Research

Optimize variant-calling pipeline

Optimize variant calling pipeline for huge datasets on HPC and GPU. Explore the best way to call variants for hundreds of WGS data using the GATK interval list and GenomicDB on both HPC and GPU resources, and organize them into Nextflow pipeline.

Brassica napus pan-genome

Combine Pacbio, HiC, and Bionano sequencing to de novo assemble high-quality genomes of two subspecies of Brassica napus: Siberian kale and rutabaga. Subsequently, we will construct species level B. napus pan-genome, and further investigate the association between SVs, PAVs, and agronomic traits. The Hi-C scaffolding protocol paper can be find at Bio-Protocol.

Brassica napus origin and diversification

Study the origin and diversification of Brassica napus (canola, rutabaga, and Siberian kale), use bioinformatic approaches to explore hundreds of RNA-seq and GSS(Genome Survey Sequencing) data to study the genetic structure, admix/introgression history, and detect the important genes contributing to Brassica napus different morphotypes formation. Paper can be find at Nature Communicaitons.

Brassica rapa domestication and its polyploidy efforts

Domestication process and selective sweeps of Brassica rapa (turnip, pak choi, napa cabbage et al.), discover genes functioned in important agricultural traits, and their relationship with the whole-genome duplication events (WGD). Paper can be find at Molecular Ecology and New Phytologist.

Brassica napus CMS mechanism

Comparative transcriptome analysis of a RIL line based on RNA-Seq help us understand the Differentially Expressed Genes(DEGs) between fertile and Cytoplasmic Male Sterility(CMS), and propose the mechanism of Polima CMS. Paper can be find at BMC Genomics.