A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird
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A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird. / Friis, Guillermo; Vizueta, Joel; Ketterson, Ellen D.; Milá, Borja.
In: G3: Genes, Genomes, Genetics, Vol. 12, No. 6, jkac083, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird
AU - Friis, Guillermo
AU - Vizueta, Joel
AU - Ketterson, Ellen D.
AU - Milá, Borja
N1 - Funding Information: Funding was provided by grant CGL-2011-25866 from the Spanish Ministerio de Ciencia e Innovación to BM and by multiple awards from the National Science Foundation to EK. Publisher Copyright: © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - dark-eyed junco
KW - genome assembly
KW - Hi-C
KW - Junco hyemalis
U2 - 10.1093/g3journal/jkac083
DO - 10.1093/g3journal/jkac083
M3 - Journal article
C2 - 35404451
AN - SCOPUS:85131220411
VL - 12
JO - G3: Genes, Genomes, Genetics (Bethesda)
JF - G3: Genes, Genomes, Genetics (Bethesda)
SN - 2160-1836
IS - 6
M1 - jkac083
ER -
ID: 343211890