cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14320404
title: Tracking a recent horizontal transfer event: The P-element reaches Brazilian populations of Drosophila simulans

description: Abstract The “cut-and-paste” P-element present in some Diptera illustrates two important transposable elements abilities: to move within genomes and to be transmitted between non-mating species, a phenomenon known as horizontal transposon transfer (HTT). Recent studies reported a HTT of the P-element from Drosophila melanogaster to D. simulans. P-elements first appeared in D. simulans European samples collected in 2006 and spread across several populations from Europe, Africa, North America and Japan within seven years. Nevertheless, no P-element was found in South American populations of D. simulans collected between 2002 and 2009. We investigated the presence of the P-element in D. simulans collected in five Brazilian localities between 2018 and 2019, using a combination of methodologies such as PCR, DNA sequencing and FISH on chromosomes. Our experiments revealed the presence of the P-element in all sampled individuals from the five localities. The number of P-elements per individual varied from 11 to 20 copies and truncated copies were also observed. Altogether, our results showed that P-element invasion in D. simulans is at an advanced stage in Brazil and, together with other recent studies, confirms the remarkable rapid invasion of P-elements across worldwide D. simulans populations.
DOI: 10.6084/m9.figshare.14320404.v1
title: Tracking a recent horizontal transfer event: The P-element reaches Brazilian populations of Drosophila simulans

description: Abstract The “cut-and-paste” P-element present in some Diptera illustrates two important transposable elements abilities: to move within genomes and to be transmitted between non-mating species, a phenomenon known as horizontal transposon transfer (HTT). Recent studies reported a HTT of the P-element from Drosophila melanogaster to D. simulans. P-elements first appeared in D. simulans European samples collected in 2006 and spread across several populations from Europe, Africa, North America and Japan within seven years. Nevertheless, no P-element was found in South American populations of D. simulans collected between 2002 and 2009. We investigated the presence of the P-element in D. simulans collected in five Brazilian localities between 2018 and 2019, using a combination of methodologies such as PCR, DNA sequencing and FISH on chromosomes. Our experiments revealed the presence of the P-element in all sampled individuals from the five localities. The number of P-elements per individual varied from 11 to 20 copies and truncated copies were also observed. Altogether, our results showed that P-element invasion in D. simulans is at an advanced stage in Brazil and, together with other recent studies, confirms the remarkable rapid invasion of P-elements across worldwide D. simulans populations.
DOI: 10.6084/m9.figshare.14320405
title: What could be the fate of secondary contact zones between closely related plant species?

description: Abstract Interspecific hybridization has been fundamental in plant evolution. Nevertheless, the fate of hybrid zones throughout the generations remains poorly addressed. We analyzed a pair of recently diverged, interfertile, and sympatric Petunia species to ask what fate the interspecific hybrid population has met over time. We analyzed the genetic diversity in two generations from two contact sites and evaluated the effect of introgression. To do this, we collected all adult plants from the contact zones, including canonicals and intermediary colored individuals, and compared them with purebred representatives of both species based on seven highly informative microsatellite loci. We compared the genetic diversity observed in the contact zones with what is seen in isolated populations of each species, considering two generations of these annual species. Our results have confirmed the genetic differentiation between the species and the hybrid origin of the majority of the intermediary colored individuals. We also observed a differentiation related to genetic variability and inbreeding levels among the populations. Over time, there were no significant differences per site related to genetic diversity or phenotype composition. We found two stable populations kept by high inbreeding and backcross rates that influence the genetic diversity of their parental species through introgression.
DOI: 10.6084/m9.figshare.14320405.v1
title: What could be the fate of secondary contact zones between closely related plant species?

description: Abstract Interspecific hybridization has been fundamental in plant evolution. Nevertheless, the fate of hybrid zones throughout the generations remains poorly addressed. We analyzed a pair of recently diverged, interfertile, and sympatric Petunia species to ask what fate the interspecific hybrid population has met over time. We analyzed the genetic diversity in two generations from two contact sites and evaluated the effect of introgression. To do this, we collected all adult plants from the contact zones, including canonicals and intermediary colored individuals, and compared them with purebred representatives of both species based on seven highly informative microsatellite loci. We compared the genetic diversity observed in the contact zones with what is seen in isolated populations of each species, considering two generations of these annual species. Our results have confirmed the genetic differentiation between the species and the hybrid origin of the majority of the intermediary colored individuals. We also observed a differentiation related to genetic variability and inbreeding levels among the populations. Over time, there were no significant differences per site related to genetic diversity or phenotype composition. We found two stable populations kept by high inbreeding and backcross rates that influence the genetic diversity of their parental species through introgression.
DOI: 10.6084/m9.figshare.14320407
title: ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2

