Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea

Abstract

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.

An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea)

“…This new reference transcriptome was improved (in terms of number of genes, percentage of CDS reconstructed and median contig length) to the one reported by Giorello et al. ().…”

“…One of the 26 individuals (PPA450) was conservatively removed from subsequent analyses because its locality of origin was mislabelled; the remaining 25 were combined with 13 samples from Giorello et al. () for a net total of 38 individuals. Reads were aligned against the reference transcriptome using Bowtie2 in paired‐end mode, implemented in rsem 1.2.19 (Li & Dewey, ).…”

“…Assembly of the 26 new libraries was performed using Trinity with default settings (Haas et al, 2013). A reference transcriptome was constructed using the transcriptome assembly of each of the 26 samples and 13 previously published transcriptomic samples and multiread assembly (an assembly constructed joining the reads of 13 libraries) of Giorello et al (2014), using custom Python scripts. For the construction of the reference transcriptome, we select the best hit between the contigs, among the 39 assembled transcriptomes and among the OMA browser mouse proteins (September 2014 database) (Altenhoff, Schneider, Gonnet, & Dessimoz, 2011).…”

“…We sampled 95 Patagonian olive mouse specimens from four localities (Figure ) to obtain urine plasma concentrations and 26 kidney samples (which were combined with 13 samples reported by Giorello et al. () for deep coverage individual transcriptome sequencing and associated sequences). Using measures of differential gene expression, population structure ( F ST ) and neutrality tests (Tajima's D), we found that (a) overall, differential expression distinguishes samples from the forest and the steppe; (b) differentially expression analyses point out that this species resorts to the “classical” gene pathways for water regulation and the expression of some key genes showed a different expression pattern of those found in desert mammals; and (c) genes that were differentially expressed showed a slight tendency to be more divergent and an excess of intermediate allele frequencies, relative to the remaining loci.…”

Peromyscus transcriptomics: Understanding adaptation and gene expression plasticity within and between species of deer mice

“…Deserts do not exhibit high mammalian biodiversity, but rodents are relatively common in deserts and thus have likely evolved many adaptations to water stress. Recently, full transcriptomes of the kidney were generated for three non-Peromyscine rodents that inhabit deserts [27,28]. Adaptive divergence and differential expression in genes related to osmoregulation were identified in two of these species [27].…”