gap-free genomes of Cabernet Sauvignon, revealing inversion events not seen in other V. vinifera genomes.

This study uses pan-metagenomics to analyze the grapevine phyllosphere microbiome, revealing its structure, diversity, and functional roles in downy mildew resistance.

The paper evaluates resistance mechanisms in grapevines against downy mildew, finding that V. riparia exhibits layered stomatal immunity that suppresses pathogen entry and development.

The paper assembles and annotates haplotype-resolved genomes of grapevines to uncover genetic diversity and disease resistance mechanisms, identifying structural variants linked to downy mildew resistance.