Genome-wide variation in recombination rate in Eucalyptus

Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside of a few model taxa, particularly in forest trees. Eucalypts are forest trees of global economic importance, and dominate many Australian ecosystems. We studied recombination rate in Eucalyptus globulus using genetic linkage maps constructed in 10 unrelated individuals, and markers anchored to the Eucalyptus reference genome. This experimental design provided the replication to study whether recombination rate varied between individuals and chromosomes, and allowed us to study the genomic attributes and population genetic parameters correlated with this variation. Results Recombination rate varied significantly between individuals (range = 2.71 to 3.51 centimorgans/megabase [cM/Mb]), but was not significantly influenced by sex or cross type (F1 vs. F2). Significant differences in recombination rate between chromosomes were also evident (range = 1.98 to 3.81 cM/Mb), beyond those which were due to variation in chromosome size. Variation in chromosomal recombination rate was significantly correlated with gene density (r = 0.94), GC content (r = 0.90), and the number of tandem duplicated genes (r = −0.72) per chromosome. Notably, chromosome level recombination rate was also negatively correlated with the average genetic diversity across six species from an independent set of samples (r = −0.75). Conclusions The correlations with genomic attributes are consistent with findings in other taxa, however, the direction of the correlation between diversity and recombination rate is opposite to that commonly observed. We argue this is likely to reflect the interaction of selection and specific genome architecture of Eucalyptus. Interestingly, the differences amongst chromosomes in recombination rates appear stable across Eucalyptus species. Together with the strong correlations between recombination rate and features of the Eucalyptus reference genome, we maintain these findings provide further evidence for a broad conservation of genome architecture across the globally significant lineages of Eucalyptus. (Résumé d'auteur

International Geomagnetic Reference Field: the 12th generation

The 12th generation of the International Geomagnetic Reference Field (IGRF) was adopted in December 2014 by the Working Group V-MOD appointed by the International Association of Geomagnetism and Aeronomy (IAGA). It updates the previous IGRF generation with a definitive main field model for epoch 2010.0, a main field model for epoch 2015.0, and a linear annual predictive secular variation model for 2015.0-2020.0. Here, we present the equations defining the IGRF model, provide the spherical harmonic coefficients, and provide maps of the magnetic declination, inclination, and total intensity for epoch 2015.0 and their predicted rates of change for 2015.0-2020.0. We also update the magnetic pole positions and discuss briefly the latest changes and possible future trends of the Earth’s magnetic fiel

Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems

Next-generation biomonitoring proposes to combine machine-learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water status to develop next-generation biomonitoring of forest ecosystems. Because phyllosphere microbial communities respond to both tree physiology and climate change, we investigated whether environmental DNA data from tree phyllosphere could be used as molecular biomarkers of tree water status in forest ecosystems. Using an amplicon sequencing approach, we analysed phyllosphere microbial communities of four tree species (Quercus ilex, Quercus robur, Pinus pinaster and Betula pendula) in a forest experiment composed of irrigated and non-irrigated plots. We used these microbial community data to train a machine-learning algorithm (Random Forest) to classify irrigated and non-irrigated trees. The Random Forest algorithm detected tree water status from phyllosphere microbial community composition with more than 90% accuracy for oak species, and more than 75% for pine and birch. Phyllosphere fungal communities were more informative than phyllosphere bacterial communities in all tree species. Seven fungal amplicon sequence variants were identified as candidates for the development of molecular biomarkers of water status in oak trees. Altogether, our results show that microbial community data from tree phyllosphere provides information on tree water status in forest ecosystems and could be included in next-generation biomonitoring programmes that would use in situ, real-time sequencing of environmental DNA to help monitor the health of European temperate forest ecosystems.</p

Early Cacao Use in the Upper Amazon of South America

The archaeological site of Santa Ana-La Florida (SALF), located in the Ecuadorian upper Amazon, is in the region of Theobroma spp. greatest genetic diversity, thus making it ideal to investigate the origins of domestication of this enigmatic tree. We present research showing that the residents of SALF were involved in the domestication of cacao, traditionally thought to have been first domesticated in Mesoamerica and/or Central America. We used three independent lines of evidence—starch grains, theobromine residues and ancient DNA—dating from approximately 5,300 years ago, to establish the earliest evidence of T. cacao use in the Americas, the first unequivocal archaeological example of its pre-Columbian use in South America and reveal the upper Amazon region as the oldest centre of cacao domestication yet identified. We suggest that new paleoethnobotanical research will expand our knowledge of this process, including the timing, locations, and uses of cacao by Indigenous South Americans

Resilience of genetic diversity in forest trees over the Quaternary

Abstract The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes.Abstract The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes

Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

<p>Abstract</p> <p>Background</p> <p>One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for <it>Quercus robur</it>, its characterization and an analysis of BAC end sequences.</p> <p>Results</p> <p>The <it>Eco</it>RI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs) were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while <it>ab initio </it>repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of <it>Arabidopsis thaliana</it>, <it>Vitis vinifera </it>and <it>Populus trichocarpa</it>. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of <it>V. vinifera.</it></p> <p>Conclusions</p> <p>This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be used in the assembly of a future genome sequence for oak.</p

