Rates of evolution in stress-related genes are associated with habitat preference in two Cardamine lineages

Abstract

Background: Elucidating the selective and neutral forces underlying molecular evolution is fundamental to understanding the genetic basis of adaptation. Plants have evolved a suite of adaptive responses to cope with variable environmental conditions, but relatively little is known about which genes are involved in such responses. Here we studied molecular evolution on a genome-wide scale in two species of Cardamine with distinct habitat preferences: C. resedifolia, found at high altitudes, and C. impatiens, found at low altitudes. Our analyses focussed on genes that are involved in stress responses to two factors that differentiate the high- and low-altitude habitats, namely temperature and irradiation.

Results: High-throughput sequencing was used to obtain gene sequences from C. resedifolia and C. impatiens. Using the available A. thaliana gene sequences and annotation, we identified nearly 3,000 triplets of putative orthologues, including genes involved in cold response, photosynthesis or in general stress responses. By comparing estimated rates of molecular substitution, codon usage, and gene expression in these species with those of Arabidopsis, we were able to evaluate the role of positive and relaxed selection in driving the evolution of Cardamine genes. Our analyses revealed a statistically significant higher rate of molecular substitution in C. resedifolia than in C. impatiens, compatible with more efficient positive selection in the former. Conversely, the genome-wide level of selective pressure is compatible with more relaxed selection in C. impatiens. Moreover, levels of selective pressure were heterogeneous between functional classes and between species, with cold responsive genes evolving particularly fast in C. resedifolia, but not in C. impatiens.

Conclusions: Overall, our comparative genomic analyses revealed that differences in effective population size might contribute to the differences in the rate of protein evolution and in the levels of selective pressure between the C. impatiens and C. resedifolia lineages. The within-species analyses also revealed evolutionary patterns associated with habitat preference of two Cardamine species. We conclude that the selective pressures associated with the habitats typical of C. resedifolia may have caused the rapid evolution of genes involved in cold response.

Figure 1

Levels of selective pressure in C. impatiens and C. resedifolia orthologous genes. Mean values of ω are reported for genes functionally characterized as cold responsive (CRG), and for genes annotated as involved in cold response (CGO), photosynthesis (PGO) and general stress responses (SGO). Text in bars denotes the number of genes; error bars denote the standard error of the mean. For each functional class, the mean residual values of the correlation between levels of selective pressure and A. thaliana gene length were compared to the mean estimated for the genes not in such functional class (identified by red dots) using a Wilcoxon test: * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Figure 2

Codon usage bias in C. impatiens and C. resedifolia orthologous genes. Mean values of the frequency of the optimal codon (Fop) are reported for genes functionally characterized as cold responsive genes (CRG), and for genes annotated as involved either in cold response (CGO), photosynthesis (PGO) and general stress responses (SGO). Text in bars denotes the number of genes; error bars denote the standard error of the mean. The mean values of each functional class were compared to the mean estimated for the genes not in that functional class (identified by red dots) using a Wilcoxon test: * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.