A high-quality genome assembly of the north American song sparrow, melospiza melodia

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dc.creatorLouha, Swarnali
dc.creatorRay, David A. (TTU)
dc.creatorWinker, Kevin
dc.creatorGlenn, Travis C.
dc.date.accessioned2023-08-24T16:54:16Z
dc.date.available2023-08-24T16:54:16Z
dc.date.issued2020
dc.description© 2020 Louha et al. cc-by
dc.description.abstractThe song sparrow, Melospiza melodia, is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species' pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We have generated a high-quality de novo genome assembly of M. melodia using Illumina short read sequences from genomic and in vitro proximity-ligation libraries. The assembled genome is 978.3 Mb, with a physical coverage of 24.9·, N50 scaffold size of 5.6 Mb and N50 contig size of 31.7 Kb. Our genome assembly is highly complete, with 87.5% full-length genes present out of a set of 4,915 universal single-copy orthologs present in most avian genomes. We annotated our genome assembly and constructed 15,086 gene models, a majority of which have high homology to related birds, Taeniopygia guttata and Junco hyemalis. In total, 83% of the annotated genes are assigned with putative functions. Furthermore, only ∼7% of the genome is found to be repetitive; these regions and other non-coding functional regions are also identified. The high-quality M. melodia genome assembly and annotations we report will serve as a valuable resource for facilitating studies on genome structure and evolution that can contribute to biomedical research and serve as a reference in population genomic and comparative genomic studies of closely related species.
dc.identifier.citationLouha, S., Ray, D.A., Winker, K., & Glenn, T.C.. 2020. A high-quality genome assembly of the north American song sparrow, melospiza melodia. G3: Genes, Genomes, Genetics, 10(4). https://doi.org/10.1534/g3.119.400929
dc.identifier.urihttps://doi.org/10.1534/g3.119.400929
dc.identifier.urihttps://hdl.handle.net/2346/95789
dc.language.isoeng
dc.subjectAssembly
dc.subjectDe novo
dc.subjectDovetail genomics
dc.subjectMelospiza melodia
dc.subjectPasseriformes
dc.subjectSequencing
dc.subjectWhole genome
dc.titleA high-quality genome assembly of the north American song sparrow, melospiza melodia
dc.typeArticle

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