Zhangjun Fei

The paper constructs a graph-based pangenome of Venturia inaequalis, identifies structural variants linked to population differentiation, and reveals gene repertoire conservation and virulence-associated diversity.

The paper generates a chromosome-scale genome and single-nucleus transcriptomic atlas of sand bean roots to study coastal adaptation, finding that salt tolerance in Beach ecotypes relies on pre-existing, spatially organized stress-response programs.

The paper constructs a graph-based pangenome of Cucurbita pepo to study adaptive evolution, identifying structural variants and showing parallel domestication and environmental adaptation.

The paper identifies the molecular identities of B and L-2 genes in squash and reveals their synergistic epistatic interaction enhances carotenoid accumulation by upregulating the rate-limiting enzyme CpPSY-A.

This study constructs a watermelon super-pangenome from 138 genomes, identifies over a million structural variants, and develops genomic prediction models for 18 traits to advance precision breeding.

The paper constructs a cucumber pangenome to analyze structural variant dynamics during domestication and breeding, finding SVs are purged more than SNPs and improving genomic prediction accuracy.

PSVGT is a framework for population-scale structural variant discovery and genotyping that integrates multiple sequencing data types and outperforms existing tools, especially in complex genomes and low-coverage long-read data.

This study presents a phased chromosome-level genome assembly of sweetpotato, revealing its origin from a wild tetraploid relative and identifying genetic relationships with other progenitors.

The paper sequenced clonal Fuji apple varieties to uncover somatic variants linked to spur-type morphology and early maturation traits.

This study presents a haplotype-resolved genome assembly and variation map of Rosa hybrida, revealing domestication history and genetic contributions from wild species.

This study presents high-quality genome assemblies and a gene family-based pangenome for two native North American apple species, providing resources for breeding and understanding their adaptation.

The paper identifies a new insect-specific flavivirus in aphids and shows that plant pathogens like PLRV and CLas suppress insect antiviral immunity against related viruses.

This study identifies Pic3 and Pic12 as PP2C phosphatases that negatively regulate tomato immunity against Pseudomonas syringae through flagellin-independent pathways.

The paper identifies one-step anthranilate methyltransferases in grapes that synthesize methyl anthranilate, revealing distinct active site residues compared to maize and citrus enzymes.

This study identifies genes regulating lateral root development in tomato under salt stress, revealing ethylene and ROS signaling as key factors.

HortGenome Search Engine provides a unified platform for querying and analyzing genomic data across 400+ horticultural crops, with tools for BLAST, batch query, enrichment analysis, and synteny viewing.

The paper identifies genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis and finds shared and unique transcriptional responses to heat, salt, and drought stresses.

This study identifies differentially expressed genes in tomato plants expressing the TYLCV C4 protein, linking them to leaf cupping symptoms.

This paper presents a chromosome-scale genome assembly for Solanum lycopersicoides and maps introgression lines to support genetic studies of traits in tomato.

This study identifies genomic bases of peach local adaptation to climate variables using re-sequencing and environmental association analyses.

The paper presents a high-quality genome of Solanum pimpinellifolium and identifies structural variants that underlie important tomato breeding traits.

This paper develops a method to assemble whole-chromosome pseudomolecules for polyploid plant genomes using genotyping-by-sequencing and reference genome data, showing improved accuracy over existing tools.

This study identifies conserved gene regulatory networks in the root cambium of radish and Arabidopsis that link environmental sensing to growth, highlighting ERF-1 as a key regulator.

A PacBio and Hi-C tomato genome rebuild shrinks gaps from 81.71Mb to 44Kb; the matching ITAG4.0 annotation adds 4,794 genes and updates most carried-over models.

The paper presents a high-quality chromosome-level genome assembly of the corn leaf aphid, providing insights into its biology and potential applications in research.

The fruitENCODE project identifies three evolutionary origins of regulatory circuits governing climacteric fruit ripening through comparative genomics and epigenetics.

The paper presents the first high-quality draft genome of pomegranate, providing insights into fruit quality traits and ovule development.

This study reports high-quality genome sequences of C. maxima and C. moschata, revealing an allotetraploidization event and long-term karyotype stability in Cucurbita genomes.