| 1. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 2. |
- Clement, Yves, et al.
(författare)
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Evolutionary forces affecting synonymous variations in plant genomes
- 2017
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Ingår i: PLOS Genetics. - : PUBLIC LIBRARY SCIENCE. - 1553-7390 .- 1553-7404. ; 13:5
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Tidskriftsartikel (refereegranskat)abstract
- Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.
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| 3. |
- Manzi, Olivier Jean Leonce, 1993, et al.
(författare)
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Drought stress recovery of hydraulic and photochemical processes in Neotropical tree saplings
- 2022
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Ingår i: Tree physiology. - : Oxford University Press (OUP). - 1758-4469. ; 42:1, s. 114-129
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Tidskriftsartikel (refereegranskat)abstract
- Climate models predict an increase in the severity and the frequency of droughts. Tropical forests are among the ecosystems that could be highly impacted by these droughts. Here, we explore how hydraulic and photochemical processes respond to drought stress and re-watering. We conducted a pot experiment on saplings of five tree species. Before the onset of drought, we measured a set of hydraulic traits, including minimum leaf conductance, leaf embolism resistance, and turgor loss point. During drought stress, we monitored traits linked to leaf hydraulic functioning (leaf water potential (ψmd) and stomatal conductance (gs)) and traits linked to leaf photochemical functioning (maximum quantum yield of photosystem II (Fv/Fm) and maximum electron transport rate (ETRmax)) at different wilting stages. After re-watering the same traits were measured after 3, 7, and 14days. Hydraulic trait values decreased faster than photochemical trait values. After re-watering, the values of the four traits recovered at different rates. Fv/Fm recovered very fast close to their initial values only three days after re-watering. This was followed by ETRmax, Ψmd and gs. Finally, we show that species with large stomatal and leaf safety margin and low πtlp are not strongly impacted by drought whereas they have a low recovery on photochemical efficiency. These results demonstrate that πtlp, stomatal and leaf safety margin are a good indicators of plant responses to drought stress and also to recovery for photochemical efficiency.
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| 4. |
- Plomion, Christophe, et al.
(författare)
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Oak genome reveals facets of long lifespan
- 2018
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Ingår i: NATURE PLANTS. - : Springer Science and Business Media LLC. - 2055-026X .- 2055-0278. ; 4:7, s. 440-452
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Tidskriftsartikel (refereegranskat)abstract
- Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes' but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times(2). With 450 species spread throughout Asia, Europe and America(3), oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical(4) and modelling(5) approaches have shown that intra-organismal genetic heterogeneity can be selected for(6) and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes(7). However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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| 5. |
- Saleh, Dounia, et al.
(författare)
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Genome-wide evolutionary response of European oaks during the Anthropocene
- 2022
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Ingår i: Evolution Letters. - : John Wiley & Sons. - 2056-3744. ; 6:1, s. 4-20
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Tidskriftsartikel (refereegranskat)abstract
- The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of parallel linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods of the Anthropocene. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last 300 years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. They provide support for adaptive evolution of long-lived species during recent climatic changes. Although we acknowledge that other sources (e.g., gene flow, generation overlap) may have contributed to temporal covariances of allelic frequency changes, the consistent and correlated response across the three forests lends support to the existence of a systematic driving force such as natural selection.
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