Estudio del polimorfismo genético de la apolipoproteína E en la población mestiza y amerindia de Panamá

Se determinaron las frecuencias alelicas y genotípicas para ApoE en muestras de las poblaciones amerindias (Ngabe Bugle, Guna Yala, Embers-Wounaan) y mestiza de la Republica de Panamá. Participaron en este estudio un total de 186 individuos, previo consentimiento informado. La identificación de los alelos fue realizada mediante PCR-RFLP y las frecuencias alelicas y genotipicas fueron determinadas mediante la utilización del programa Popgen32 versión 1.32. El alelo con mayor frecuencia en la población no segregada fue: E3 con 0.868, seguido por E4 con una frecuencia de 0.114 y E2 con 0.018; este ultimo presente solo en la población mestiza. El alelo E3 se presento con una frecuencia de 1 en las poblaciones Ngabe Bugle y Guna Yala, seguida de la población Embera-Wounaan con frecuencia de 0.95 y los mestizos con frecuencia de 0.60. Las frecuencias del alelo E4 en las poblaciones mestiza y Embera-Wounaan fueron 0.336 y 0.053, respectivamente, mientras que en las poblaciones Ngdbe Bugle y Guna Yala el alelo estuvo ausente. El alelo E2 solo se observo en los mestizos con 0.05 de frecuencia. Las frecuencias genotipicas observadas fueron: E3/E3; 0.52 en mestizos; 0.897 en la poblaciOn Embera Wounaan y 1 en las poblaciones de Guna Yala y Ngabe Bugle. El genotipo E31E4 se presento en la población mestiza con una frecuencia de 0.13 y 0.10 en la Embera-Wounaan. Los genotipos E2/E2, E2/E3 y E4/E4 solo se presentaron en la población mestiza con frecuencias de 0,019 0.077, 0.269, respectivamente. La población mestiza presento la mayor heterocigosidad esperada (He= 0.527), seguida por la población Embera-Wounaan (He= 0.101). Se registraron valores de He = 0 en las poblaciones de Guna Yala y Ngabe Bugle en las cuales solo se observe" el alelo E3. Nuestros resultados sugieren que entre la población no segregada, la población mestiza tiene mayor predisposición genética de padecer enfermedades aterogenicas y Alzheimer. Los grupos amerindios por su parte, presentan el alelo salvaje E3 fijado o en mayor frecuencia, lo que indica que estos grupos tienen menor riesgo de padecer estas enfermedades

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water.

BACKGROUND: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. RESULTS: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. CONCLUSIONS: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders

The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Background: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. Results: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. Conclusions: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders

Les bases génétiques de la pigmentation dans les embryons de punaise d'eau

The principal aim of this doctoral thesis was to understand the genetic basis for the diversification of the extra-ocular pigmentation in Gerromorpha embryos. Most of the semi-aquatic bugs develop a variability of yellow or red colours patterns in legs and antennas during the embryonic stage. Since the red colour in appendages was similar to the one present in eyes, we hypothesized that the extra-ocular colours could be produced by the co-option of the eye pigments biosynthesis pathway. First we inferred the evolutionary history of this trait based on its presence or absence in embryos of 34 species. We found that the ancestral state of the trait in Gerromorpha was yellow and that six independent lineages evolved bright red colour, while two lineages lost the colour. Using RNAi and in situ hybridisation on homologous genes from the pteridine and ommochrome biosynthesis pathways, we described the genetic pathway involved in the production of pigments in eyes and extra-ocular tissues in Limnogonus franciscanus embryos. After that, we performed a screening of three genes from this pathway in five other species with different extra-ocular colours and patterns. We discovered that the same pathway was recruited once to produce the diversity of patterns in Gerromorpha. Furthermore, we identified by UPLC-HRMS that xanthopterin and erythropterin pigments produce the variability of colours and patterns in different species. Our next step aimed to understand how the recruitment of a conserved pathway could produce this striking diversity of colour patterns. Using RNA-Seq technology and bioinformatics tools, we identified 167 transcription factors that are co-expressed in eyes, antennas and legs of embryos in Limnogonus franciscanus. These proteins might be involved in the regulation of genes responsible for the different colour patterns. We have started an RNAi screen of these transcription factors. This project is still ongoing but in this thesis I will present the preliminary results and conclusions.In conclusion, the pigmentation of semi-aquatic bugs during the embryonic stage is a good model to understand the co-option of pre-existing genetic pathways and underlying the question of how a conserved pathway could be regulated to produce diverse morphological phenotypes.Le but de ce doctorat était de comprendre les bases génétiques de la diversification de la pigmentation extra-oculaire chez les embryons des Gerromorphes. La plupart des punaises semi-aquatiques présentent une variabilité de pattern de couleur jaune ou/et rouge dans les pattes et les antennes au stade embryonnaire. La couleur rouge observée dans les appendices étant similaire à celle présente dans les yeux, nous avons émis l'hypothèse que les couleurs extra-oculaires pouvaient être produites par la co-option des voies de synthèse des pigments des yeux. Nous avons d'abord déterminé l'histoire évolutive de ce trait à partir de sa présence ou de son absence dans les embryons de 34 espèces. Grâce à l'analyse génétique par interférence ARN et hybridation in situ, nous avons identifié les voies impliquées dans la pigmentation des yeux et des organes extra-oculaires dans l'espèce Limnogonus franciscanus. Nous avons ensuite testé par interférence ARN et hybridation in situ trois gènes de la voie ptéridine dans cinq autres espèces de Gerromorphes présentant des colorations extra-oculaires différentes. Les résultats suggèrent que la même voie a été recrutée une seule fois pour produire la diversité de pattern. De plus, grâce à une analyse chimique par ultra-chromatographie couplée à de la spectrométrie de masse, nous avons identifié que la xanthopterin et l’erythropterin sont les deux pigments responsables de la couleur chez différentes espèces. Nous nous sommes aussi demandé comment le recrutement d'une seule et même voie conservée pouvait produire une telle diversité de pattern. En utilisant la technologie de transcriptomique du RNA-seq, nous avons identifié 167 facteurs de transcription co-exprimés dans les yeux, les antennes et les pattes des embryons de Limnogonus franciscanus. Ces protéines pourraient intervenir dans la régulation des gènes impliqués dans la formation des patterns de couleur embryonnaire. Nous avons initié un crible ARNi de ces facteurs de transcription. En conclusion, la pigmentation des punaises semi-aquatiques au stade embryonnaire est un bon modèle pour comprendre la co-option des voies génétiques et la question sous-jacente de la façon dont une voie conservée pourrait être réglementée pour produire divers phénotypes

