{"id":"b6900166-ded6-4f7a-8734-484b6f77b2f1","uri":"https://catalogue.ceh.ac.uk/id/b6900166-ded6-4f7a-8734-484b6f77b2f1","type":"dataset","title":"Comparative transcriptomics of a complex of four European pine species","description":"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\n  1) transcriptome sequence of a reference Scots pine sample generated using Illumina paired-end sequencing technology and\n  2) information about single nucleotide polymorphisms (SNPs) in 17 samples collected across the European range, compared to the reference Scots pine sample.\n\nThese genomic resources were produced to advance the study of the genetic basis of adaptive variation and speciation in pines. ","metadataDate":"2026-03-09T17:39:01","resourceIdentifiers":[{"code":"1412239567948","codeSpace":"CEH:EIDC:"},{"code":"https://catalogue.ceh.ac.uk/id/b6900166-ded6-4f7a-8734-484b6f77b2f1"},{"code":"10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1","codeSpace":"doi:"}],"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. \n\n2. The single nucleotide polymorphism (SNP) data file was prepared by aligning sixteen samples to the reference, a sample set that included P. sylvestris (four samples), P. mugo (five samples), P. uncinata (four samples) and P. uliginosa (three samples). Samples collected between 2006 and 2010.","spatialRepresentationTypes":["textTable"],"datasetLanguages":["eng"],"topicCategories":[{"value":"biota","uri":"http://inspire.ec.europa.eu/metadata-codelist/TopicCategory/biota"}],"keywordsPlace":[{"value":"Europe"}],"keywordsTheme":[{"value":"Evolutionary ecology","uri":"http://onto.nerc.ac.uk/CEHMD/topic/19"}],"keywordsOther":[{"value":"Pinus sylvestris","uri":"http://www.wikidata.org/entity/Q133128"},{"value":"Pinus mugo","uri":"http://www.wikidata.org/entity/Q147475"},{"value":"Pinus uliginosa","uri":"http://www.wikidata.org/entity/Q160727"},{"value":"Pinus uncinata","uri":"http://www.wikidata.org/entity/Q149548"}],"distributionFormats":[{"name":"Variant Call Format (VCF)","type":"text/plain","version":"unknown"}],"inspireThemes":[{"theme":"Environmental Monitoring Facilities","uri":"http://inspire.ec.europa.eu/theme/ef"}],"boundingBoxes":[{"westBoundLongitude":-5.5,"eastBoundLongitude":29.5,"southBoundLatitude":40,"northBoundLatitude":61.5,"bounds":"{\"type\": \"Feature\",      \"properties\": {},      \"geometry\": {        \"type\": \"Polygon\",        \"coordinates\": [[[-5.5, 40], [-5.5, 61.5], [29.5, 61.5], [29.5, 40], [-5.5, 40]]]      }}","coordinates":"[[[-5.5, 40], [-5.5, 61.5], [29.5, 61.5], [29.5, 40], [-5.5, 40]]]"}],"distributorContacts":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"distributor","email":"info@eidc.ac.uk"}],"responsibleParties":[{"familyName":"Wachowiak","givenName":"W.","organisationName":"Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","fullName":"Wachowiak, W."},{"familyName":"Trivedi","givenName":"U.","organisationName":"The University of Edinburgh","role":"author","email":"enquiries@ceh.ac.uk","fullName":"Trivedi, U."},{"familyName":"Telford","givenName":"A.","organisationName":"Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","fullName":"Telford, A."},{"familyName":"Cavers","givenName":"S.","organisationName":"Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","nameIdentifier":"https://orcid.org/0000-0003-2139-9236","fullName":"Cavers, S."},{"familyName":"Wachowiak","givenName":"Witold","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"pointOfContact","email":"enquiries@ceh.ac.uk","address":{"deliveryPoint":"Bush Estate","city":"Penicuik","administrativeArea":"Midlothian","postalCode":"EH26 0QB","country":"United Kingdom"},"fullName":"Wachowiak, W.","pointOfContact":"UK Centre for Ecology & Hydrology"},{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"custodian","email":"info@eidc.ac.uk"},{"organisationName":"NERC Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"publisher","email":"info@eidc.ac.uk"},{"organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"rightsHolder","email":"enquiries@ceh.ac.uk"}],"temporalExtents":[{"begin":"2006-01-01","end":"2008-12-31"}],"onlineResources":[{"url":"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","type":"OTHER"},{"url":"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","type":"OTHER"}],"spatialReferenceSystems":[{"code":"http://www.opengis.net/def/crs/EPSG/0/4326","title":"WGS 84"}],"incomingCitations":[{"description":"Wachowiak, W., Trivedi, U., Perry, A., & Cavers, S. (2015). Comparative transcriptomics of a complex of four European pine species. BMC Genomics, 16(1). ","url":"https://doi.org/10.1186/s12864-015-1401-z"},{"description":"Liu, J.-J., Schoettle, A. W., Sniezko, R. A., Sturrock, R. N., Zamany, A., Williams, H., … Kegley, A. (2016). Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping. BMC Genomics, 17(1).","url":"https://doi.org/10.1186/s12864-016-3079-2"}],"datasetReferenceDate":{"publicationDate":"2014-10-10"},"resourceMaintenance":[{"frequencyOfUpdate":"notPlanned"}],"useConstraints":[{"value":"This resource is made available under the terms of the Open Government Licence ","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"},{"value":"© UK Centre for Ecology & Hydrology","code":"copyright"}],"resourceType":{"value":"dataset"},"accessLimitation":{"value":"no limitations to public access","code":"Available","uri":"http://purl.org/coar/access_right/c_abf2"},"notGEMINI":false,"licences":[{"value":"This resource is made available under the terms of the Open Government Licence ","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"}],"topics":["http://onto.nerc.ac.uk/CEHMD/topic/19"],"incomingCitationCount":2,"publishers":[{"organisationName":"NERC Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"publisher","email":"info@eidc.ac.uk"}],"authors":[{"familyName":"Wachowiak","givenName":"W.","organisationName":"Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","fullName":"Wachowiak, W."},{"familyName":"Trivedi","givenName":"U.","organisationName":"The University of Edinburgh","role":"author","email":"enquiries@ceh.ac.uk","fullName":"Trivedi, U."},{"familyName":"Telford","givenName":"A.","organisationName":"Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","fullName":"Telford, A."},{"familyName":"Cavers","givenName":"S.","organisationName":"Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"author","email":"enquiries@ceh.ac.uk","nameIdentifier":"https://orcid.org/0000-0003-2139-9236","fullName":"Cavers, S."}],"publicationDate":"2014-10-10T00:00:00.000+00:00","availability":"Available","custodians":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"custodian","email":"info@eidc.ac.uk"}],"infoLinks":[{"url":"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","type":"OTHER"}],"pointsOfContact":[{"familyName":"Wachowiak","givenName":"Witold","organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"pointOfContact","email":"enquiries@ceh.ac.uk","address":{"deliveryPoint":"Bush Estate","city":"Penicuik","administrativeArea":"Midlothian","postalCode":"EH26 0QB","country":"United Kingdom"},"fullName":"Wachowiak, W.","pointOfContact":"UK Centre for Ecology & Hydrology"}],"rightsHolders":[{"organisationName":"UK Centre for Ecology & Hydrology","organisationIdentifier":"https://ror.org/00pggkr55","role":"rightsHolder","email":"enquiries@ceh.ac.uk"}],"citation":{"authors":["Wachowiak, W.","Trivedi, U.","Telford, A.","Cavers, S."],"doi":"10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1","title":"Comparative transcriptomics of a complex of four European pine species","publisher":"NERC Environmental Information Data Centre","resourceTypeGeneral":"dataset","year":2014,"month":10,"day":10,"bibtex":"https://catalogue.ceh.ac.uk/documents/b6900166-ded6-4f7a-8734-484b6f77b2f1/citation?format=bib","ris":"https://catalogue.ceh.ac.uk/documents/b6900166-ded6-4f7a-8734-484b6f77b2f1/citation?format=ris","url":"https://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1"}}