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Transcriptome assembly and polymorphism detection in Silene ciliata (Caryophyllaceae)

Published online by Cambridge University Press:  30 April 2019

Sandra Sacristán-Bajo ,
Alfredo García-Fernández ,
Jose M. Iriondo  and
Carlos Lara-Romero Open the ORCID record for Carlos Lara-Romero [Opens in a new window]
Sandra Sacristán-Bajo
Affiliation:
Biodiversity and Conservation Area, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, Madrid, Spain
Alfredo García-Fernández
Affiliation:
Biodiversity and Conservation Area, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, Madrid, Spain
Jose M. Iriondo
Affiliation:
Biodiversity and Conservation Area, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, Madrid, Spain
Carlos Lara-Romero*
Affiliation:
Biodiversity and Conservation Area, Superior School of Experimental Science and Technology (ESCET), Rey Juan Carlos University, Madrid, Spain Global Change Research Group, Mediterranean Institute of Advanced Studies (CSIC–IUB), Esporles, Mallorca, Spain
*
*Corresponding author. E-mail: carlos.lara.romero@gmail.com
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Abstract

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.

Keywords

adaptationalpine plantsfunctional annotationSNPs
Type
Short Communication
Information
Plant Genetic Resources , Volume 17 , Issue 5 , October 2019 , pp. 452 - 455
Copyright
Copyright © NIAB 2019 

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