Dataset
Comparative transcriptomics of a complex of four European pine species

This resource is made available under the terms of the Open Government Licence

Wachowiak, W.; Trivedi, U.; Telford, A.; Cavers, S. (2014)
https://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1

Data from whole transcriptome sequencing of the four European pine species - Pinus sylvestris (Scots pine), P. mugo (Dwarf mountain pine), P. uliginosa (Mountain pine) and P. uncinata (Peat-bog pine). Those data include 1) transcriptome sequence of a reference Scots pine sample generated using Illumina paired-end sequencing technology and 2) information about single nucleotide polymorphisms (SNPs) in 17 samples collected across the European range, compared to the reference Scots pine sample. These genomic resources were produced to advance the study of the genetic basis of adaptive variation and speciation in pines.

Publication date: 2014-10-10

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This resource is made available under the terms of the Open Government Licence

You must cite: Wachowiak, W.; Trivedi, U.; Telford, A.; Cavers, S. (2014). Comparative transcriptomics of a complex of four European pine species. NERC Environmental Information Data Centre. https://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1

 

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Where/When

Study area
Temporal extent
2006-01-01    to    2008-12-31

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Supporting Information
Supporting information available to assist in re-use of this dataset

Quality

Lineage
1.Lineage of the reference transcriptome sequence of Scots pine samples from Glen Tanar (Scotland). Total Ribonucleic acid (RNA) was extracted from needles using Spectrum (TM) Plant Total RNA Kit (Sigma). A template complementary DNA (cDNA) library was prepared using ®TruSeq RNA Sample Preparation Kit (Illumina). The cDNA library was sequenced using Illumina HiSeq 2000 platform at Edinburgh Genomics, the University of Edinburgh, Scotland (Illumina, San Diego, California). 100 base, paired-end reads were generated and assembled de novo into contigs using Trinity (version r2012-06-08). The reference transcript sequence contains 40798 contigs in total. 2.The single nucleotide polymorphism (SNP) data file was prepared by aligning 16 samples to the reference, a sample set that included P. sylvestris (4 samples), P. mugo (5 samples), P. uncinata (4 samples) and P. uliginosa (3 samples). Samples collected between 2006 and 2010

Authors

Centre for Ecology & Hydrology
The University of Edinburgh
Centre for Ecology & Hydrology
Centre for Ecology & Hydrology

Other contacts

Point Of Contact
Centre for Ecology & Hydrology
Custodian
Publisher
Distributor

Spatial

Spatial Reference System
WGS 84

Keywords

Topic Categories
Biota
Other keywords
Pinus sylvestris
Scots pine
Pinus mugo
Dwarf mountain pine
Pinus uliginosa
Mountain pine
Pinus uncinata
Peat-bog pine
pine complex
nucleotide divergence
Local adaption
next-generation sequencing
Other keywords
Ecological Processes and Resilience
Other keywords
Evolutionary ecology
Discipline keywords
transcriptomics
Speciation
Place keywords
Europe

Dataset identifiers

CEH:EIDC:#1412239567948
https://catalogue.ceh.ac.uk/id/b6900166-ded6-4f7a-8734-484b6f77b2f1
doi:10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1

Metadata

Record identifier
b6900166-ded6-4f7a-8734-484b6f77b2f1
Record created by
Centre for Ecology & Hydrology
Record last updated
2017-06-20T10:21:41
Metadata standard
NERC profile of ISO19115:2003 version 1.0