Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares

João P Marques,Hannes Jenny,Neil Reid,Mafalda S Ferreira,José Melo-Ferreira,W Ian Montgomery,Paulo C Alves,Colin M Callahan,Jeffrey M Good,Liliana Farelo,Klaus Hackländer

doi:10.1038/sdata.2017.178

Abstract

We report the first mountain hare (Lepus timidus) transcriptome, produced by de novo assembly of RNA-sequencing reads. Data were obtained from eight specimens sampled in two localities, Alps and Ireland. The mountain hare tends to be replaced by the invading European hare (Lepus europaeus) in their numerous contact zones where the species hybridize, which affects their gene pool to a yet unquantified degree. We characterize and annotate the mountain hare transcriptome, detect polymorphism in the two analysed populations and use previously published data on the European hare (three specimens, representing the European lineage of the species) to identify 4 672 putative diagnostic sites between the species. A subset of 85 random independent SNPs was successfully validated using PCR and Sanger sequencing. These valuable genomic resources can be used to design tools to assess population status and monitor hybridization between species.

Highlights

Background & SummaryThe mountain hare (Lepus timidus) is an Arcto-alpine species that was the most common and widely distributed hare species across Europe during the last glacial periods[1]
The mountain hare is distributed from Fennoscandia to Eastern Siberia, and occurs in isolated/refuge populations (e.g., Ireland, Scotland, the Alps, Poland, the Baltics and Japan), and in places where it has been introduced (Iceland, England, Faroe Islands and New Zealand)
Even though they are a popular game species and abundant within its range, mountain hares have sharply declined in some regions, in areas of contact with the European hare (Lepus europaeus), where the latter tends to invade and replace the range of the former[1,2,3,4]

Summary

Introduction

Background & SummaryThe mountain hare (Lepus timidus) is an Arcto-alpine species that was the most common and widely distributed hare species across Europe during the last glacial periods[1]. We use high-throughput RNA sequencing to: i) generate genomic resources for the mountain hare; and, ii) use published data on the European hare[18] to pinpoint candidate fixed differences between the species that can be used to build genotyping tools to monitor gene exchange in the contact zones.

Results

Conclusion