Transcriptome assembly and polymorphism detection in Silene ciliata (Caryophyllaceae)

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.

Linking ecological niche models and common garden experiments to predict phenotypic differentiation in stressful environments: Assessing the adaptive value of marginal populations in an alpine plant

“…Although common garden experiments such as this one only can demonstrate the existence of genetically based differentiation (not adaptation per se ), the information from other studies mentioned above provides additional evidence toward the conclusion that the phenological differentiation found here likely is the result of divergent selection (Giménez‐Benavides et al, 2011; Morente‐López et al, 2019; Sacristán‐Bajo et al, 2019). Alternatively, such differentiation could result from neutral processes unrelated to selection, such as genetic drift (Garcia‐Ramos & Kirkpatrick, 1997).…”

“…The patterns of phenological differentiation found are also congruent with results obtained in subsequent experiments implemented with plants grown from seeds derived from the cuttings used in the present study (unpublished results). Moreover, a parallel transcriptomic study with the same populations identified SNPs (single nucleotide polymorphisms) with unusually high allele‐frequency differentiation between marginal and optimal environments, for candidate genes in the flower development pathway (Sacristán‐Bajo et al, 2019). In addition, the phenotypic differentiation found in this study adds to recent evidence of the adaptive potential of marginal populations at early life stages (i.e., seedlings).…”

Ecological niche models as hypothesis generators of functional genetic differentiation and potential local adaptation in a Mediterranean alpine ecosystem

“…selected for early flowering) (see also chapter 3). In this vein, a parallel transcriptomic study using material collected from the same study’s populations identified a set of candidate SNPs with unusually high allele frequency differentiation between marginal and optimal environments (Sacristán-Bajo et al, 2019). Many of these SNPs derived from candidate genes in the flower development pathway (Sacristán-Bajo et al, 2019).…”

“…In this vein, a parallel transcriptomic study using material collected from the same study’s populations identified a set of candidate SNPs with unusually high allele frequency differentiation between marginal and optimal environments (Sacristán-Bajo et al, 2019). Many of these SNPs derived from candidate genes in the flower development pathway (Sacristán-Bajo et al, 2019). Thus, these selection analysis and genomic approaches provide increased evidence that genetically-based phenological differentiation found in this study is the result of divergent selection between marginal and optimal populations.…”

Áreas marginales en ecosistemas alpinos: definición y valor evolutivo en un contexto de cambio climático

“…En este sentido, en un estudio paralelo del transcriptoma (RNA-seq) realizado con las mismas poblaciones de S. ciliata se identificó un conjunto de genes candidatos con una diferenciación en la frecuencia de alelos (Single Nucleotide Polymorphisms, en adelante SNPs) inusualmente alta entre ambientes marginales y óptimos (Sacristán-Bajo et al 2019), lo que respalda la existencia de presiones selectivas de naturaleza ambiental. Muchos de estos genes candidatos están asociados con las rutas de desarrollo de la flor y procesos de respuesta al estrés abiótico (Sacristán-Bajo et al 2019). Algunos de estos genes han sido nuevamente identificados como candidatos a encontrarse bajo selección en un estudio de secuenciación masiva de ADN aplicando métodos de detección de variantes genéticas sujetas a selección y de estructura genética (Lara-Romero, datos sin publicar).…”