This file contains recombination rates values according to two estimations: Fiston-Lavier et al. ... more This file contains recombination rates values according to two estimations: Fiston-Lavier et al. 2010 and Comeron et al. 2012 for D. melanogaster genome release 6.
VCF file generated for searching selection signatures on TEs in 46 D. melanogaster genomes (the 3... more VCF file generated for searching selection signatures on TEs in 46 D. melanogaster genomes (the 32 sequenced in this work + the 14 genomes sequenced by Chakraborty et al. 2019. SNPs were called using the GATK (v4.0) (McKenna et al. 2010) HaplotypeCaller best practices for variant discovery (Van der Auwera et al. 2013) and the haplotype phasing was performed using SHAPEIT4 (Delaneau et al. 2019).
ABSTRACTBackgroundClimate change is one of the main factors shaping the distribution and biodiver... more ABSTRACTBackgroundClimate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Integrating transcriptomics and physiology is key to advancing our knowledge on how species cope with desiccation stress, and these studies are still best accomplished in model organisms.ResultsHere, we characterized the natural variation of European D. melanogaster populations across climate zones and found that strains from arid regions were similar or more tolerant to desiccation compared with strains from temperate regions. Tolerant and sensitive strains differed not only in their transcriptomic response to stress but also in their basal expression levels. We further showed that gene expression change...
Sequencing statistics for all the strains analyzed in this work, and expression values for all di... more Sequencing statistics for all the strains analyzed in this work, and expression values for all differentially expressed genes in each strain. Genes previously reported as oxidative stress responsive genes are also listed.
Differentially expressed TE families and their distribution regarding nearby differentially expre... more Differentially expressed TE families and their distribution regarding nearby differentially expressed genes. The analysis of differentially expressed TE families in response to DDT is also given.
Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby ge... more Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby genes in the strains analyzed in this work. The expression level of the genes nearby candidate TEs are also given.
Venn diagrams showing the overlap of differentially expressed genes among strains for all genes, ... more Venn diagrams showing the overlap of differentially expressed genes among strains for all genes, and for up-regulated and down-regulated genes separately.
Significant gene ontology clusters according to DAVID functional annotation tool for pairs of str... more Significant gene ontology clusters according to DAVID functional annotation tool for pairs of strains and for individual strains
<i>Cytohubba</i> results for individual strains, and list of the unique hubs genes fo... more <i>Cytohubba</i> results for individual strains, and list of the unique hubs genes found across strains including those located nearby a TE
ABSTRACTIncreases in industrialization and anthropogenic activity have resulted in an increase of... more ABSTRACTIncreases in industrialization and anthropogenic activity have resulted in an increase of pollutants released into the environment. Of these pollutants, heavy metals such as copper are particularly concerning due to their bio-accumulative nature. Due to its highly heterogeneous distribution and its dual nature as an essential micronutrient and toxic element, the genetic basis of copper tolerance is likely shaped by a complex interplay of genetic and environmental factors.In this study, we utilized the natural variation present in multiple populations of Drosophila melanogaster collected across Europe to screen for variation in copper tolerance. We found that latitude and the degree of urbanization at the collection sites, rather than any other combination of environmental factors, were linked to copper tolerance. While previously identified copper-related genes were not differentially expressed in tolerant vs. sensitive strains, genes involved in metabolism, reproduction, an...
ABSTRACTSignatures of spatially varying selection have been investigated both at the genomic and ... more ABSTRACTSignatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. InDrosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, populations in these two continents showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection is challenging when analyzing these populations. European populations could be a suitable system to identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden), and Castellana Grotte, (Southern Italy). We found low levels of population structure and no evi...
Mapping genotype to phenotype is challenging because of the difficulties in identifying both the ... more 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 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 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations ofDrosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. In...
In the present study, we investigated the induced systemic resistance (ISR) activated by the bene... more In the present study, we investigated the induced systemic resistance (ISR) activated by the beneficial fungus Trichoderma atroviride in maize plants, and the early immunological responses triggered after challenge with the ear rot pathogen Fusarium verticillioides. By transcriptional analysis, we were able to identify the gene core set specifically modulated in silks of maize plants expressing ISR. Our results showed that the main transcriptional reprogramming falls into genes involved in five main functional categories: cell structure or cell wall, amino acid and protein metabolism, stress responses, signaling, and transport. Among these ISR-related genes, it is important to highlight novel findings regarding hormone metabolism and signaling. The expression of hormone-dependent genes was in good agreement with the abscisic acid, jasmonic acid, and salicylic acid (SA) levels detected in the plants under study. The experimental design allowed the identification of novel regulatory e...
