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.
Enlace
Doi: 10.1007/s11103-018-0742-9

Resumen:

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.

Leer más

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.
Enlace
Doi: 10.1111/nph.13496

Resumen:

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.

Leer más

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.
Enlace
Doi: 10.1111/j.1365-294X.2012.05532.x

Resumen:

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.

Leer más

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.
Enlace
Doi: 10.1093/aob/mcr298

Resumen:

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.

Leer más

Genetic effects of chronic habitat fragmentation revisited: Strong genetic structure in a temperate tree, Taxus baccata (Taxaceae), with great dispersal capability

Dubreuil M., Riba M., González-Martínez S.C., Vendramin G.G., Sebastiani F., Mayol M. (2010) Genetic effects of chronic habitat fragmentation revisited: Strong genetic structure in a temperate tree, Taxus baccata (Taxaceae), with great dispersal capability. American Journal of Botany. 97: 303-310.
Enlace
Doi: 10.3732/ajb.0900148

Resumen:

Tree species are thought to be relatively resistant to habitat fragmentation because of their longevity and their aptitude for extensive gene flow, although recent empirical studies have reported negative genetic consequences, in particular after long-term habitat fragmentation in European temperate regions. Yet the response of each species to habitat loss may differ greatly depending on their biological attributes, in particular seed dispersal ability. In this study, we used demographic and molecular data to investigate the genetic consequences of chronic habitat fragmentation in remnant populations of Taxus baccata in the Montseny Mountains, northeast Spain. The age structure of populations revealed demographic bottlenecks and recruitment events associated with exploitation and management practices. We found a strong genetic structure, both at the landscape and within-population levels. We also detected high levels of inbreeding for a strictly outcrossing species. Chronic forest fragmentation resulting from long-term exploitation in the Montseny Mountains seems the most plausible explanation for the strong genetic structure observed. Our results support the view that, contrary to some predictions, tree species are not buffered from the adverse effects of habitat fragmentation, even in the case of species with a high dispersal potential.

Leer más

Spatial genetic structure of Taxus baccata L. in the western Mediterranean Basin: Past and present limits to gene movement over a broad geographic scale

González-Martínez S.C., Dubreuil M., Riba M., Vendramin G.G., Sebastiani F., Mayol M. (2010) Spatial genetic structure of Taxus baccata L. in the western Mediterranean Basin: Past and present limits to gene movement over a broad geographic scale. Molecular Phylogenetics and Evolution. 55: 805-815.
Enlace
Doi: 10.1016/j.ympev.2010.03.001

Resumen:

English yew (Taxus baccata L., Taxaceae), a Tertiary relict, provides a seminal example of a widespread albeit locally endangered (often close to extinction) tree species. In order to gain detailed insights into the evolutionary dynamics of the species on a broad geographical scale, over 1000 trees from 91 populations of English yew in the western Mediterranean were analyzed using seven nuclear microsatellite markers. Our results revealed contrasting patterns of genetic structure at different spatial scales: genetic variation was highly structured at the local scale, while only a low proportion of the observed variation was attributed to regional differences. We also found a geographic gradient of decreasing diversity and increasing population divergence from northwest (central Europe and northern Iberian Peninsula) to southeast (Mediterranean Iberia and North Africa). The patterns revealed in this study probably reflect the combined effects of Quaternary climatic changes and recent impact of human activities, and potentially also more ancient events dating back to the Tertiary. Both climatic and anthropogenic factors seem to have conducted to a long history of population isolation, which may have contributed significantly to enhance population divergence through restricted gene flow and genetic drift. © 2010 Elsevier Inc. All rights reserved.

Leer más

Isolation and characterization of polymorphic nuclear microsatellite loci in Taxus baccata L.

Dubreuil M., Sebastiani F., Mayol M., González-Martínez S.C., Riba M., Vendramin G.G. (2008) Isolation and characterization of polymorphic nuclear microsatellite loci in Taxus baccata L.. Conservation Genetics. 9: 1665-1668.
Enlace
Doi: 10.1007/s10592-008-9515-3

Resumen:

Seven polymorphic nuclear microsatellite markers for Taxus baccata L. (English yew) were developed using an enriched-library method. An additional polymorphic SSR was obtained by testing eight primer pairs from the congeneric species Taxus sumatrana. Mendelian inheritance for the seven Taxus baccata SSRs was proved by genotyping 17 individuals and 124 megagametophytes (conifer seed haploid tissue). A total of 96 individuals from 5 different populations (10-26 samples per population) were used to estimate genetic diversity parameters. High levels of genetic diversity, with values ranging from 0.533 to 0.929 (6-28 alleles per SSR) were found. No linkage disequilibrium between pairs of loci was detected. All loci but one showed significant departures from Hardy-Weinberg equilibrium. Excess of homozygosity was probably due to high inbreeding in English yew populations, an outcome of low effective population size and/or fragmented distribution. Highly polymorphic SSRs will be used to conduct population genetic studies at different geographical scales and to monitor gene flow. © 2008 Springer Science+Business Media B.V.

Leer más