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Zonotrichia albicollis

ABSTRACT: The Brain Transcriptome of the White-throated Sparrow, a Vertebrate Model of Inversion Polymorphism

PROVIDER: PRJNA231930 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1200893_1.fastq.gz	Fastqsanger.gz
	SRR1200893_2.fastq.gz	Fastqsanger.gz
	SRR1200734.fastq.gz	Fastqsanger.gz
	SRR1200894_1.fastq.gz	Fastqsanger.gz
	SRR1200894_2.fastq.gz	Fastqsanger.gz

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Zonotrichia albicollis

Project description:The white-throated sparrow is a passerine bird native to North America

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Zonotrichia albicollis

Project description:Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

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Zonotrichia albicollis isolate:Super-white morph

Project description:Whole genome sequencing of the white-throated sparrow (super white morph)

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Genes located in a chromosomal inversion are correlated with territorial song in white-throated sparrows

Project description:The genome of the white-throated sparrow (Zonotrichia albicollis) contains an inversion polymorphism on chromosome 2 that is linked to predictable variation in a suite of phenotypic traits including plumage color, aggression, and parental behavior. Differences in gene expression between the two color morphs, which represent the two common inversion genotypes (ZAL2/ZAL2 and ZAL2/ZAL2m), are therefore of potential interest toward understanding the molecular underpinnings of these phenotypes. To identify genes that are differentially expressed between the two morphs and correlated with behavior, we quantified both behavior and gene expression in a population of free-living white-throated sparrows. We quantified behavioral responses to simulated territorial intrusions (STIs) early during the breeding season. In the same birds, we then performed a transcriptomewide analysis of gene expression in two behaviorally relevant brain regions, the medial amygdala and hypothalamus. Using network analyses, we identified modules of genes that were correlated with both morph and STI-induced singing behavior. The majority of these genes were located within the inversion, demonstrating the profound effect the inversion has on the expression of genes captured by the rearrangement. Gene pathway analyses revealed that in the medial amygdala, the most prominent pathways were those related to steroid hormone receptor activity. Within these pathways, the only gene encoding such a receptor was ESR1 (estrogen receptor alpha). Our results thus suggest that ESR1 and related genes are important for behavioral differences between the morphs.

2017-11-06 | GSE77186 | GEO

Project description:White-throated sparrow nestling transcriptomics

| PRJNA546611 | ENA

Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis).

Project description:BackgroundThe level of nucleotide diversity observed across the genome is positively correlated with the local rate of recombination. Avian karyotypes are typified by large variation in chromosome size and the rate of recombination in birds has been shown to be negatively correlated with chromosome size. It has thus been predicted that nucleotide diversity is negatively correlated with chromosome size in aves. However, there is limited empirical evidence to support this prediction.ResultsHere we sequenced 27 autosomal and 12 sex chromosome-linked loci in the white-throated sparrow (Zonotrichia albicollis) to quantify and compare patterns of recombination, linkage disequilibrium (LD), and genetic diversity across the genome of this North American songbird. Genetic diversity on the autosomes varied up to 8-fold, with the lowest diversity observed on the macrochromosomes and the highest diversity on the microchromosomes. Genetic diversity on the sex chromosomes was reduced compared to the autosomes, the most extreme difference being a ~300-fold difference between the W chromosome and the microchromosomes. LD and population structure associated with a common inversion polymorphism (ZAL2/2m) in this species were found to be atypical compared to other macrochromosomes, and nucleotide diversity within this inversion on the two chromosome arrangements was more similar to that observed on the Z chromosome.ConclusionsA negative correlation between nucleotide diversity and autosome size was observed in the white-throated sparrow genome, as well as low levels of diversity on the sex chromosomes comparable to those reported in other birds. The population structure and extended LD associated with the ZAL2/2m chromosomal polymorphism are exceptional compared to the rest of the white-throated sparrow genome.

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Zonotrichia albicollis

Project description:Zonotrichia albicollis Transcriptome or Gene expression

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Zonotrichia albicollis

Project description:Zonotrichia albicollis Raw sequence reads

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Zonotrichia albicollis

Project description:Zonotrichia albicollis Transcriptome or Gene expression

| PRJNA217789 | ENA

Project description:Whole-genome bisulfite sequencing of the white-throated sparrow

| PRJNA540850 | ENA