Recent years have seen a surge in plant genome sequencing projects and the comparison
of multiple related individuals. The high degree of genomic variation observed led to the …

Climate change is a threat to global food security due to the reduction of crop productivity
around the globe. Food security is a matter of concern for stakeholders and policymakers as …

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages
the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies …

Background Despite the prevalence and recurrence of polyploidization in the speciation of
flowering plants, its impacts on crop intraspecific genome diversification are largely …

The pangenome provides genomic variations in the cultivated gene pool for a given species.
However, as the crop's gene pool comprises many species, especially wild relatives with …

Background Millennia of directional human selection has reshaped the genomic architecture
of cultivated cotton relative to wild counterparts, but we have limited understanding of the …

As large-scale genomic studies have progressed, it has been revealed that a single
reference genome pattern cannot represent genetic diversity at the species level. While …

The pangenome refers to a collection of genomic sequence found in the entire species or
population rather than in a single individual; the sequence can be core, present in all …

Plants and pathogens constantly adapt to each other. As a consequence, many members of
the plant immune system, and especially the intracellular nucleotide-binding site leucine …

Structural variations (SVs) including gene presence/absence variations and copy number
variations are a common feature of genomes in plants and, together with single nucleotide …