De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses

Olsson S., Pinosio S., González-Martínez S.C., Abascal F., Mayol M., Grivet D., Vendramin G.G. (2018) De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses. Plant Molecular Biology. 97: 337-345.
Link
Doi: 10.1007/s11103-018-0742-9

Abstract:

Key message: We provide novel genomic resources for Taxus baccata in the form of a reference transcriptome, SSR and SNP markers, and orthologous single-copy genes, useful for phylogenomic and population genomic applications. Abstract: English yew (T. baccata) is the only European representative of the Taxaceae family, a conifer group originated in the Jurassic period. The wide extent of environmental heterogeneity within the species’ range, together with its long presence in Europe, make English yew an ideal species to investigate adaptive evolution in conifers. To enlarge the genomic resources available for this species, we used Illumina short read sequencing followed by de novo assembly to build the transcriptome of English yew. In addition to a fully annotated transcriptome as well as large sets of new potential SSR and SNP markers for T. baccata, we provide a data set of orthologous single-copy genes across three Taxus species using Picea sitchensis as outgroup, and discuss ortholog uses and limitations for phylogenomic and population genomic applications. © 2018, Springer Science+Business Media B.V., part of Springer Nature.

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Adapting through glacial cycles: Insights from a long-lived tree (Taxus baccata)

Mayol M., Riba M., Gonzalez-Martinez S.C., Bagnoli F., de Beaulieu J.-L., Berganzo E., Burgarella C., Dubreuil M., Krajmerova D., Paule L., Romsakova I., Vettori C., Vincenot L., Vendramin G.G. (2015) Adapting through glacial cycles: Insights from a long-lived tree (Taxus baccata). New Phytologist. : 0-0.
Link
Doi: 10.1111/nph.13496

Abstract:

Despite the large body of research devoted to understanding the role of Quaternary glacial cycles in the genetic divergence of European trees, the differential contribution of geographic isolation and/or environmental adaptation in creating population genetic divergence remains unexplored. In this study, we used a long-lived tree (Taxus baccata) as a model species to investigate the impact of Quaternary climatic changes on genetic diversity via neutral (isolation-by-distance) and selective (isolation-by-adaptation) processes. We applied approximate Bayesian computation to genetic data to infer its demographic history, and combined this information with past and present climatic data to assess the role of environment and geography in the observed patterns of genetic structure. We found evidence that yew colonized Europe from the East, and that European samples diverged into two groups (Western, Eastern) at the beginning of the Quaternary glaciations, c. 2.2 Myr before present. Apart from the expected effects of geographical isolation during glacials, we discovered a significant role of environmental adaptation during interglacials at the origin of genetic divergence between both groups. This process may be common in other organisms, providing new research lines to explore the effect of Quaternary climatic factors on present-day patterns of genetic diversity. © 2015 New Phytologist Trust.

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Recent population decline and selection shape diversity of taxol-related genes

Burgarella C., NavascuÉs M., Zabal-Aguirre M., Berganzo E., Riba M., Mayol M., Vendramin G.G., González-MartÍnez S.C. (2012) Recent population decline and selection shape diversity of taxol-related genes. Molecular Ecology. 21: 3006-3021.
Link
Doi: 10.1111/j.1365-294X.2012.05532.x

Abstract:

Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane-related genes are unknown. We examined variation at five main genes of Taxus baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site frequency spectrum (SFS) and Zeng's compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT and balancing selection for DBAT. In addition, neutrality tests based on SFS found that while a recent reduction in population size may explain most statistics' values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defence-related genes. Such natural selection processes may have produced taxane variants still undiscovered. © 2012 Blackwell Publishing Ltd.

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Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

Mayol M, Palau C, Rosselló JA, González-Martínez SC, Molins A, Riba M (2012) Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands. Annals of Botany 109: 429-441.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: Insights on evolutionary processes leading to diversification in continental islands

Mayol M., Palau C., Rosselló J.A., González-Marítnez S.C., Molins A., Riba M. (2012) Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: Insights on evolutionary processes leading to diversification in continental islands. Annals of Botany. 109: 429-441.
Link
Doi: 10.1093/aob/mcr298

Abstract:

Background and Aims Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Methods Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Key Results Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Conclusions Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands. © 2011 The Author.

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Recent population decline and selection shape diversity of taxol-related genes.

Burgarella C, Navascués M, Zabal-Aguirre M, Berganzo E, Riba M, Mayol M, Vendramin GG, González-Martínez SC (2012) Recent population decline and selection shape diversity of taxol-related genes. Molecular Ecology 21: 3006-3021.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

Mayol M, Palau C, Rosselló JA, González-Martínez SC, Molins A, Riba M (2011) Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands. Annals of Botany doi: 10.1093/aob/mcr298.

Molecular phylogeography of Thymus herba-barona (Lamiaceae): Insight into the evolutionary history of the flora of the western Mediterranean islands.

Molins A, Bacchetta G, Rosato M, Rosselló JA, Mayol M (2011) Molecular phylogeography of Thymus herba-barona (Lamiaceae): Insight into the evolutionary history of the flora of the western Mediterranean islands. Taxon 60: 1295-1305.

Variabilidad genética de Taxus baccata en el Mediterráneo occidental: el papel de los procesos históricos y de la fragmentación del paisaje. En: A. Caritat (ed.), II Jornades sobre el teix a la Mediterrània occidental.

Mayol M, Dubreuil M, González-Martínez SC, Sebastiani F, Vendramin GG, Riba M (2011) Variabilidad genética de Taxus baccata en el Mediterráneo occidental: el papel de los procesos históricos y de la fragmentación del paisaje. En: A. Caritat (ed.), II Jornades sobre el teix a la Mediterrània occidental. Documents de la delegació de la Garrotxa de la Institució Catalana d’Història Natural, 1, Olot, pp. 103-106. ISBN: 978-84-9965-053-1.

Aspectos genéticos y demográficos de Taxus baccata en la Red de Parques Nacionales. En: L. Ramírez y B. Asensio (eds.), Proyectos de Investigación en Parques Nacionales 2007-2010.

Burgarella C, Berganzo E, Zabal-Aguirre M, Prada A, Iglesias S, Riba M, Mayol M, Vendramin GG, González-Martínez SC (2011) Aspectos genéticos y demográficos de Taxus baccata en la Red de Parques Nacionales. En: L. Ramírez y B. Asensio (eds.), Proyectos de Investigación en Parques Nacionales 2007-2010. Organismo Autónomo de Parques Nacionales, pp. 125-137. ISBN: 978-84-8014-805-4.

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