A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia
The 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 candi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2020-04-01
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| Series: | G3: Genes, Genomes, Genetics |
| Subjects: | |
| Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.119.400929 |
| _version_ | 1819149663358418944 |
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| author | Swarnali Louha David A. Ray Kevin Winker Travis C. Glenn |
| author_facet | Swarnali Louha David A. Ray Kevin Winker Travis C. Glenn |
| author_sort | Swarnali Louha |
| collection | DOAJ |
| description | The 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. |
| first_indexed | 2024-12-22T14:05:11Z |
| format | Article |
| id | doaj.art-4639e2b72bfd494388802461d56fdefb |
| institution | Directory Open Access Journal |
| issn | 2160-1836 |
| language | English |
| last_indexed | 2024-12-22T14:05:11Z |
| publishDate | 2020-04-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | G3: Genes, Genomes, Genetics |
| spelling | doaj.art-4639e2b72bfd494388802461d56fdefb2022-12-21T18:23:19ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362020-04-011041159116610.1534/g3.119.4009292A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodiaSwarnali LouhaDavid A. RayKevin WinkerTravis C. GlennThe 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.http://g3journal.org/lookup/doi/10.1534/g3.119.400929melospiza melodiadovetail genomicspasseriformeswhole genome sequencingde novo assembly |
| spellingShingle | Swarnali Louha David A. Ray Kevin Winker Travis C. Glenn A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia G3: Genes, Genomes, Genetics melospiza melodia dovetail genomics passeriformes whole genome sequencing de novo assembly |
| title | A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia |
| title_full | A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia |
| title_fullStr | A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia |
| title_full_unstemmed | A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia |
| title_short | A High-Quality Genome Assembly of the North American Song Sparrow, Melospiza melodia |
| title_sort | high quality genome assembly of the north american song sparrow melospiza melodia |
| topic | melospiza melodia dovetail genomics passeriformes whole genome sequencing de novo assembly |
| url | http://g3journal.org/lookup/doi/10.1534/g3.119.400929 |
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