Patterns of pan-genome occupancy and gene co-expression under water-deficit in Brachypodium distachyon

Abstract

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequence complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome, which demonstrate that many genes are absent from the reference genomes whose analysis has dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and investigated network topology and differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable occupancy in the pan-genome (genes which are either present in all studied genotypes or missing in some genotypes) show different distributions among co-expression modules. Co-expression analysis united drought genes expressed in drought-stressed plants into 9 modules covering 343 hub genes (440 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 724 hub genes (911 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

“…We made use of data from an extensive transcriptome study of 32 B. distachyon ecotypes [39], which enabled us to explore intraspecific variation in how Bdhn genes are expressed in response to drought in mature plants. Development and tissue specific expression analysis of dehydrin genes was performed in 32 out of the 54 genomically sequenced ecotypes of B. distachyon (Supplementary Table S4).…”

“…Expression analysis of dehydrin genes was performed from a transcriptome study of 32 ecotypes of B. distachyon [39] (Supplementary Table S4) using replicates of the plant materials employed in the ecophysiological study of [2]. Seeds were stratified at 6 • C for two weeks and then grown in the greenhouse at soil field water capacity for 3 weeks.…”

“…RNA-Sequencing of 3 cDNA tag libraries (with fragment of 300-500 bp) was conducted on an Illumina HiSeq2500 platform obtaining 100 bp Single-End (SE) reads. This method yielded only one sequence per expressed transcript in the RNA pool, allowing for higher sequencing coverage per gene [39]. SE reads were checked for quality with FastQC and adapters and low quality reads were removed and filtered with Trimmomatic-0.32 [77].…”

“…Thus, 60 wheat dehydrin gene sequences [82] were retrieved through Blast analysis from the Wheat@URGI portal https://wheat-urgi.versailles.inrae.fr, 29 November 2021, [83]. Orthology of the expressed B. distachyon and T. aestivum dehydrin genes was primarily retrieved from Ensembl Plants using BioMart, and only few cases were retrieved using Blast and the homoeologies previously established in [39] (Supplementary Table S10).…”