Identification

Title

Comparative transcriptomics of a complex of four European pine species

Abstract

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

Resource type

dataset

Resource locator

https://data-package.ceh.ac.uk/data/b6900166-ded6-4f7a-8734-484b6f77b2f1

name: Download the data

description: Download a copy of this data

function: download

https://data-package.ceh.ac.uk/sd/b6900166-ded6-4f7a-8734-484b6f77b2f1.zip

name: Supporting Information

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

function: information

Unique resource identifier

code

1412239567948

codeSpace

CEH:EIDC:

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

biota

Keywords

Keyword set

keyword value

Environmental Monitoring Facilities

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

originating controlled vocabulary

title

Wikidata

reference date

date type

creation

effective date

2012-10-29

Keyword set

keyword value

Europe

Scots pine

Dwarf mountain pine

Mountain pine

Peat-bog pine

pine complex

nucleotide divergence

Local adaption

next-generation sequencing

transcriptomics

speciation

Geographic location

West bounding longitude

-5.5

East bounding longitude

29.5

North bounding latitude

61.5

South bounding latitude

Temporal reference

Temporal extent

Begin position

2006-01-01

End position

2008-12-31

Dataset reference date

date type

publication

effective date

2014-10-10

Frequency of update

notPlanned

Quality and validity

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

Conformity

Conformity report

specification

title

Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services

reference date

date type

publication

effective date

2010-12-08

degree

explanation

Data format

name of format

Variant Call Format (VCF)

version of format

Constraints related to access and use

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

Constraint set

Limitations on public access

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

owner

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

email address

info@eidc.ac.uk

responsible party role

pointOfContact

Metadata date

2021-06-25T18:38:50

Metadata language

eng