PT  - JOURNAL ARTICLE
AU  - Nicholas A. Mason
AU  - Paulo Pulgarin
AU  - Carlos Daniel Cadena
AU  - Irby J. Lovette
TI  - Genome Report: <em>De novo</em> assembly of a high-quality reference genome for the Horned Lark (<em>Eremophila alpestris</em>)
AID  - 10.1101/811745
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 811745
4099  - http://biorxiv.org/content/early/2019/10/21/811745.short
4100  - http://biorxiv.org/content/early/2019/10/21/811745.full
AB  - The Horned Lark (Eremophila alpestris) is a species of small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris and related species have been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for horned larks and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for horned larks generated from blood samples 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 2708 contigs with an N50 of 10.58 Mb and a L50 of 29. After polishing the genome, we were able to identify 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, indicating that our de novo assembly is near complete. 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 a widespread, yet understudied lineage of songbirds.