Signatures of spatially varying selection have been investigated both at the genomic and transcri... more Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no ev...
Identifying the genomic basis of adaptive evolution is a growing field of research. The number of... more Identifying the genomic basis of adaptive evolution is a growing field of research. The number of statistics and methodologies aimed at identifying adaptive loci continues to increase. Moreover, the availability of whole‐genome sequences allows us to make inferences of selection on a diverse set of species. However, detecting footprints of selection has mostly been restricted to one type of genomic variation: single‐nucleotide polymorphisms (SNPs). Other genomic variants such as transposable element (TE) insertions that are likely to contribute to adaptive evolution have been largely ignored. Here, we present an overview of different approaches that can be used to infer selection acting on TE insertions. We focused on five main approaches: (i) DNA sequence conservation analysis; (ii) selection on linked polymorphisms; (iii) environmental association analyses; (iv) estimation of allele age; and (v) functional assays to identify the molecular and fitness effects. For each of these five approaches, we focus on the latest developments and illustrate them with recent examples from the literature. We also identify the data requirements and the limitations associated with the different methodologies. We conclude that the availability of third‐generation sequencing technologies should allow for a systematic analysis of TE insertions as sources of adaptive mutations. Incorporating the knowledge of the role of TE insertions in adaptive evolution will allow us to get a more complete picture of the adaptive process.
Molecular plant-microbe interactions : MPMI, Jan 11, 2015
Plant pathogens have the capacity to manipulate the host immune system through the secretion of e... more Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host's nucleus as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems and roots. Genetic, molecular and biochemical studies confirmed that this effector targets the host's nucleus, and defines a novel class of dsDNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process with evidence for episodes of positive selection. We detected CgEP1 homologs in sever...
This file contains recombination rates values according to two estimations: Fiston-Lavier et al. ... more This file contains recombination rates values according to two estimations: Fiston-Lavier et al. 2010 and Comeron et al. 2012 for D. melanogaster genome release 6.
VCF file generated for searching selection signatures on TEs in 46 D. melanogaster genomes (the 3... more VCF file generated for searching selection signatures on TEs in 46 D. melanogaster genomes (the 32 sequenced in this work + the 14 genomes sequenced by Chakraborty et al. 2019. SNPs were called using the GATK (v4.0) (McKenna et al. 2010) HaplotypeCaller best practices for variant discovery (Van der Auwera et al. 2013) and the haplotype phasing was performed using SHAPEIT4 (Delaneau et al. 2019).
ABSTRACTBackgroundClimate change is one of the main factors shaping the distribution and biodiver... more ABSTRACTBackgroundClimate change is one of the main factors shaping the distribution and biodiversity of organisms, among others by greatly altering water availability, thus exposing species and ecosystems to harsh desiccation conditions. Insects are especially threatened by these challenging dry environments, because of their small size and thus large surface area to volume ratio. Integrating transcriptomics and physiology is key to advancing our knowledge on how species cope with desiccation stress, and these studies are still best accomplished in model organisms.ResultsHere, we characterized the natural variation of European D. melanogaster populations across climate zones and found that strains from arid regions were similar or more tolerant to desiccation compared with strains from temperate regions. Tolerant and sensitive strains differed not only in their transcriptomic response to stress but also in their basal expression levels. We further showed that gene expression change...
Sequencing statistics for all the strains analyzed in this work, and expression values for all di... more Sequencing statistics for all the strains analyzed in this work, and expression values for all differentially expressed genes in each strain. Genes previously reported as oxidative stress responsive genes are also listed.
Differentially expressed TE families and their distribution regarding nearby differentially expre... more Differentially expressed TE families and their distribution regarding nearby differentially expressed genes. The analysis of differentially expressed TE families in response to DDT is also given.
Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby ge... more Presence/absence of the reference TE insertions and distribution of these TEs regarding nearby genes in the strains analyzed in this work. The expression level of the genes nearby candidate TEs are also given.
Venn diagrams showing the overlap of differentially expressed genes among strains for all genes, ... more Venn diagrams showing the overlap of differentially expressed genes among strains for all genes, and for up-regulated and down-regulated genes separately.
