Maria Bogaerts Marquez

Maria Bogaerts Marquez
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Centre de Biologie pour la Gestion des Populations (CBGP)

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37
Publications
2,133
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162
Citations
Citations since 2016
37 Research Items
162 Citations
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20162017201820192020202120220102030405060
20162017201820192020202120220102030405060
20162017201820192020202120220102030405060

Publications

Publications (37)
Article
Full-text available
Using a combination of biochemical, transcriptomic, and physiological analyses, we elucidated the mechanisms of physical and chemical withering of tea shoots subjected to UV-C and ethylene treatments. UV-C irradiation (15 kJ m–2) initiated oxidation of catechins into theaflavins, increasing theaflavin-3-monogallate and theaflavin digallate by 5- an...
Article
Full-text available
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipeli...
Article
Full-text available
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipeline...
Preprint
Full-text available
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic...
Article
Full-text available
While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded w...
Article
Full-text available
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations cost...
Article
Full-text available
Motivation: Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. Accurate genotyping of TEs in genomes is therefore crucial for a complete identification of the genetic differences among indivi...
Article
Full-text available
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transp...
Data
Histogram showing the number of TEs (y axis) and the number of samples for which we were able to estimate its frequency. (PDF)
Data
19 TEs showing significant correlation with the expression of nearby genes. Results are divided in correlations obtained with male and female expression data (Huang et al. 2015). beta: Effect size estimate, t-stat: Test statistic (t-statistic of T-test), p-value: p-value for the linear regression. FDR: False discovery rate estimated with Benjamini–...
Data
Genomic location of different TE categories. Percentages and rigth-tail p-values are showed when the Chi-square test is significant. (A) Localization of TEs regarding the nearest gene across categories. (B) Localization of intragenic TEs across TE categories. (XLSX)
Data
Enrichment test for TE families. For each family, table shows the number of TEs at each category. HighFreq TEs correspond to the sum of AF, AF-NA, AF-OOA and OOA. p-value (Bonf.) indicates Bonferroni corrected p-values for Chi-square test when comparing HighFreq, AF-OOA and OOA TEs against All TEs. In red p-values < 0.05. (XLSX)
Data
Boxplots showing the distribution of TE ratio percentages (percentage of the length of the TE insertion regarding the length of the canonical family sequence) for each TE category and colored by Age (A) and TE class (B). (PDF)
Data
Correlation between frequencies estimated with data obtained using different sequencing strategies in the Stockholm (Sweden) population. Frequencies calculated using individual strain sequencing (x) (Mateo et al 2018) and pool sequencing (y). Pearson correlation coefficient r = 0.98, p-value < 2.2e-16. (PDF)
Data
Number of TEs showing significant values in the selection tests for each HighFreq category. For each sweep test (iHS, H12 and nSL), “Continent” column indicates population used for the analysis: NA: North America or EU: Europe. For each HighFreq category, table shows the number of significant TEs / number of TEs for which the test was calculated. “...
Data
List of 36 TEs showing at least one significant (highlighted in red) selective sweep test (iHS, H12 or nSL). (XLSX)
Data
List of the 254 HighFreq TEs with at least one pairwise FST calculation performed. Category indicates the classification of the TE according to Fig 2. For each continent, two pairwise comparisons were performed. Values for each comparison are the FST (in red the significant ones). Concordant FST indicates whether TEs with significant FST were at hi...
Data
Summary results for Fixed TEs showing significant Tajima´s D values on neighbour windows. Significance was dermined by the 5% quantile of Tajima´s D values from all high recombination regions in the genome (-1.65 for Autosomes and -1.82 for chromosome X). (XLSX)
Data
Enrichment of genes previously described as associated with different stress-related and behaviour-related traits in the different datasets analyzed. A) Genes the 65 TEs with evidence of selection. B) Genes nearby the 300 HighFreq TEs. C) Genes nearby the 174 OOA TEs. D) Genes nearby the 111 AF-OOA TEs. (XLSX)
Data
Genomic coordinates of cosmopolitan inversion (Kapun et al. 2016) analyzed in order to determine its influence on the transposable elements frequency calculation. (XLSX)
