Data Descriptor: 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

doi:10.1038/sdata.2017.178

Data Descriptor: 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

Division of Biological and Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

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.

Original language	English
Article number	170178
Journal	Scientific data
Volume	4
DOIs	https://doi.org/10.1038/sdata.2017.178
State	Published - Dec 5 2017

Funding

This work was funded by project HybridAdapt with reference FCT-ANR/BIA-EVF/0250/2012, supported by Portuguese National Funds through the Fundação para a Ciência e a Tecnologia, FCT. Additional support was obtained from POPH-QREN funds, from the European Social Fund and FCT (IF/ 00033/2014/CP1256/CT0005 FCT Investigator grant to JM-F, and SFRH/BD/115089/2016 and PD/BD/ 108131/2015 PhD grants to JPM and MSF respectively). Instrumentation, laboratory and computational support was provided by CIBIO NEW-GEN sequencing platform, supported by European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 286431. Laboratory work at the University of Montana was performed in the UM Genomics Core, supported with a grant from the M.J. Murdock Charitable Trust. Transcriptome sequencing was performed through the Vincent J. Coates Genomics Sequencing Laboratory at University of California Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. Support was additionally obtained from FLAD (Luso-American Foundation) travel grant to MSF. We are grateful to René Gadient and local hunters in Grisons for their tremendous effort in collecting samples under Alpine conditions. Laura Claffey issued the licence to take animals for scientific purposes in Ireland (dated 31/10/2012) from the Wildlife Licensing Unit, National Parks & Wildlife Service (NPWS), Department of Arts, Heritage & the Gaeltacht, and Mr Jimi Conroy, the local NPWS Conservation Officer consented to sampling within his jurisdiction. We thank the Irish Coursing Club (ICC) for providing hares, and in particular Mr D.J. Histon, Chief Executive and Secretary, for supporting the research. Thanks also to Mr William Fitzgerald, Department of Agriculture, Food and the Marine for dispatching animals in a humane manner.

Funder number
S10RR027303, S10RR029668
286431
SFRH/BD/115089/2016, IF/ 00033/2014/CP1256/CT0005, PD/BD/ 108131/2015

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10.1038/sdata.2017.178

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Marques, J. P., Ferreira, M. S., Farelo, L., Callahan, C. M., Hackländer, K., Jenny, H., Montgomery, W. I., Reid, N., Good, J. M., Alves, P. C., & Melo-Ferreira, J. (2017). Data Descriptor: Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. Scientific data, 4, Article 170178. https://doi.org/10.1038/sdata.2017.178

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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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AU - Callahan, Colin M.

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AU - Jenny, Hannes

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

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