Abstract
BackgroundWith its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen.ResultsWe characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression (n = 182; 2% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response.ConclusionsThe two house finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house finch and zebra finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.
Highlights
With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions
We present high coverage spleen transcriptomes from two populations of the house finch, one representing birds from a population in Arizona (AZ) that has never been exposed to MG and the other representing birds from a population in Alabama (AL) that had been exposed to MG for 15 years at the time of collection
Using the topGO package in the Bioconductor project frame [38] and applying a false discovery rate (FDR) of 0.05 and a minimum fold change of at least two in either direction for the 8,981 transcripts with noticeable expression (>1 CPM) we found that 182 (~2%) transcripts were differentially expressed between the house finch populations (Figure 4, Additional file 1: Table S4)
Summary
With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. Understanding the hereditary components underlying trait variation in natural populations is key to answering a range of fundamental questions in evolutionary biology, but advancing basic insight into evolutionary relevant genotype-phenotype interactions is not trivial Two essentials of this endeavor are quantification of phenotypic variation in traits that influence individual fitness in natural settings [1] and collection of information on DNA sequences, linkage maps, gene expression profiles or other genomic resources spanning the genome of the focal organism [eg. The recent progress in data collection in evolutionary genetics research, mediated predominantly by advancements in DNA sequencing, allows one to rapidly generate vast amounts of genomic data at reasonable cost, even for organisms that are genetically poorly known [4]. The implications of this trend are that taxa for which long-term ecological data have already been collected (ecological model species) will be at the forefront of evolutionary genomics research on natural populations [1]
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