Data
Summary statistics for the pairwise FST calculations. TEs with FST: Number of TEs for which it was possible to calculate FST. Signif. (Africa H/L): Total number of significant TEs. Between brackets: H: Number of significant TEs identified using the distribution of neutral SNPs that are at high frequency in Africa. L: Number of significant TEs ident...
Data
Venn diagrams for the 36 HighFreq TEs with significant evidence of selective sweeps. A) Overlapping between TEs showing significant results for the different selective sweeps statistics (iHS, H12 and nSL). B) Overlapping between TEs showing at least one significant test in the North American (NA) and/or the European (EU) population. The percentage...
Data
Functional enrichment analysis of genes nearby OOA and AF-OOA TEs. A) Significant Gene Ontology Clusters according to DAVID functional annotation tool. Only the top six significant clusters are showed (enrichment score > 1.3). The horizontal axis represents DAVID enrichment score (see S9C and S9D Table for details). B) Significantly overrepresented...
Data
Distribution of the number of TEs (y axis) by the number of strains for which T-lex2 estimated frequencies in the 8 individually-sequenced populations. (PDF)
Data
Distribution of mapped reads for the presence module (red), absence module (green) and total number of reads (blue) for each one of the 48 DrosEU samples (Kapun et al. 2018). (PDF)
Data
Information for the 91 samples used in this study. (XLSX)
Data
TE classes across different TE categories. P-values and percentages are showed in bold when significant enrichment according to Chi-square test p-value < 0.05 when comparing with All TEs. (XLSX)
Data
Distribution of number of TEs that are present at >0.10 and < 0.95 frequency by number of populations in which they are present at that frequency. We considered TEs to be present at high frequency (HighFreq) when they fulfil the frequency condition in at least three samples (represented by blue bars in the figure). (PDF)
Data
Comparison of age estimations obtained by Bergman and Bensasson (2007) and the estimations obtained in this work. Only the 417 TEs that are common between the two studies are plotted. A) TE age distribution of the 417 TEs based on Bergman and Bensasson (2007) and in this work. Note that there are 10 insertions that showed extreme age values in our...
Data
Venn diagrams showing the overlap between TEs showing significant FST values in at least one pair of populations. A) TEs present at high frequency in populations located at low latitude locations. B) TEs present at high frequency in populations located at high latitude locations. (PDF)
Data
TE frequencies estimated using all strains (x axis) vs frequencies estimated after removing strains that contain inversions (y axis) for different individually-sequenced populations. A) Zambia (Lack et al., 2015), B) France (Pool et al., 2012), C) DGRP (Raleigh) (Huang et al. 2014; Mackay et al. 2012), D) Italy (Bari) and E) Sweden (Stockholm) (Mat...
Data
Distribution of iHS values obtained for TEs (red) and neutral SNPs (cyan) in the North American population (DGRP, Raleigh, North Carolina). A) Distribution of iHS values for all TEs and neutral SNPs. B) Distribution of iHS values for TEs and neutral SNPs at high frequency (> 0.10) in the OOA population (Raleigh) and in the African population (Zambi...
Data
Frequency estimations using Tlex2 for the 1,615 TEs at each of the 91 samples. NA indicates that the frequency could not be estimated for that TE in the given sample. Recombination estimates according to Comeron et al. (2012) and Fiston-Lavier et al. (2010) are showed for each TE. Class column indicates the category at which each TE was classified....
Data
TE length ratio statistics. At the top, mean and median TE Length Ratio (%) for each TE category. At the bottom, results for the Wilcoxon rank sum test and Kruskal Wallis test among different TE categories. The results are shown for All TEs (A), for onlt young TEs (B), for only old TEs (C), for only TEs of the class DNA (D), for only TEs of the cla...
Data
A Results of gene ontology (GO) enrichment test for the 83 genes nearby the 65 TEs showing evidence of selection (ES). B Table. Results of gene ontology (GO) enrichment test for the 363 genes nearby the 300 HigFreq TEs. C Table: Results of gene ontology (GO) enrichment test for the 215 genes nearby the 174 OOA TEs. D Table. Results of gene ontology...
Data
Gene association studies analyzing different fitness-related phenotypes. (XLSX)
Preprint
Full-text available
Mapping genotype to phenotype is challenging because of the difficulties in identifying both the traits under selection and the specific genetic variants underlying these traits. Most of the current knowledge of the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence fo...

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