Genetic Basis of Extra-Ocular Pigmentation in Semi-Aquatic Embryos

Le but de ce doctorat était de comprendre les bases génétiques de la diversification de la pigmentation extra-oculaire chez les embryons des Gerromorphes. La plupart des punaises semi-aquatiques présentent une variabilité de pattern de couleur jaune ou/et rouge dans les pattes et les antennes au stade embryonnaire. La couleur rouge observée dans les appendices étant similaire à celle présente dans les yeux, nous avons émis l'hypothèse que les couleurs extra-oculaires pouvaient être produites par la co-option des voies de synthèse des pigments des yeux. Nous avons d'abord déterminé l'histoire évolutive de ce trait à partir de sa présence ou de son absence dans les embryons de 34 espèces. Grâce à l'analyse génétique par interférence ARN et hybridation in situ, nous avons identifié les voies impliquées dans la pigmentation des yeux et des organes extra-oculaires dans l'espèce Limnogonus franciscanus. Nous avons ensuite testé par interférence ARN et hybridation in situ trois gènes de la voie ptéridine dans cinq autres espèces de Gerromorphes présentant des colorations extra-oculaires différentes. Les résultats suggèrent que la même voie a été recrutée une seule fois pour produire la diversité de pattern. De plus, grâce à une analyse chimique par ultra-chromatographie couplée à de la spectrométrie de masse, nous avons identifié que la xanthopterin et l’erythropterin sont les deux pigments responsables de la couleur chez différentes espèces. Nous nous sommes aussi demandé comment le recrutement d'une seule et même voie conservée pouvait produire une telle diversité de pattern. En utilisant la technologie de transcriptomique du RNA-seq, nous avons identifié 167 facteurs de transcription co-exprimés dans les yeux, les antennes et les pattes des embryons de Limnogonus franciscanus. Ces protéines pourraient intervenir dans la régulation des gènes impliqués dans la formation des patterns de couleur embryonnaire. Nous avons initié un crible ARNi de ces facteurs de transcription. En conclusion, la pigmentation des punaises semi-aquatiques au stade embryonnaire est un bon modèle pour comprendre la co-option des voies génétiques et la question sous-jacente de la façon dont une voie conservée pourrait être réglementée pour produire divers phénotypes.The principal aim of this doctoral thesis was to understand the genetic basis for the diversification of the extra-ocular pigmentation in Gerromorpha embryos. Most of the semi-aquatic bugs develop a variability of yellow or red colours patterns in legs and antennas during the embryonic stage. Since the red colour in appendages was similar to the one present in eyes, we hypothesized that the extra-ocular colours could be produced by the co-option of the eye pigments biosynthesis pathway. First we inferred the evolutionary history of this trait based on its presence or absence in embryos of 34 species. We found that the ancestral state of the trait in Gerromorpha was yellow and that six independent lineages evolved bright red colour, while two lineages lost the colour. Using RNAi and in situ hybridisation on homologous genes from the pteridine and ommochrome biosynthesis pathways, we described the genetic pathway involved in the production of pigments in eyes and extra-ocular tissues in Limnogonus franciscanus embryos. After that, we performed a screening of three genes from this pathway in five other species with different extra-ocular colours and patterns. We discovered that the same pathway was recruited once to produce the diversity of patterns in Gerromorpha. Furthermore, we identified by UPLC-HRMS that xanthopterin and erythropterin pigments produce the variability of colours and patterns in different species. Our next step aimed to understand how the recruitment of a conserved pathway could produce this striking diversity of colour patterns. Using RNA-Seq technology and bioinformatics tools, we identified 167 transcription factors that are co-expressed in eyes, antennas and legs of embryos in Limnogonus franciscanus. These proteins might be involved in the regulation of genes responsible for the different colour patterns. We have started an RNAi screen of these transcription factors. This project is still ongoing but in this thesis I will present the preliminary results and conclusions.In conclusion, the pigmentation of semi-aquatic bugs during the embryonic stage is a good model to understand the co-option of pre-existing genetic pathways and underlying the question of how a conserved pathway could be regulated to produce diverse morphological phenotypes

