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Evolutionary relevance of lineages in the European black pine (Pinus nigra) in the transcriptomic era

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European black pine (Pinus nigra J.F.Arnold) is an ecologically and economically important conifer growing across southern Europe and the Mediterranean Basin in a variety of habitats. Its morphological and ecological variabilities as well as geographic origin are the basis for subspecies level taxonomic identification and forestry practice recommendations. Yet, no true consensus exists and genomic resources are lacking for resolving the taxonomy of P. nigra and assessing its adaptive potential. To provide genetic tools for further research, we generated novel genomic resources using six de novo transcriptomic assemblies representing major biogeographic regions where the species is growing naturally. Using two closely related species, Pinus sylvestris and Pinus halepensis, as outgroups, we identified a set of 2200 nuclear, putatively orthologous, single-copy genes. In addition, we identified a set of 405,624 polymorphic SNPs for P. nigra. Based on these resources, we were able to confirm the division of P. nigra into two wide geographical population groups and to provide new insights into evolutionary dynamics of the species.

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Two anonymous reviewers and the associate editor are acknowledged for their helpful comments that improved the final version of this article. We thank M. Lingrand (INRA URFM, Avignon, France) for sample collection and preparation. Collection of material was made before the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity and was legally implemented by signatory countries. We thank IGAtech (Udine, Italy) for transcriptome sequencing and de novo assembly. We acknowledge Supercomputing Centre of Galicia (CESGA) as well as CSC—Finnish IT Center and the Finnish grid infrastructure (FGI) for Science for the allocation of computational resources.


Funding was provided by the project INIA-MAPAMA EG17-048 co-financed by FEADER (75%) according to EU Regulation 1305/2013. SO received funding from the Spanish Ministry of Economy and Competitiveness (MINECO) under PTA2015-10836-I contract. We received financial support from GenTree. This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 676876.

Author information

BF and GGV conceived the study; FC and VV produced the data and assembled the reference transcriptome; SO performed transcriptomic data analyses; DG contributed to genetic analyses; SO, BF and DG wrote the manuscript with the help of GG; all authors revised and edited the text, and approved the final manuscript.

Correspondence to Sanna Olsson or Bruno Fady.

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The raw reads and the contamination filtered reference transcriptome have been deposited in the European Nucleotide Archive (ENA) under bioproject PRJEB33411.

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Olsson, S., Grivet, D., Cattonaro, F. et al. Evolutionary relevance of lineages in the European black pine (Pinus nigra) in the transcriptomic era. Tree Genetics & Genomes 16, 30 (2020).

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  • Orthologous gene
  • Nuclear genetic marker
  • SNP
  • Transcriptome
  • Phylogeny