Dataset Information

A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird.

ABSTRACT: The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.

SUBMITTER: Friis G

PROVIDER: S-EPMC9157146 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird.

Friis Guillermo G Vizueta Joel J Ketterson Ellen D ED Milá Borja B

G3 (Bethesda, Md.) 20220501 6

The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generat ...[more]

PMID: 35404451

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Project description:BACKGROUND:Though genomic-level data are becoming widely available, many of the metazoan species sequenced are laboratory systems whose natural history is not well documented. In contrast, the wide array of species with very well-characterized natural history have, until recently, lacked genomics tools. It is now possible to address significant evolutionary genomics questions by applying high-throughput sequencing to discover the majority of genes for ecologically tractable species, and by subsequently developing microarray platforms from which to investigate gene regulatory networks that function in natural systems. We used GS-FLX Titanium Sequencing (Roche/454-Sequencing) of two normalized libraries of pooled RNA samples to characterize a transcriptome of the dark-eyed junco (Junco hyemalis), a North American sparrow that is a classically studied species in the fields of photoperiodism, speciation, and hormone-mediated behavior. RESULTS:From a broad pool of RNA sampled from tissues throughout the body of a male and a female junco, we sequenced a total of 434 million nucleotides from 1.17 million reads that were assembled de novo into 31,379 putative transcripts representing 22,765 gene sets covering 35.8 million nucleotides with 12-fold average depth of coverage. Annotation of roughly half of the putative genes was accomplished using sequence similarity, and expression was confirmed for the majority with a preliminary microarray analysis. Of 716 core bilaterian genes, 646 (90?%) were recovered within our characterized gene set. Gene Ontology, orthoDB orthology groups, and KEGG Pathway annotation provide further functional information about the sequences, and 25,781 potential SNPs were identified. CONCLUSIONS:The extensive sequence information returned by this effort adds to the growing store of genomic data on diverse species. The extent of coverage and annotation achieved and confirmation of expression, show that transcriptome sequencing provides useful information for ecological model systems that have historically lacked genomic tools. The junco-specific microarray developed here is allowing investigations of gene expression responses to environmental and hormonal manipulations - extending the historic work on natural history and hormone-mediated phenotypes in this system.

Project description:Plumage color plays a prominent role in reproductive isolation and thus understanding the genetic basis of pigmentation patterns can provide critical insight into speciation. Subspecies of the dark-eyed junco (Junco hyemalis) show marked differences in melanic plumage coloration known to have evolved rapidly since the Last Glacial Maximum just 18,000 years ago. To understand this rapid radiation we studied the pigment composition and the genetic basis of coloration in two divergent subspecies, the slate-colored and Oregon juncos. We used HPLC and light microscopy to investigate pigment deposition patterns in feathers from four body areas. RNA-seq data generated under common garden experimental conditions were then used to compare the relative roles of differential gene expression in growing feathers and sequence divergence in loci expressed during feather development. Junco feathers were found to differ in eumelanin and pheomelanin content and distribution, producing a range of black, gray and brown colors. Transcriptomic data revealed marked regulatory differences among subspecies and among body-parts within subspecies in known melanin-pathway genes (including PMEL, TYR, TYRP1, OCA2, MLANA), but also in several novel or poorly known loci (EDAR, VPS33B, HPS1). Within subspecies, lighter feathers expressed less melanin synthesis genes, more ASIP, and showed differential expression of Wnt signaling genes. Feathers from different body regions also showed differential expression of Hox genes. The two subspecies differed in expression of ASIP and three other genes (MFSD12, KCNJ13, HAND2) previously associated with color development. Sequence variation in the expressed genes was not related to color differences between junco subspecies. Our findings suggest that differential expression of a few genes can account for marked differences in plumage color and pattern, a mechanism that can account for the rapid diversification of juncos. Several novel candidate pigmentation genes found in juncos may contribute to the expression of melanic coloration in other vertebrates.

Dataset Information

A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird.

Publications

A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird.

Similar Datasets

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