POTENTIAL APPLICATION OF TRANSCRIPTOMIC ANALYSIS OF PEST INSECT MANAGEMENT PLANS AFFECTING THE AGRICULTURAL SECTOR OF PANAMA

Background. Insect pests, as well as other arthropods, constitute a constant threat to public health and food security and food sovereignty in a country. Although various techniques are currently used for integrated pest management, the search for new management alternatives is constant. In this sense, transcriptome analysis, which consists of the analysis of gene expression profiles of certain living organisms, could provide new alternatives. Objective. To determine the potential applications of transcriptomic analysis against insect pests in the agricultural sector in Panama. Methodology. The study was developed through the search for relevant information on transcriptome analysis applied within entomology. Search was performed in SciELO (Scientific Electronic Library Online), Dialnet, Web of Science, Springer Link, Ciencia.Science.gov, Scopus, Google Schoolar and ERIC (Institute of Education Sciences). Main findings. The analysis of transcriptomes is a tool to understand different biological, physiological, and molecular aspects of insects and other arthropods identified as pests in the Republic of Panama that put at risk the agricultural production of the country. Implications. Harmful arthropods have become more relevant in recent years due to climate change, invasive species and anthropogenic factors that increase the populations of these pest in Panama. Conclusion. The results indicate that transcriptomic analysis generates information about the existence of candidate genes, including those of harmful arthropods and natural enemies as predators, parasitoids and entomopathogenic microorganisms that could be used as targets to reduce the damage caused by arthropods to the agricultural sector

Cooption of the pteridine biosynthesis pathway underlies the diversification of embryonic colors in water striders

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Transcriptome-based phylogeny of the semi-aquatic bugs (Hemiptera Heteroptera: Gerromorpha) reveals patterns of lineage expansion in a series of new adaptive zones

Key innovations enable access to new adaptive zones and are often linked to increased species diversification. As such, innovations have attracted much attention, yet their concrete consequences on the subsequent evolutionary trajectory and diversification of the bearing lineages remain unclear. Water striders and relatives (Hemiptera: Heteroptera: Gerromorpha) represent a monophyletic lineage of insects that transitioned to live on the water-air interface and that diversified to occupy ponds, puddles, streams, mangroves and even oceans. This lineage offers an excellent model to study the patterns and processes underlying species diversification following the conquest of new adaptive zones. However, such studies require a reliable and comprehensive phylogeny of the infraorder. Based on whole transcriptomic datasets of 97 species and fossil records, we reconstructed a new phylogeny of the Gerromorpha that resolved inconsistencies and uncovered strong support for previously unknown relationships between some important taxa. We then used this phylogeny to reconstruct the ancestral state of a set of adaptations associated with water surface invasion (fluid locomotion, dispersal and transition to saline waters) and sexual dimorphism. Our results uncovered important patterns and dynamics of phenotypic evolution, revealing how the initial event of water surface invasion enabled multiple subsequent transitions to new adaptive zones on the water surfaces. This phylogeny and the associated transcriptomic datasets constitute highly valuable resources, making Gerromorpha an attractive model lineage to study phenotypic evolution

Transcriptome-based phylogeny of the semi-aquatic bugs (Hemiptera: Heteroptera: Gerromorpha) reveals patterns of lineage expansion in a series of new adaptive zones Authors

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