An annotated de novo draft genome of the mountain hare (Lepus timidus)

  • João Marques (Contributor)
  • Fernando Seixas (Contributor)
  • Liliana Farelo (Contributor)
  • Colin Callahan (Contributor)
  • Jeffrey Good (Contributor)
  • Reid, N. (Participant)
  • Paulo C Alves (Contributor)
  • Pierre Boursot (Contributor)
  • José Melo-Ferreira (Presenter)

Activity: Talk or presentation typesOral presentation


Generating genomic resources for Lagomorphs provides fundamental tools to study relevant questions related with the biology and evolution of these organisms. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus). We assembled the genome using the ALLPATHS-LG protocol, combining overlapping pair and mate pair reads from Illumina sequencing (77x coverage). After de novo assembly, a reference-guided ordering of the obtained scaffolds based on the available European rabbit (Oryctolagus cuniculus) genome allowed reconstructing long scaffolds, 22 of which have a direct correspondence with the rabbit chromosomes. 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. This hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Given that previous genomic studies on hares had relied on comparisons to the rabbit reference genome, we then performed analyses of hare whole-genome re-sequencing data based on the density of variants along the genome, using either the hare or the rabbit genomes as reference. Our results show similar inferences in either case, which validates previous reference-based strategies, and suggests that the chromosome-scale hare draft genome can be used for chromosome-wide analyses and genome scans on hares.
Period06 Jul 202010 Jul 2020
Event title6th World Lagomorph Conference
Event typeConference
LocationMontpellier, France
Degree of RecognitionInternational