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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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References

Altschul, SF, Gish, W, Miller, W, Myers, EW and Lipman, DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.Google Scholar
Bairoch, A and Apweiler, R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 28: 45–48.Google Scholar
Bernasconi, G, Antonovics, J, Biere, A, Charlesworth, D, Delph, LF, Filatov, D, Giraud, T, Hood, ME, Marais, GAB, McCauley, D, Pannell, JR, Shykoff, JA, Vyskot, B, Wolfe, LM and Widmer, A (2009) Silene as a model system in ecology and evolution. Heredity 103: 5–14.Google Scholar
Bolger, AM, Lohse, M and Usadel, B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (Oxford, England) 30: 2114–2120.Google Scholar
Council Directive 92/43/EEC of 21 May 1992. On the conservation of natural habitats and of wild fauna and flora. Official Journal of the European Union 206: 7–50.Google Scholar
Danecek, P, Auton, A, Abecasis, G, Albers, CA, Banks, E, DePristo, MA, Handsaker, RE, Lunter, G, Marth, GT, Sherry, ST and McVean, G (2011) The variant call format and VCFtools. Bioinformatics (Oxford, England) 27: 2156–2158.Google Scholar
Dray, AM (1985) Plantas a proteger en Portugal continental. Serviço Nacional de Parques, Reservas e Conservaçao da Natureza, Lisboa.Google Scholar
Escudero, A, Gimenez-Benavides, L, Iriondo, JM and Rubio, A (2005) Patch dynamics and islands of fertility in a high mountain Mediterranean community. Arctic, Antarctic and Alpine Research 36: 518–527.Google Scholar
Fernández, AP, Prieto, JAC, Altuna, JG, Arregui, JL, Gutiérrez, LO, Sánchez, SP and Janices, JV (2007) Flora amenazada presente en la región eurosiberiana de la Comunidad Autónoma del País Vasco. Naturalia Cantabricae 3: 79–91.Google Scholar
García-Fernández, A, Segarra-Moragues, JG, Widmer, A, Escudero, A and Iriondo, JM (2012) Unravelling genetics at the top: mountain islands or isolated belts? Annals of Botany 110: 1221–1232.Google Scholar
García-Fernández, A, Escudero, A, Lara-Romero, C and Iriondo, JM (2015) Effects of the duration of cold stratification on early life stages of the Mediterranean alpine plant Silene ciliata. Plant Biology 17: 344–350.Google Scholar
Gayral, P, Melo-Ferreira, J, Glemin, S, Bierne, N, Carneiro, M, Nabholz, B, Lourenco, JM, Alves, PC, Ballenghien, M, Faivre, N, Belkhir, K, Cahais, V, Loire, E, Bernard, A and Galtier, N (2013) Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap. PLoS Genetics 9: e1003457.Google Scholar
Giménez-Benavides, L, Escudero, A and Iriondo, JM (2007) Local adaptation enhances seedling recruitment along an altitudinal gradient in a high mountain Mediterranean plant. Annals of Botany 99: 723–734.Google Scholar
Giménez-Benavides, L, Escudero, A, García-Camacho, R, García-Fernández, A, Iriondo, JM, Lara-Romero, C and Morente-López, J (2018) How does climate change affect regeneration of Mediterranean high-mountain plants? An integration and synthesis of current knowledge. Plant Biology 20(Suppl. 1): 50–62.Google Scholar
Kyrkou, I, Iriondo, JM and García-Fernández, A (2015) A glacial survivor of the alpine Mediterranean region: phylogenetic and phylogeographic insights into Silene ciliata Pourr. (Caryophyllaceae). PeerJ 3: e1193.Google Scholar
Lara-Romero, C, García-Fernández, A, Robledo-Arnuncio, JJ, Roumet, M, Morente- López, J, López-Gil, A and Iriondo, JM (2016) Individual spatial aggregation correlates with between-population variation in fine-scale genetic structure of Silene ciliata (Caryophyllaceae). Heredity 116: 417–423.Google Scholar
Légifrance (2019) 10 mai 1990. Relatif à la liste des espèces végétales protégées en région Auvergne complétant la liste nationale. Journal Officiel de la République Française. NOR: PRME9061196A.Google Scholar
Li, H and Durbin, R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics (Oxford, England) 26: 589–595.Google Scholar
López-Moreno, JI, Vicente-Serrano, JI and Lanjeri, S (2007) Mapping snowpack distribution over large areas using GIS and interpolation techniques. Climate Research 33: 257–270.Google Scholar
Marano, LA, Marcorin, L, Castelli, EC and Mendes-Junior, CT (2017) Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project. Genetics and Molecular Biology 40: 530–539.Google Scholar
Muller, MH, Latreille, M and Tollon, C (2011) The origin and evolution of a recent agricultural weed: population genetic diversity of weedy populations of sunflower (Helianthus annuus L.) in Spain and France. Evolutionary Applications 4: 499–514.Google Scholar
Sanz, JMH, Carreño, MÁC and Albacete, EA (2010) Conservación de flora amenazada en Castilla-La Mancha. Foresta 47: 16–28.Google Scholar
Stölting, KN, Paris, M, Meier, C, Heinze, B, Castiglione, S, Bartha, D and Lexer, C (2015) Genome-wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree. New Phytologist 207: 723–734.Google Scholar
Swarts, K, Li, H, Romero Navarro, JA, An, D, Romay, MC, Hearne, S, Acharya, C, Glaubitz, JC and Mitchell, S (2014) Novel methods to optimize genotypic imputation for low-coverage, next-generation sequence data in crop plants. The Plant Genome 7: 1–12.Google Scholar
Turner, TL, Bourne, EC, Von Wettberg, EJ, Hu, TT and Nuzhdin, SV (2010) Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics 42: 260.Google Scholar
Ye, J, Zhang, Y, Cui, H, Liu, J, Wu, Y, Cheng, Y, Xu, H, Huang, X, Li, S, Zhou, A, Zhang, X, Bolund, L, Chen, Q, Wang, J, Yang, H, Fang, L and Shi, C (2018) WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. Nucleic Acids Research 46: W71–W75.Google Scholar
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