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Sci Data. 2017 Dec 05;4:170178. doi: 10.1038/sdata.2017.178.

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

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

Affiliations

  1. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal.
  2. Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal.
  3. Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA.
  4. Institute of Wildlife Biology and Game Management, BOKU-University of Natural Resources and Life Sciences, Vienna 1180, Austria.
  5. Amt für Jagd und Fischerei Graubünden, Chur 7001, Switzerland.
  6. Institute of Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5BN, UK.
  7. School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK.

PMID: 29206218 PMCID: PMC5716010 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.

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