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

Abstract

Emberizid sparrows (emberizidae) have played a prominent role in the study of avian vocal communication and social behavior. We present here brain transcriptomes for three emberizid model systems, song sparrow Melospiza melodia, white-throated sparrow Zonotrichia albicollis, and Gambel’s white-crowned sparrow Zonotrichia leucophrys gambelii. Each of the assemblies covered fully or in part, over 89% of the previously annotated protein coding genes in the zebra finch Taeniopygia guttata, with 16,846, 15,805, and 16,646 unique BLAST hits in song, white-throated and white-crowned sparrows, respectively. As in previous studies, we find tissue of origin (auditory forebrain versus hypothalamus and whole brain) as an important determinant of overall expression profile. We also demonstrate the successful isolation of RNA and RNA-sequencing from post-mortem samples from building strikes and suggest that such an approach could be useful when traditional sampling opportunities are limited. These transcriptomes will be an important resource for the study of social behavior in birds and for data driven annotation of forthcoming whole genome sequences for these and other bird species.

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

“…To investigate the long-term evolutionary history of chromosomes 2 and 2 m , we examined genome-wide patterns of divergence between the white-throated sparrow and its close relatives. For comparison, we analyzed closely-related taxa with previously [16, 17] or newly sequenced transcriptomes or genomes (Figure 1B). As in previous studies [11], we find that the relationship of chromosomes 2 and 2 m conflicts with the species tree and suggests more recent common ancestry of chromosome 2 with other taxa than with 2 m .…”

Parent and offspring genotypes influence gene expression in early life

“…Additionally, we identified morphspecific gene expression driven by innate immunity genes and genes located in the chromosome 2 inversion. As adults, the genes within the inversion strongly influence the WTSP neural transcriptome (Balakrishnan et al, 2014;Zinzow-Kramer et al, 2015). Our results here suggest that as nestlings, parental genotypes and associated behaviours, rather than nestling genotype, have the strongest influence on the nestling transcriptome.…”

Mapping Molecular Datasets Back to the Brain Regions They are Extracted from: Remembering the Native Countries of Hypothalamic Expatriates and Refugees

“…Left- and right-handedness in cichlid fish, for example, is correlated strongly with hemispheric and regional asymmetry of gene expression [241]. In songbirds, clustering analyses performed on retrieved sets of genes demonstrate a strong association of gene expression with brain region [25, 96, 359]. This also holds true for mammalian brain.…”