Recent molecular studies have found striking differences between desert-adapted species and model mammals regarding water conservation. In particular, aquaporin 4, a classical gene involved in water regulation of model species, is absent or not expressed in the kidneys of desert-adapted species. To further understand the molecular response to water availability, we studied the Patagonian olive mouse Abrothrix olivacea, a species with an unusually broad ecological tolerance that exhibits a great urine concentration capability. The species is able to occupy both the arid Patagonian steppe and the Valdivian and Magellanic forests. We sampled 95 olive mouse specimens from four localities (two in the steppe and two in the forests) and analysed both phenotypic variables and transcriptomic data to investigate the response of this species to the contrasting environmental conditions. The relative size of the kidney and the ratio of urine to plasma concentrations were, as expected, negatively correlated with annual rainfall. Expression analyses uncovered nearly 3,000 genes that were differentially expressed between steppe and forest samples and indicated that this species resorts to the "classical" gene pathways for water regulation. Differential expression across biomes also involves genes that involved in immune and detoxification functions. Overall, genes that were differentially expressed showed a slight tendency to be more divergent and to display an excess of intermediate allele frequencies, relative to the remaining loci. Our results indicate that both differential expression in pathways involved in water conservation and geographical allelic variation are important in the occupation of contrasting habitats by the Patagonian olive mouse.
BackgroundThe olive mouse Abrothrix olivacea is a
cricetid rodent of the subfamily Sigmodontinae that inhabits a wide range of
contrasting environments in southern South America, from aridlands to temperate
rainforests. Along its distribution, it presents different geographic forms that
make the olive mouse a good focal case for the study of geographical variation in
response to environmental variation. We chose to characterize the kidney
transcriptome because this organ has been shown to be associated with multiple
physiological processes, including water reabsorption.ResultsTranscriptomes of thirteen kidneys from individuals from Argentina and Chile
were sequenced using Illumina technology in order to obtain a kidney reference
transcriptome. After combining the reads produced for each sample, we explored
three assembly strategies to obtain the best reconstruction of transcripts,
TrinityNorm and DigiNorm, which include its own normalization algorithms for
redundant reads removal, and Multireads, which simply consist on the assembly of
the joined reads. We found that Multireads strategy produces a less fragmented
assembly than normalization algorithms but recovers fewer number of genes. In
general, about 15000 genes were annotated, of which almost half had at least one
coding sequence reconstructed at 99% of its length. We also built a list of highly
expressed genes, of which several are involved in water conservation under
laboratory conditions using mouse models.ConclusionBased on our assembly results, Trinity's in
silico normalization is the best algorithm in terms of cost-benefit
returns; however, our results also indicate that normalization should be avoided
if complete or nearly complete coding sequences of genes are desired. Given that
this work is the first to characterize the transcriptome of any member of
Sigmodontinae, a subfamily of cricetid rodents with about 400 living species, it
will provide valuable resources for future ecological and evolutionary genomic
analyses.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-446) contains supplementary material, which is available to authorized
users.
Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.
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