Résumé
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 24,578 protein coding genes by combining ab-initio predictions,
homology search, and transcriptome data, of which 683 were solely derived
from hare-specific transcriptome data. The hare reference genome is
therefore a new resource to discover and investigate hare-specific
variation. Similar estimates of heterozygosity and inferred demographic
history 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. Our results validate previous
reference-based strategies and suggest that the chromosome-scale hare
draft genome should enable chromosome-wide analyses and genome scans on
hares.