Jonathan F. Wendel

The paper reports four new chromosome-level genome assemblies of wild Gossypium hirsutum from Yucatan, highlighting their genetic diversity and potential for improving cotton resistance traits.

This paper provides a systems-level proteomic and transcriptomic resource for cotton fiber development, revealing post-transcriptional control and gene expression dynamics.

This study compares multi-omics data from two cotton species to identify differences in polysaccharide composition and glycosyltransferases linked to fiber quality traits.

This study examines genetic diversity and population structure of wild and introgressed Gossypium hirsutum in Puerto Rico and Guadeloupe, revealing patterns of genetic variation and inbreeding.

The paper analyzes gene regulatory networks in cotton fiber development using multi-omics data to reveal subgenomic regulatory dynamics in allopolyploid cotton.

This study uses population genomics to assess genetic diversity and structure in three critically endangered Kokia species in Hawaii, informing conservation strategies.

This study compares nanoscale mechanical properties of cotton fibers between two species and develops machine learning models to predict phenotypic traits using multi-omics data.

This study presents a high-resolution transcriptomic analysis of cotton fiber development, identifying key gene expression shifts and regulatory networks during secondary wall synthesis.

This study profiles the glycome and transcriptome of cotton fibers daily to identify polysaccharide structures and glycosyltransferases critical for fiber growth and quality.

The paper uses quantitative phenotyping and computational modeling to study cotton fiber growth variability and links it to gene expression and agronomic traits.

The paper provides genome assemblies for three extant Kokia species, revealing genetic diversity and divergence patterns in the Hawaiian Islands endemic genus.

The paper sequenced and analyzed the G. herbaceum cv Wagad genome to study domestication changes and gene expression in diploid cotton.

The paper presents a high-quality genome assembly of Gossypium anomalum and identifies genomic regions associated with hybrid lethality using synthetic allopolyploids.

pSONIC improves ortholog identification in polyploid species by incorporating synteny, placing 75-90% of genes into orthologous groups with higher accuracy than methods without synteny.

The paper presents a high-quality genome sequence for Gossypium stocksii and compares it with G. somalense to explore pest resistance in cotton.

The paper presents a high-quality genome assembly of Gossypium longicalyx to study reniform nematode immunity and fiber evolution in cotton.

The paper evaluates bioinformatic methods for quantifying homoeologous gene expression in polyploids using cotton transcriptomic data, finding that GSNAP-PolyCat provides the most accurate results and highlights methodological impacts on co-expression network analysis.

This study identifies 120 QTL associated with domestication traits in cotton using an F2 population, revealing subgenome-specific distribution and environmental variability.

The paper introduces an analytical framework to understand regulatory changes in allopolyploids by disentangling cis and trans regulatory interactions across subgenomes.