Linking gene expression patterns with survival studies elucidates adaptive potential in changing environments

AbstractLatitudinal variation has been known to create strong selection pressure for genomic variation that enables the adaptation and survival of organisms. By altering gene expression patterns, organisms can modify their adaptive potential to heterogeneous environmental conditions along a latitudinal gradient; however, there is a gap in our understanding of how physiological consequences in wild species are affected and how changing environmental conditions act on multiple species. Here, we investigated how seven stream stonefly species sampled from four geographical regions in Japan differ in their responses to latitudinal variations by measuring gene expression (RNA-sequencing) differences within species and gene co-expression among species. We found that a large number of genes (622) were differentially expressed along the latitudinal gradient. The high species-specific gene expression diversity found at higher latitude regions was probably associated with low temperatures and high water discharge, which suggests the adaptive potential of stonefly specie. In contrast, similar gene expression patterns among species was observed at lower latitudes, which suggests that strong environmental stress occurs in warmer regions. Weighted gene co-expression network analysis (WGCNA) identified 22 genes with similar expression patterns among species along the latitudinal gradient. Among the four geographical regions, high differential expression patterns in the co-expressed genes from two regions were found, suggesting that the local environment strongly affects gene expression patterns among species in these regions. Respiration, metabolism, and developmental co-expressed genes exhibited a latitudinal cline, showing clear evidence of divergent adaptive responses to latitude. Our findings demonstrate that stonefly species are differentially adapted to local environmental conditions, and imply that adaptation in gene expression could be shared by multiple species under environmental stress conditions. This study highlights the importance of considering multiple species when evaluating the consequences of environmental changes on aquatic insect communities, and possible mechanisms to cope with environmental changes.

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Homogenization of sub-genome secretome gene expression patterns in the allodiploid fungus Verticillium longisporum

10.1101/341636 ◽

2018 ◽

Cited By ~ 4

Author(s):

Jasper R.L. Depotter ◽

Fabian van Beveren ◽

Luis Rodriguez-Moreno ◽

Grardy C.M. van den Berg ◽

Thomas A. Wood ◽

...

Keyword(s):

Gene Expression ◽

Plant Pathogens ◽

Genome Duplication ◽

Expression Patterns ◽

Secreted Proteins ◽

Plant Colonization ◽

Gene Expression Patterns ◽

Adaptive Potential ◽

Verticillium Longisporum ◽

Genes Encoding

AbstractAllopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. The increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their ongoing quest for host immune response evasion. To this end, plant pathogens secrete a plethora of molecules that enable host colonization. Allodiploidization has resulted in the new plant pathogen Verticillium longisporum that infects different hosts than haploid Verticillium species. To reveal the impact of allodiploidization on plant pathogen evolution, we studied the genome and transcriptome dynamics of V. longisporum using next-generation sequencing. V. longisporum genome evolution is characterized by extensive chromosomal rearrangements, between as well as within parental chromosome sets, leading to a mosaic genome structure. In comparison to haploid Verticillium species, V. longisporum genes display stronger signs of positive selection. The expression patterns of the two sub-genomes show remarkable resemblance, suggesting that the parental gene expression patterns homogenized upon hybridization. Moreover, whereas V. longisporum genes encoding secreted proteins frequently display differential expression between the parental sub-genomes in culture medium, expression patterns homogenize upon plant colonization. Collectively, our results illustrate of the adaptive potential of allodiploidy mediated by the interplay of two sub-genomes.Author summaryHybridization followed by whole-genome duplication, so-called allopolyploidization, provides genomic flexibility that is beneficial for survival under stressful conditions or invasiveness into new habitats. Allopolyploidization has mainly been studied in plants, but also occurs in other organisms, including fungi. Verticillium longisporum, an emerging fungal pathogen on brassicaceous plants, arose by allodiploidization between two Verticillium spp. We used comparative genomics to reveal the plastic nature of the V. longisporum genomes, showing that parental chromosome sets recombined extensively, resulting in a mosaic genome pattern. Furthermore, we show that non-synonymous substitutions frequently occurred in V. longisporum. Moreover, we reveal that expression patterns of genes encoding secreted proteins homogenized between the V. longisporum sub-genomes upon plant colonization. In conclusion, our results illustrate the large adaptive potential upon genome hybridization for fungi mediated by genomic plasticity and interaction between sub-genomes.

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