De Novo Assembly of a High-Quality Reference Genome for the Horned Lark ( Eremophila alpestris )

• Published in: G3 Genes|Genomes|Genetics
• Main Authors: Mason, Nicholas A, Pulgarin, Paulo, Cadena, Carlos Daniel, Lovette, Irby J
• Format: Article in Journal/Newspaper
• Language: English
• Published: Oxford University Press (OUP) 2020
• Subjects: Genetics (clinical); Genetics; Molecular Biology; Eremophila alpestris
• Online Access: http://dx.doi.org/10.1534/g3.119.400846; http://academic.oup.com/g3journal/article-pdf/10/2/475/37180639/g3journal0475.pdf

Abstract The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds.