Publication details.

Paper

Year:2019
Author(s):S. Sacristán-Bajo, A. García-Fernández, J. Iriondo, C. Lara-Romero
Title:Transcriptome assembly and polymorphism detection in Silene ciliata (Caryophyllaceae)
Journal:Plant Genetic Resources-Characterization and Utilization
ISSN:1479-2621
JCR Impact Factor:0.869
Volume:17
Issue No.:5
Pages:452-455
D.O.I.:10.1017/S1479262119000157
Web:https://dx.doi.org/10.1017/S1479262119000157
Abstract:Copyright © 2019 NIAB.Silene ciliata (Caryophyllaceae) is a key species to test evolutionary hypotheses in a global warming context. The recent advances in Next Generation Sequencing technologies can help in providing clues about climate-mediated local adaptation. In the present study, we analysed the full transcriptome of six individuals of S. ciliata from Central Spain, by aligning it with the transcriptome of S. latifolia. We aimed (a) to identify Single Nucleotide Polymorphisms (SNPs) in the transcriptome of the species, (b) to describe the biological function of the polymorphic genes expressed and (c) to identify loci that may be involved in local adaptation processes at optimal and marginal populations of the species. We identified a total of 147,118 SNPs distributed throughout 12,688 sequences. The number of polymorphic sequences annotated was 8023. One hundred thirty sequences containing polymorphisms strongly associated with optimal and marginal conditions were selected. Gene ontology searches were successful for 118, and many of these were related to responses to stress (n = 19) and abiotic stimulus (n = 16). Genomic data generated provide a starting point for further research on the identification of candidate genes related to local adaptation and other processes in the species.

Related departments

  • Oceanography and Global Change
  • Related research groups

  • Global Change Research