Data from: An annotated draft genome of the mountain hare (Lepus timidus) ...

• Main Authors: Marques, João Pedro, Seixas, Fernando A., Good, Jeffrey M., Farelo, Liliana, Callahan, Colin M., Montgomery, W. Ian, Reid, Neil, Alves, Paulo C., Boursot, Pierre, Melo-Ferreira, José
• Format: Dataset
• Language: English
• Published: Dryad 2020
• Subjects: FOS Biological sciences; whole-genome sequencing; de novo Assembly; annotation; Hares; Leporids; Lagomorpha; Lepus timidus; mountain hare
• Online Access: https://dx.doi.org/10.5061/dryad.j0zpc86bk; https://datadryad.org/stash/dataset/doi:10.5061/dryad.j0zpc86bk

Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated ... : DNA Sampling, Extraction, and Sequencing One female mountain hare (Lepus timidus hibernicus) specimen (NCBI BioSample ID SAMN12621015) was captured from the wild for scientific research purposes by the Irish Coursing Club (ICC) at Borris-in-Ossory, County Laois under National Parks & Wildlife (NPWS) license no. C 337/2012 issued by the Department of Arts, Heritage and the Gaeltacht (dated October 31, 2012). Genomic DNA was extracted from kidney, muscle, and ear tissue using the JETquick Tissue DNA Spin Kit (GENOMED), with RNAse and proteinase K to remove RNA and protein contamination. Genomic libraries of different insert lengths were generated following the standard ALLPATHS-LG protocol (Gnerre et al. 2011): one Illumina TruSeq DNA library of 180 bp fragments was sequenced with overlapping paired-end (OPE) reads, and three Illumina TruSeq DNA mate-pair (MP) libraries of 2.5, 4.5, and 8.0 kb insert sizes. Whole-genome sequencing was performed at The Genome Analysis Center (TGAC, currently Earlham ...