Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. However, 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 de novo 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 using the rabbit genome as reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb, with 22 scaffolds corresponding to the rabbit chromosomes. 24,578 protein coding genes were annotated by combining ab-initio predictions, homology search and transcriptome data, of which 683 were solely annotated based on hare-specific transcriptome data. Similar estimates of heterozygosity and PSMC-inferred demographic profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. These results suggest that the hare draft genome should allow similar performance in chromosome-wide analyses and genome scans on hares. In addition, the hare reference genome is a new resource of hare-specific variation, valuable for studies at finer genomic scales.
- whole genome sequencing
- de novo assembly