Differentially regulated orthologs in sorghum and the subgenomes of maize

Abstract

Cross-species comparisons of transcriptional regulation have the potential to identify functionally constrained transcriptional regulation and genes for which a change in transcriptional regulation correlates with a change in phenotype. Conventional differential gene expression analysis and a different approach based on identifying differentially regulated orthologs (DROs) are compared using paired time course gene expression data from two species which respond similarly to cold – maize (Zea mays) and sorghum (Sorghum bicolor). Both approaches suggest that, for genes conserved at syntenic positions for millions of years, the majority of cold responsive transcriptional regulation is species specific, although initial transcriptional responses to cold appear to be more conserved between the two species than later responses. In maize, the promoters of genes with both species specific and conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. However, genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions consistent with this population of genes experiencing stronger purifying selection. We hypothesize that cold responsive transcriptional regulation is a fast evolving and largely neutral molecular phenotype for the majority of genes in Andropogoneae, while a smaller core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold responsive regulation.

Parallels between natural selection in the cold‐adapted crop‐wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

“…Hence, data from Sorghum , an outgroup to maize and T. dactyloides were also generated and included. As previously reported (Zhang et al ., ), no gene ontology (GO) terms were significantly enriched among differentially regulated orthologs (DROs) of maize and Sorghum , during cold stress. GO enrichment analysis on the DROs between T. dactyloides −maize (t‐m) and T. dactyloides − Sorghum (t‐s) showed many GO terms enriched at 3 h and 6 h post‐stress (19 and 45 in t‐m, and 17 and 6 in t‐s, respectively) than at 1 and 24 h (0 and 2 in t‐m, and 2 and 0 in t‐s, respectively).…”

“…Raw fastq sequences for maize and Sorghum cold stress treatment are those published in Zhang et al . (). All data were realigned and reanalyzed using Trimmomatic (Bolger et al ., ), GSNAP (Wu et al ., ) and HTSeq (Anders et al ., ).…”

IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae

“…The quota was set to –quota = 1:2 for maize and teff, and –quota = 1:1 for all other species. Pairwise syntenic block data were merged and polished using the methodology previously described in (Zhang et al, ) to obtain the final set of high confidence syntenic ortholog groups employed for all downstream analysis.…”

Parallel natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

“…In some cases a single consensus tripsacum sequence spanned two or more maize gene models ( Figure S3). Maize genes were sorted based on their expression levels using an existing short read RNA-seq dataset from maize seedling tissue (Zhang et al, 2017). Of the 13,089 most highly expressed maize genes, 8,191 (62.6%) were aligned with at least one tripsacum transcript indicating that the expression level of a gene in maize is a relatively good predictor of how likely that gene was to be captured in the tripsacum isoseq data.…”

“…Secondly, the tripsacum gene must have been uniquely mapped to a single sorghum gene using BLASTN. Thirdly, the maize and sorghum genes must be syntenic orthologs of each other using a previously published dataset (Schnable et al, 2016;Zhang et al, 2017). As a result of the maize WGD shared by maize and tripsacum, in some cases multiple tripsacum sequences mapped to unique maize genes on different maize subgenomes, but to the single shared co-ortholog of these two maize genes in sorghum.…”