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 …

Genetic variation ranging from single-nucleotide polymorphisms to large structural variants
(SVs) can cause variation of gene content among individuals within the same species. There …

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural
variation, a single reference genome assembly cannot capture the full complement of …

Domesticated plants have long served as excellent models for studying evolution. Many
genes and mutations underlying important domestication traits have been identified, and …

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By
combining high-throughput sequencing, recent developments in parallel computing, and …

Highlights•Plant NLR immune receptors are rapidly diversifying modular proteins.•There is a
vast diversity in NLR copy number and allelic variation across species.•NLRs are sensors of …

Crop genomics has seen dramatic advances in recent years due to improvements in
sequencing technology, assembly methods, and computational resources. These advances …

Differences between plant genomes range from single nucleotide polymorphisms to large-
scale duplications, deletions and rearrangements. The large polymorphisms are termed …

Key message Structural genome variation is a major determinant of useful trait diversity. We
describe how genome analysis methods are enabling discovery of trait-associated structural …

Background The plant immune system is innate and encoded in the germline. Using it
efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens …