Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

[Abstract] Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5’-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.[Author Summary] The presence of several transposable element insertions in the promoter region of a Drosophila melanogaster gene has only been described in heat shock protein genes. In this work, we have discovered and characterized in detail several naturally occurring independent transposable element insertions in the promoter region of a cold-stress response gene in the fruitfly Drosophila melanogaster. The nine transposable element insertions described are clustered in a small 368 bp region and all belong to the same family of transposable elements: the roo family. Each individual insertion is present at relatively low population frequencies, ranging from 1% to 17%. However, the majority of strains analyzed contain one of these nine roo insertions suggesting that this region might be evolving under positive selection. Although the sequence of these insertions is highly similar, their molecular and functional consequences are different. Only one of them, FBti0019985, is associated with increased viability in nonstress and in cold-stress conditions.This work was supported by the Ministerio de Economía y Competitividad (MINECO: http://www.idi.mineco.gob.es) BFU-2011-24397 and RYC-2010-07306 to JG, and BES-2012-052999 to AU, Ministerio de Economía y Competitividad and Fondo Europeo de Desarrollo Regional (MINECO/FEDER:http://www.idi.mineco.gob.es) BFU2014-57779-P, the European Commission (https://ec.europa.eu) FP7-PEOPLE-2011-CIG-293860, the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (http://agaur.gencat.cat) 2014-SGR-201 to JG, and by the Agence Nationale de la Recherche (http://www.agence-nationale-recherche.fr) ANR-14-CE02-0003 to MARdC.USD 2250 APC fee funded by the EC FP7 Post-Grant Open Access PilotPeer reviewe

Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

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 pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.We thank four reviewers and the handling editor for helpful comments on previous versions of our manuscript. We are grateful to the members of the DrosEU and DrosRTEC consortia for their long-standing support, collaboration, and for discussion. DrosEU was funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). M.K. was supported by the Austrian Science Foundation (grant no. FWF P32275); J.G. by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); T.F. by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of Münster; AOB by the National Institutes of Health (R35 GM119686); M.K. by Academy of Finland grant 322980; V.L. by Danish Natural Science Research Council (FNU) (grant no. 4002-00113B); FS Deutsche Forschungsgemeinschaft (DFG) (grant no. STA1154/4-1), Project 408908608; J.P. by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; A.U. by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) (grant no. 1737/17); M.S.V., M.S.R. and M.J. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); A.P., K.E. and M.T. by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551. The authors acknowledge Research Computing at The University of Virginia for providing computational resources and technical support that have contributed to the results reported within this publication (https://rc.virginia.edu, last accessed September 6, 2021)

Servicios ecosistémicos en el Chaco Húmedo Paraguayo: retos para el manejo basado en los ecosistemas

Para contar con información necesaria para promover estrategias de gestión basada en ecosistemas, se evaluaron servicios ecosistémicos en un área ganadera en el Chaco Húmedo Paraguayo. Se estudió captura de carbono en biomasa forestal, captura de carbono en el suelo de humedales, calidad del agua de humedales, conectividad funcional de isletas forestales, valoración económica de un sistema silvopastoril basado en pasturasy bosques nativos, e infiltración y evaporación del agua en el suelo. Para ello, se aplicaron diferentes metodologías con un enfoque multidisciplinario. Los resultados informan sobre estos servicios ecosistémicos y su interacción con la ganadería, actividad instalada desde hace varias generaciones,aprovechando pastizales naturales inundables. A partir de esta evaluación, se realizaron recomendaciones para la continuidad de estos servicios, con actualización cartográfica de las unidades de vegetación. Los humedales del sitio de estudio, además de capturar carbono, se encuentran en un buen estado de conservación. La ganadería ha tenido impactos negativos ocasionales y puntuales en la calidad del agua que, sin embargo, son corregibles. Las isletas forestales del área de estudio permiten la conectividad biológica para Alouatta caraya, sin embargo, es aún necesario realizar estudios similares para otras especies. Los pastizales con palmares ofrecen un mayor valor forrajero en comparación con los pastizales con bosque, por otro lado, la captura de carbono en el bosque resultó en un valor económico que supera en más del doble al del palmar ocupando una superficie seis veces menor. Los ensayos de infiltración destacaron el papel de los bosques y árboles individuales en la mejora de este servicio, especialmente relevante para los suelos inundables de esta región. El mosaico de formaciones vegetales naturales del Chaco Húmedo plantea la necesidad del manejo basado en el conocimiento del funcionamiento de los distintos ecosistemas.In order to obtain necessary information to promote ecosystem-based management strategies, ecosystem services were assessed in a cattle rangeland in the Paraguayan Humid Chaco. Carbon sequestration in forest biomass, carbon sequestration in wetlands soil, water quality in wetlands, functional connectivity of forest islets, economic valuation of a silvopastoral system based on native savannas and forests, and infiltration and evaporation of water in the soil were studied. Different methodologies were applied with a multidisciplinary approach. Results give information about these ecosystem services and their interaction with livestock rearing, activity installed for several generations, taking advantage of frequently-flooded native savannas. From these assessments, recommendations were made for the improvement and restoration of these services, with cartographic updating of the vegetation units. Wetlands in the study site, in addition to carbon sequestration, are in a good state of conservation. Livestock rearing has had occasional and isolated negative impacts on water quality, which, nonetheless can be corrected. Forest islets present in the study area allow biological connectivity of Alouatta caraya, however, it’s still necessary to conduct similar analysis for other species. Regarding livestock production, palm groves/savannas systems offer a higher fodder value than forests/savannas, on the other hand, carbon sequestration in the forest resulted in an economic value that is more than double that of the palm groves occupying a surface six times smaller. Infiltration trials emphasized the role of individual forests and trees in improving infiltration, especially relevant to floodable soils in this region. The mosaic of natural plant formations in the Humid Chaco raises the need for a management based on the knowledge of the functioning of the different ecosystems

Drosophila evolution over space and time (DEST):A new population genomics resource

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 pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.DrosEU is funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). MK (M. Kapun) was supported by the Austrian Science Foundation (grant no. FWF P32275); JG by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); TF by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of Münster; AOB by the National Institutes of Health (R35 GM119686); MK (M. Kankare) by Academy of Finland grant 322980; VL by Danish Natural Science Research Council (FNU) grant 4002-00113B; FS Deutsche Forschungsgemeinschaft (DFG) grant STA1154/4-1, Project 408908608; JP by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; AU by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) grant 1737/17; MSV, MSR and MJ by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); AP, KE and MT by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551.Peer reviewe

Corrigendum to: Drosophila Evolution over Space and Time (DEST): a New Population Genomics Resource

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 pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.DrosEU is funded by a Special Topic Networks (STN) grant from the European Society for Evolutionary Biology (ESEB). MK (M. Kapun) was supported by the Austrian Science Foundation (grant no. FWF P32275); JG by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (H2020-ERC-2014-CoG-647900) and by the Spanish Ministry of Science and Innovation (BFU-2011-24397); TF by the Swiss National Science Foundation (SNSF grants PP00P3_133641, PP00P3_165836, and 31003A_182262) and a Mercator Fellowship from the German Research Foundation (DFG), held as a EvoPAD Visiting Professor at the Institute for Evolution and Biodiversity, University of Münster; AOB by the National Institutes of Health (R35 GM119686); MK (M. Kankare) by Academy of Finland grant 322980; VL by Danish Natural Science Research Council (FNU) grant 4002-00113B; FS Deutsche Forschungsgemeinschaft (DFG) grant STA1154/4-1, Project 408908608; JP by the Deutsche Forschungsgemeinschaft Projects 274388701 and 347368302; AU by FPI fellowship (BES-2012-052999); ET Israel Science Foundation (ISF) grant 1737/17; MSV, MSR and MJ by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178); AP, KE and MT by a grant from the Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007); and TM NSERC grant RGPIN-2018-05551.Peer reviewe

EGEO : la estructura geográfica de una base de conocimiento

En la presente contribución se describe la Estructura Geográfica (EGEO) que forma parte del banco de contenidos (BCP) desarrollado en el grupo Planeta. Dicha descripción incide tanto en las bases formales y constructivas del EGEO en sí, como en su interrelación funcional y de diseño con la base de conocimiento en general

A benchmark of transposon insertion detection tools using real data

Background: Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. Therefore, identifying TE polymorphisms is key to better understand the link between genotype and phenotype. However, most genotype-to-phenotype analyses have concentrated on single nucleotide polymorphisms as they are easier to reliable detect using short-read data. Many bioinformatic tools have been developed to identify transposon insertions from resequencing data using short reads. Nevertheless, the performance of most of these tools has been tested using simulated insertions, which do not accurately reproduce the complexity of natural insertions. Results: We have overcome this limitation by building a dataset of insertions from the comparison of two high-quality rice genomes, followed by extensive manual curation. This dataset contains validated insertions of two very different types of TEs, LTR-retrotransposons and MITEs. Using this dataset, we have benchmarked the sensitivity and precision of 12 commonly used tools, and our results suggest that in general their sensitivity was previously overestimated when using simulated data. Our results also show that, increasing coverage leads to a better sensitivity but with a cost in precision. Moreover, we found important differences in tool performance, with some tools performing better on a specific type of TEs. We have also used two sets of experimentally validated insertions in Drosophila and humans and show that this trend is maintained in genomes of different size and complexity. Conclusions: We discuss the possible choice of tools depending on the goals of the study and show that the appropriate combination of tools could be an option for most approaches, increasing the sensitivity while maintaining a good precision.This work was supported in part by grants from the Ministerio de Economia y Competitividad (AGL2016–78992-R). Fabio Barteri and Pol Vendrell hold a FPI (Formación de Personal Investigador) fellowship from the Spanish Ministerio de Economia y Competitividad. Raúl Castanera holds a Juan de la Cierva Postdoctoral fellowship from the Spanish Ministerio de Economia y Competitividad. JG is funded by the European Commission (H2020-ERC-2014-CoG-647900) and the Spanish Ministerio de Ciencia, Innovación y Universidades/AEI/FEDER, EU (BFU2017–82937-P)

ANTRO : un sistema de reconocimiento y gestión de antropónimos

En este artículo se describe ANTRO, una herramienta que permite identificar los antropónimos susceptibles de aparecer en cualquier tipo de texto, así como gestionarlos adecuadamente dentro de un sistema general de procesamiento del lenguaje natural