Gene expression differs in codominant prairie grasses under drought

Abstract

Grasslands of the central United States are expected to experience severe droughts and other climate extremes in the future, yet we know little about how these grasses will respond in terms of gene expression. We compared gene expression in Andropogon gerardii and Sorghastrum nutans, two closely related codominant C grasses responsible for the majority of ecosystem function, using RNA-seq. We compared Trinity assemblies within each species to determine annotated functions of transcripts responding to drought. Subsequently, we compared homologous annotated gene-groups across the two species using cross-species meta-level analysis and functional clustering based on key terms. The majority of variation was found between species, as opposed to between drought and watered treatments. However, there is evidence for differential responses; Andropogon allocated gene expression differently compared to Sorghastrum, suggesting Andropogon focuses on stress alleviation (such as oxygen radical scavenging) rather than prevention. In contrast, Sorghastrum may employ a drought avoidance strategy by modulating osmotic response, especially with hormonal regulation. We found Sorghastrum tended to be more sensitive within 10 key gene-groups related to stress, abscisic acid and trichomes, suggesting gene expression may mechanistically parallel sensitivity at the physiological level. Our findings corroborate phenotypic and physiological differences in the field and may help explain the phenotypic mechanisms of these two species in the tallgrass prairie community under future drought scenarios.

Comparative analysis of two sister Erythrophleum species (Leguminosae) reveal contrasting transcriptome-wide responses to early drought stress

“…Assuming that a large part of these genes may be encoding for signaling and metabolic pathways but not unannotated using GO and KEGG databases from E. suaveolens transcriptome, we suggest that these sets of up-regulated genes could be involved in the response to drought at its different stages and may confer better drought tolerance to this species. This is in line with previous comparative studies performed in Oryza sativa (Poaceae) (Lenka et al, 2011) and Trifolium pratense (Fabaceae) (Yates et al, 2014) genotypes and as well as two Corchorus species (Tiliaceae) and two tallgrass species (Hoffman and Smith, 2018) with contrasting drought tolerance in which an increased number of up-regulated genes encoding for signaling and metabolism-related pathways was observed in the tolerant genotypes.…”

Peer Review #2 of "Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie (v0.1)"

“…First, we used stringent criteria by excluding spots with signal to noise ratios less than 3 or larger than 10 to decrease the inclusion of crosshybridization artefacts (Verdnik et al 2002). Second, the cDNA sequences of the maize microarray SAM1.2 (18,862 sequences) were aligned against the de novo RNA-seq transcriptome data sets of A. gerardii and S. nutans (Hoffman and Smith 2017), previously generated using Trinity (version 2.1.1, Haas et al 2013). We only included BLASTN (Altschul et al 1990;Altschul et al 1997) hits with an e-value cutoff of 1e -10 and alignment length larger than 150 base pairs from the A. gerardii and S. nutans transcript data sets.…”

“…Specifically, S. nutans was more responsive to both a year-round 2°C increase in temperature and more variable precipitation patterns (and lower average soil water availability) than A. gerardii (Smith et al 2016). Sorghastrum nutans also showed greater plasticity for dealing with water stress at the gene level (Hoffman and Smith 2017). To date, much of the research assessing sensitivity of these grasses to heat and water stress has focused on chronic, subtle changes in temperature (2°C increase in temperature) and water availability (on average 14% reduction in soil moisture; Fay et al 2011).…”

“…However, A. gerardii and S. nutans differ in physiological response and abundance under different temperature and water availability (Silletti and Knapp 2002;Silletti et al 2004;Swemmer et al 2006;Nippert et al 2009;Hoover et al 2014b;Hoover et al 2014a). At the level of gene regulation, A. gerardii has been shown to be more sensitive to thermal stress (Travers et al 2007;Travers et al 2010; but see Smith et al 2016) while S. nutans is more sensitive to moderate water stress (Smith et al 2016;Hoffman and Smith 2017). Specifically, S. nutans was more responsive to both a year-round 2°C increase in temperature and more variable precipitation patterns (and lower average soil water availability) than A. gerardii (Smith et al 2016).…”

“…As in past research (Travers et al 2007;Travers et al 2010;Smith et al 2016), we measured gene expression using heterologous hybridization with cDNA microarrays designed for a closely related model species, Zea mays. We coupled the microarray data with filtering through each species' RNA-seq transcriptome (Hoffman and Smith 2017). We hypothesized that gene regulation (number of genes, functional groups) would differ between A. gerardii and S. nutans in response to the heat wave under both watered and drought conditions, with these grasses employing different strategies for coping with extreme heat and water stress.…”