Comparative transcriptomics of a complex of four European pine species

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. Full details about this dataset can be found at https://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1

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Identification info

Metadata Language
English (en)
Character set
utf8
Dataset Reference Date ()
2014-10-10
Identifier
CEH:EIDC: / 1412239567948
Identifier
https://catalogue.ceh.ac.uk/id/b6900166-ded6-4f7a-8734-484b6f77b2f1
Identifier
doi: / 10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1
Other citation details
Wachowiak, W., Trivedi, U., Telford, A., Cavers, S. (2014). Comparative transcriptomics of a complex of four European pine species. NERC Environmental Information Data Centre 10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1
  Centre for Ecology & Hydrology - Wachowiak, W.
  The University of Edinburgh - Trivedi, U.
  Centre for Ecology & Hydrology - Telford, A.
  Centre for Ecology & Hydrology - Cavers, S.
  UK Centre for Ecology & Hydrology - Witold Wachowiak
  NERC EDS Environmental Information Data Centre
  NERC Environmental Information Data Centre
  UK Centre for Ecology & Hydrology
Maintenance and update frequency
notPlanned
GEMET - INSPIRE themes, version 1.0 ()
  • Environmental Monitoring Facilities
Wikidata
Keywords
  • Evolutionary ecology
  • Europe
  • Scots pine
  • Dwarf mountain pine
  • Mountain pine
  • Peat-bog pine
  • pine complex
  • nucleotide divergence
  • Local adaption
  • next-generation sequencing
  • transcriptomics
  • speciation
Limitations on Public Access
otherRestrictions
Other constraints
no limitations
Use constraints
otherRestrictions
Other constraints
This resource is made available under the terms of the Open Government Licence
Use constraints
otherRestrictions
Other constraints
© UK Centre for Ecology & Hydrology
Use constraints
otherRestrictions
Other constraints
If you reuse this data, you should 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
Spatial representation type
textTable
Topic category
  • Biota
N
S
E
W


Begin date
2006-01-01
End date
2008-12-31
 
Code
WGS 84

Distribution Information

Data format
  • Variant Call Format (VCF) ()

Resource Locator
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Supporting Information

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

Resource Locator
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Supporting Information

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

 
Quality Scope
dataset
Other
dataset

Report

Dataset Reference Date ()
2010-12-08
Statement
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

Metadata

File identifier
b6900166-ded6-4f7a-8734-484b6f77b2f1 XML
Metadata Language
English (en)
Character set
ISO/IEC 8859-1 (also known as Latin 1)
Resource type
dataset
Hierarchy level name
dataset
Metadata Date
2022-05-20T10:40:35
Metadata standard name
UK GEMINI
Metadata standard version
2.3
  Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK
 
 

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