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 - Publisher Copyright:
© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America
PY - 2022/6
Y1 - 2022/6
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 - Hi-C
KW - Junco hyemalis
KW - dark-eyed junco
KW - genome assembly
UR - http://www.scopus.com/inward/record.url?scp=85131220411&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85131220411&partnerID=8YFLogxK
U2 - 10.1093/g3journal/jkac083
DO - 10.1093/g3journal/jkac083
M3 - Article
C2 - 35404451
AN - SCOPUS:85131220411
SN - 2160-1836
VL - 12
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 6
M1 - jkac083
ER -