ArticleBMC genomics2015
Comparative transcriptomics of a complex of four European pine species.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Genome-wide association study reveals genomic regions associated withFrontiers in plant science · 2026Article
- Adaptive Potential and Genomic Vulnerability of Keystone Forest Tree Species to Climate Change: A Case Study in Scots Pine.Evolutionary applications · 2025Article
- Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).Molecular ecology · 2025Article
- Molecular signatures of adaptive introgression and selection in contact zones of closely related pine species (Pinus genus).BMC plant biology · 2025Article
- Article
- Early-Stage Infection-SpecificInternational journal of molecular sciences · 2024Article
- Roast: a tool for reference-free optimization of supertranscriptome assemblies.BMC bioinformatics · 2024Article
- Full-Length Transcriptome Sequencing-Based Analysis ofInsects · 2022Article
- Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.The Plant journal : for cell and molecular biology · 2022Article
- Identifying and testing marker-trait associations for growth and phenology in three pine species: Implications for genomic prediction.Evolutionary applications · 2022Article
- Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches.Plant molecular biology · 2021Article
- Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa.International journal of molecular sciences · 2021Article
- Transcript Dynamics in Wounded and Inoculated Scots Pine.International journal of molecular sciences · 2021Article
- Article
- 275 years of forestry meets genomics inEvolutionary applications · 2020Review
- Utilization of Tissue Ploidy Level Variation inG3 (Bethesda, Md.) · 2019Article
- Early phenology and growth trait variation in closely related European pine species.Ecology and evolution · 2018Article
- Chemical characterization and identification of Pinaceae pollen by infrared microspectroscopy.Planta · 2018Article
- Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping.BMC genomics · 2016Article
Corrections and comments
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4 authors.
Funding
Abstract
backgroundPinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology.
resultsDe novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes.
conclusionsThe study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes.
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