Brain transcriptome of the violet-eared waxbillUraeginthus granatinaand recent evolution in the songbird genome

Abstract

Songbirds are important models for the study of social behaviour and communication. To complement the recent genome sequencing of the domesticated zebra finch, we sequenced the brain transcriptome of a closely related songbird species, the violet-eared waxbill (Uraeginthus granatina). Both the zebra finch and violet-eared waxbill are members of the family Estrildidae, but differ markedly in their social behaviour. Using Roche 454 RNA sequencing, we generated an assembly and annotation of 11 084 waxbill orthologues of 17 475 zebra finch genes (64%), with an average transcript length of 1555 bp. We also identified 5985 single nucleotide polymorphisms (SNPs) of potential utility for future population genomic studies. Comparing the two species, we found evidence for rapid protein evolution (ω) and low polymorphism of the avian Z sex chromosome, consistent with prior studies of more divergent avian species. An intriguing outlier was putative chromosome 4A, which showed a high density of SNPs and low evolutionary rate relative to other chromosomes. Genome-wide ω was identical in zebra finch and violet-eared waxbill lineages, suggesting a similar demographic history with efficient purifying natural selection. Further comparisons of these and other estrildid finches may provide insights into the evolutionary neurogenomics of social behaviour.

Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior

“…This was notable as a previous 454-based whole brain transcriptome of another songbird did not detect any olfactory receptor genes at all (Balakrishnan et al, 2013). The detection of such genes here suggests that the increased sequencing depth provided by the Illumina platform has aided in this regard.…”

“…For comparison we also included previously published RNAseq read data from the zebra finch auditory forebrain (Balakrishnan et al, 2013). White-throated sparrow reads mapped at a lower rate (average = 83% of reads mapped) than reads from Gambel’s white-crowned sparrow (90%), song sparrow (94%) and zebra finch (93%).…”

Avian transcriptomics: opportunities and challenges

“…In contrast to mammals, birds have evolved a female heterogametic sex system, with females having two distinct sex chromosomes (ZW) and males two copies of the Z chromosome (ZZ) (Ellegren 2000). The distinct pattern of inheritance in sex chromosomes means that they experience evolutionary forces different from the rest of the genome (Mank et al 2010), and they have hence been subject to a number of evolutionary studies in birds (Wang et al 2014;Zhou et al 2014), also using transcriptomic data (Balakrishnan et al 2013;Künstner et al 2010;Ramstad et al 2016;Wright et al 2015). Wright et al (2015) studied sequence and expression data of sex chromosomes simultaneously in six species of birds using RNA-seq data.…”

“…SNPs are abundant in the genome and can be found especially in non-coding but also in coding regions, and are hence valuable markers for many types of research questions or to see whether genetic variants are associated with a certain trait or disease. SNPs have been discovered using transcriptomics in many avian species (Balakrishnan et al 2013;Ekblom and Wang 2017;Ekblom et al 2014;Hagen et al 2013;Kaiser et al 2017;Lundberg et al 2013;Ramstad et al 2016;Santure et al 2011;Srivastava 2011;Srivastava et al 2012;Vijayakumar et al 2014;Zhang et al 2014b) (Box 3). Whole body transcriptomics was used to find candidate loci explaining the divergence between two subspecies of songbirds with several phenotypically different characteristics inhabiting either the mainland or islands of Alaska (Srivastava 2011).…”

“…This classification scheme was initiated to generate consistent descriptions of gene products that can be used across species boundaries (Gene Ontology Consortium 2004). GO analyses are frequently used in transcriptome studies to help reduce complexity and highlight biological processes , and also, of course, in avian studies (Balakrishnan et al 2013;Ekblom et al 2014;Peterson et al 2012;Santure et al 2011;Vijayakumar et al 2014;Wright et al 2015). By classifying the genes that were differentially expressed between migratory and sedentary Dark-eyed Juncos Junco hyemalis through GO analysis, Fudickar et al (2016) found that genes involved in lipid transport and metabolism were overrepresented in migrant individuals while genes involved in reproductive processes were overrepresented in resident individuals.…”