Gene Expression Profiles Characterize Inflammation Stages in the Acute Lung Injury in Mice

Acute Lung Injury (ALI) carries about 50 percent mortality and is frequently associated with an infection (sepsis). Life-support treatment with mechanical ventilation rescues many patients, although superimposed infection or multiple organ failure can result in death. The outcome of a patient developing sepsis depends on two factors: the infection and the pre-existing inflammation. In this study, we described each stage of the inflammation process using a transcriptional approach and an animal model. Female C57BL6/J mice received an intravenous oleic acid injection to induce an acute lung injury (ALI). Lung expression patterns were analyzed using a 9900 cDNA mouse microarray (MUSV29K). Our gene-expression analysis revealed marked changes in the immune and inflammatory response metabolic pathways, notably lipid metabolism and transcription. The early stage (1 hour–1.5 hours) is characterized by a pro-inflammatory immune response. Later (3 hours–4 hours), the immune cells migrate into inflamed tissues through interaction with vascular endothelial cells. Finally, at late stages of lung inflammation (18 hours–24 hours), metabolism is deeply disturbed. Highly expressed pro-inflammatory cytokines activate transcription of many genes and lipid metabolism. In this study, we described a global overview of critical events occurring during lung inflammation which is essential to understand infectious pathologies such as sepsis where inflammation and infection are intertwined. Based on these data, it becomes possible to isolate the impact of a pathogen at the transcriptional level from the global gene expression modifications resulting from the infection associated with the inflammation

Resilience of genetic diversity in forest trees over the Quaternary

The effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasting European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size, Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories of Ne over time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity over time. Altogether, our results indicate that forest trees have been able to retain their evolutionary potential over very long periods of time despite strong environmental changes

Between but not within species variation in the distribution of fitness effects

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is therefore of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, i.e., whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterised the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence and genetic background. We find statistical support for there being variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and that evolutionarily recent events, such as demographic changes and local adaptation, have little impact

Etude du transcriptome du mutant de la levure dna2-1 vieillissant prématurement à l'aide d'un nouveau système permettant l'analyse comparative du puces à ADN

Cette these decrit une methode originale de comparaison automatique d'experiences de transcriptome appliquee a la determination des causes du vieillissement de l'organisme eucaryote modele: Saccharomyces cerevisiae. Les experiences de transcriptome, qui peuvent etre realisees a l'aide de microarrays, permettent au biologiste d'etudier simultanement les variations globales d'expression de milliers de genes dans de nombreuses conditions experimentales. Ces experiences a grande echelle realisees a haut-debit generent une quantite importante de donnees. En consequence, les biologistes ont besoin d'outils informatiques pour les interpreter. L'utilisation de microarrays pour l'etude des causes du vieillissement chez la levure nous a permis d'identifier les outils informatiques necessaires a l'interpretation des donnees de transcriptome. Independemment de son interet biologique, le vieillissement est un probleme particulierement bien adapte a une double approche biologique et informatique. Nous avons analyse le transcriptome des cellules de levure au cours de leur vieillissement. Deux souches ont ete etudiees: l'une d'elles est une souche sauvage et l'autre un mutant, dna2-1, vieillissant prematurement, et dont la replication de l'ADN est deficiente. Plusieurs outils existants d'analyse de donnees microarrays nous ont permis d'interpreter nos resultats. Nous avons constate un stockage d'energie associe au vieillissement: les genes impliques dans la gluconeogenese, le cycle du glyoxylate, le metabolisme lipidique, et la production de glycogene sont actives dans les vieilles cellules. Nous avons egalement observe une reponse generalisee au stress connue sous le nom ESR (Reponse Environnementale au Stress) decrite auparavant dans d'autres etudes. De plus, Nous avons observe l'induction d'un ensemble de genes qui reparent l'ADN et connus sous le nom de signature de degradation de l'ADN. Plusieurs genes ayant un role dans la production d'energie sont actives dans la souche mutante dna2-1. La reponse au vieillissement observee chez dna2-1 est similaire a celle decrite dans un mutant dont la telomerase est disfonctionnelle (TDR). Elle est constituee par un ensemble de genes dont l'expression change durant la senescence cellulaire. Ces resultats suggerent indirectement que les cellules agees repondent a une instabilite du genome. Le travail d'interpretation de ces donnees nous a permis d'identifier des besoins informatiques specifiques parmis lesquels la necessite de comparer des experiences microarray de facon automatique. Pour cette raison, nous avons developpe, dans la deuxieme partie de cette these, une methode permettant de comparer des experiences microarray de facon automatique. Cette methode originale repose sur une ontologie pour experiences microarrays associee a un modele de cout evaluant le degre de compatibilite de deux experiences. La validation de cette methode a conduit au developpement d'une plateforme de test, Malako, qui associe les outils informatiques classiques d'analyses de donnees microarray a un systeme de comparaison automatique d'experiences microarray.BORDEAUX1-BU Sciences-Talence (335222101) / SudocSudocFranceF