Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

Abstract

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes

“…When the B. distachyon plastome genealogy was compared to an SNP‐based nuclear pan‐genome genealogy generated in our parallel study (Fig. a, Nuclear tree; Gordon et al ., ), the plastome tree revealed 11 cases of potential chloroplast capture and introgression. Seven cases (BdTR11A, BdTR11I, BdTR11G, BdTR13A, BdTR13C, BdTR3C, Bis1) corresponded to nuclear T+ ecotypes nested within the plastid EDF+ clade, two cases (ABR3, Uni2) to nuclear S+ ecotypes nested within the plastid T+ group, and two cases (Arn1, Mon3) to introgressed nuclear EDF+ ecotypes nested (and introgressed) within the plastid S+T+ clade (Fig.…”

“…Genomic structure plots showing percentages of membership of plastomes’ profiles to K = 2 and K = 4 genomic groups (center). Chloroplast capture and introgression events detected through topological contrast of the plastome and the nuclear trees (nuclear DNA ( nDNA ) tree from Gordon et al ., ) (right). Discontinuous and continuous lines mark potential chloroplast capture events and introgression events, respectively.…”

“…Flowering time data were obtained from Gordon et al . (). Briefly, flowering time was measured as the number of days elapsed from the end of vernalization to inflorescence heading, in the growth chamber, and assigned to flowering time classes following Ream et al .…”

“…In parallel with the creation of the nuclear pan‐genome of B. distachyon from 53 diverse lines (Gordon et al ., ), and the genome sequencing of its close congeners B. stacei and B. hybridum ( Brachypodium stacei v1.1 DOE‐JGI, http://phytozome.jgi.doe.gov/ and B. hybridum early access available through Phytozome), we isolated ptDNA sequences from WGS paired‐end reads to assemble the corresponding plastomes. Our aim was to compile a large plastome data set and investigate the evolutionary relationships of the annual Brachypodium species within the grass phylogenetic framework.…”

Computational aspects underlying genome to phenome analysis in plants

“…A recent study used more than 60 diverse rice ( Oryza sativa ) accessions together with a wild relative ( Oryza rufipogon ) to assemble multiple genomes, revealing gene loss and gain (Zhao et al ., ). In a similar approach, 54 Brachypodium lines were all assembled de novo (Gordon et al ., ). While illustrating the power of a multiple‐reference genome approach, these projects required multiple time‐intensive analysis pipelines, and several ad‐hoc developments.…”