Kapeel M. Chougule

The paper presents high-quality genome assemblies and annotations for two Yarrowia lipolytica strains, using a combination of short-read and long-read sequencing technologies.

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

The paper presents an HPC-based workflow for genome variant calling using GATK, demonstrating SNP detection in four plant species and identifying novel SNPs in rice.

The paper constructs a pan-genome inversion index for Asian rice using 16 genomes and finds a high inversion rate with functional implications.

The paper presents 10 new high-quality genome assemblies for sorghum genotypes, identifying structural variants and SNPs linked to bioenergy traits.

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

The paper tracks structural mutations in rice over a century of breeding, showing exonic mutations are removed more rapidly than other mutation types during selection.

This study constructs high-quality sorghum genome assemblies and identifies structural variations and resistance genes associated with sugarcane aphid resistance.

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

The paper develops a tool for haplotype phasing and expression analysis in maize using single-molecule long-read sequencing, revealing allele-specific and imprinted gene expression.

The paper benchmarks TE annotation methods and develops a pipeline called EDTA to create a comprehensive, condensed TE library for both intact and fragmented elements in rice genomes.

The paper identifies poorly annotated genes in maize using a double triage approach combining quality metrics and gene tree visualization, revealing 4,000 novel annotations.