Pan-genomes: estimating the true genomic diversity of plant species

Abstract

A pan-genome is defined as the union of all the genes and non-coding DNA found in all individuals of a species or broader taxon. While pan-genomes have been extensively studied in bacteria, and related to their ecological and pathogenic properties, our knowledge of pan-genomes in wild plants and crops is still limited. In this talk I will review how genome and RNA sequencing of both monocot and dicot models (Brachypodium distachyon and Arabidopsis thaliana) and crops (Hordeum vulgare) show that plants, as microorganisms, contain core genes, detected in all accessions, and also accessory sequences, which are present only in some of them. Core genes are more likely to be involved in essential biological functions, whereas accessory loci evolve faster and are conditionally expressed with roles in defense and development. Comparison of de-novo genome assemblies of B. distachyon accessions indicates that accessory genes accumulate in pericentromeric regions, close to transposable elements, in agreement with expression and enrichment analyses in barley. Our results demonstrate that pan-genomes are useful to explore germplasm diversity and show that mobile genetic elements play a key role in shaping plant genomes.