Significant gene ontology clusters according to DAVID functional annotation tool for pairs of str... more Significant gene ontology clusters according to DAVID functional annotation tool for pairs of strains and for individual strains
<i>Cytohubba</i> results for individual strains, and list of the unique hubs genes fo... more <i>Cytohubba</i> results for individual strains, and list of the unique hubs genes found across strains including those located nearby a TE
ABSTRACTIncreases in industrialization and anthropogenic activity have resulted in an increase of... more ABSTRACTIncreases in industrialization and anthropogenic activity have resulted in an increase of pollutants released into the environment. Of these pollutants, heavy metals such as copper are particularly concerning due to their bio-accumulative nature. Due to its highly heterogeneous distribution and its dual nature as an essential micronutrient and toxic element, the genetic basis of copper tolerance is likely shaped by a complex interplay of genetic and environmental factors.In this study, we utilized the natural variation present in multiple populations of Drosophila melanogaster collected across Europe to screen for variation in copper tolerance. We found that latitude and the degree of urbanization at the collection sites, rather than any other combination of environmental factors, were linked to copper tolerance. While previously identified copper-related genes were not differentially expressed in tolerant vs. sensitive strains, genes involved in metabolism, reproduction, an...
ABSTRACTSignatures of spatially varying selection have been investigated both at the genomic and ... more ABSTRACTSignatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. InDrosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, populations in these two continents showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection is challenging when analyzing these populations. European populations could be a suitable system to identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden), and Castellana Grotte, (Southern Italy). We found low levels of population structure and no evi...
Mapping genotype to phenotype is challenging because of the difficulties in identifying both the ... more 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 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 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations ofDrosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. In...
In the present study, we investigated the induced systemic resistance (ISR) activated by the bene... more In the present study, we investigated the induced systemic resistance (ISR) activated by the beneficial fungus Trichoderma atroviride in maize plants, and the early immunological responses triggered after challenge with the ear rot pathogen Fusarium verticillioides. By transcriptional analysis, we were able to identify the gene core set specifically modulated in silks of maize plants expressing ISR. Our results showed that the main transcriptional reprogramming falls into genes involved in five main functional categories: cell structure or cell wall, amino acid and protein metabolism, stress responses, signaling, and transport. Among these ISR-related genes, it is important to highlight novel findings regarding hormone metabolism and signaling. The expression of hormone-dependent genes was in good agreement with the abscisic acid, jasmonic acid, and salicylic acid (SA) levels detected in the plants under study. The experimental design allowed the identification of novel regulatory e...
Signatures of spatially varying selection have been investigated both at the genomic and transcri... more Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no ev...
Identifying the genomic basis of adaptive evolution is a growing field of research. The number of... more Identifying the genomic basis of adaptive evolution is a growing field of research. The number of statistics and methodologies aimed at identifying adaptive loci continues to increase. Moreover, the availability of whole‐genome sequences allows us to make inferences of selection on a diverse set of species. However, detecting footprints of selection has mostly been restricted to one type of genomic variation: single‐nucleotide polymorphisms (SNPs). Other genomic variants such as transposable element (TE) insertions that are likely to contribute to adaptive evolution have been largely ignored. Here, we present an overview of different approaches that can be used to infer selection acting on TE insertions. We focused on five main approaches: (i) DNA sequence conservation analysis; (ii) selection on linked polymorphisms; (iii) environmental association analyses; (iv) estimation of allele age; and (v) functional assays to identify the molecular and fitness effects. For each of these five approaches, we focus on the latest developments and illustrate them with recent examples from the literature. We also identify the data requirements and the limitations associated with the different methodologies. We conclude that the availability of third‐generation sequencing technologies should allow for a systematic analysis of TE insertions as sources of adaptive mutations. Incorporating the knowledge of the role of TE insertions in adaptive evolution will allow us to get a more complete picture of the adaptive process.
Molecular plant-microbe interactions : MPMI, Jan 11, 2015
Plant pathogens have the capacity to manipulate the host immune system through the secretion of e... more Plant pathogens have the capacity to manipulate the host immune system through the secretion of effectors. We identified 27 putative effector proteins encoded in the genome of the maize anthracnose pathogen Colletotrichum graminicola that are likely to target the host's nucleus as they simultaneously contain sequence signatures for secretion and nuclear localization. We functionally characterized one protein identified as CgEP1. This protein is synthesized during the early stages of disease development and is necessary for anthracnose development in maize leaves, stems and roots. Genetic, molecular and biochemical studies confirmed that this effector targets the host's nucleus, and defines a novel class of dsDNA-binding protein. We show that CgEP1 arose from a gene duplication in an ancestor of a lineage of monocot-infecting Colletotrichum spp. and has undergone an intense evolution process with evidence for episodes of positive selection. We detected CgEP1 homologs in sever...
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Papers by Gabriel Rech