description: Abstract The recent emergence of SARS-CoV-2 is responsible for the current pandemic of COVID-19, which uses the human membrane protein ACE2 as a gateway to host-cell infection. We performed a comparative genomic analysis of 70 ACE2 placental mammal orthologues to identify variations and contribute to the understanding of evolutionary dynamics behind this successful adaptation to infect humans. Our results reveal that 4% of the ACE2 sites are under positive selection, all located in the catalytic domain, suggesting possibly taxon-specific adaptations related to the ACE2 function, such as cardiovascular physiology. Considering all variable sites, we selected 30 of them located at the critical ACE2 binding sites to the SARS-CoV-like viruses for analysis in more detail. Our results reveal a relatively high diversity of ACE2 between placental mammal species, while showing no polymorphism within human populations, at least considering the 30 inter-species variable sites. A perfect scenario for natural selection favored this opportunistic new coronavirus in its trajectory of infecting humans. We suggest that SARS-CoV-2 became a specialist coronavirus for human hosts. Differences in the rate of infection and mortality could be related to the innate immune responses, other unknown genetic factors, as well as non-biological factors.
DOI: 10.6084/m9.figshare.14320407.v1
title: ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2

description: Abstract The recent emergence of SARS-CoV-2 is responsible for the current pandemic of COVID-19, which uses the human membrane protein ACE2 as a gateway to host-cell infection. We performed a comparative genomic analysis of 70 ACE2 placental mammal orthologues to identify variations and contribute to the understanding of evolutionary dynamics behind this successful adaptation to infect humans. Our results reveal that 4% of the ACE2 sites are under positive selection, all located in the catalytic domain, suggesting possibly taxon-specific adaptations related to the ACE2 function, such as cardiovascular physiology. Considering all variable sites, we selected 30 of them located at the critical ACE2 binding sites to the SARS-CoV-like viruses for analysis in more detail. Our results reveal a relatively high diversity of ACE2 between placental mammal species, while showing no polymorphism within human populations, at least considering the 30 inter-species variable sites. A perfect scenario for natural selection favored this opportunistic new coronavirus in its trajectory of infecting humans. We suggest that SARS-CoV-2 became a specialist coronavirus for human hosts. Differences in the rate of infection and mortality could be related to the innate immune responses, other unknown genetic factors, as well as non-biological factors.
DOI: 10.6084/m9.figshare.14320408
title: Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development

description: Abstract Tsetse flies are responsible for the transmission of Trypanossoma sp. to vertebrate animals in Africa causing huge health issues and economic loss. The availability of the genome sequence of Glossina morsitans enabled the discovery of several genes related to medically important phenotypes and novel physiological features. However, a genome-wide scan for coding regions that underwent positive selection is still missing, which is surprising given the evolution of traits associated with the hematophagy in this lineage. In this study, we employed an experimental design that controlled for the rate of false positives and we performed a scan of 3,318 G. morsitans genes. We found 145 genes with significant historical signal of positive selection. These genes were categorized into 18 functional classes after careful manual annotation. Based on their attributed functions, we identified candidate genes related with feeding habits and embryonic development. When our results were contrasted with gene expression data, we confirmed that most genes that underwent adaptive molecular evolution were frequently expressed in organs associated with key physiological evolutionary innovations in the G. morsitans lineage, namely, the salivary gland, the midgut, fat body tissue, and in the spermatophore.
DOI: 10.6084/m9.figshare.14320408.v1
title: Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development

description: Abstract Tsetse flies are responsible for the transmission of Trypanossoma sp. to vertebrate animals in Africa causing huge health issues and economic loss. The availability of the genome sequence of Glossina morsitans enabled the discovery of several genes related to medically important phenotypes and novel physiological features. However, a genome-wide scan for coding regions that underwent positive selection is still missing, which is surprising given the evolution of traits associated with the hematophagy in this lineage. In this study, we employed an experimental design that controlled for the rate of false positives and we performed a scan of 3,318 G. morsitans genes. We found 145 genes with significant historical signal of positive selection. These genes were categorized into 18 functional classes after careful manual annotation. Based on their attributed functions, we identified candidate genes related with feeding habits and embryonic development. When our results were contrasted with gene expression data, we confirmed that most genes that underwent adaptive molecular evolution were frequently expressed in organs associated with key physiological evolutionary innovations in the G. morsitans lineage, namely, the salivary gland, the midgut, fat body tissue, and in the spermatophore.
DOI: 10.6084/m9.figshare.14320410
title: Global phylogeography of the critically endangered hawksbill turtle (Eretmochelys imbricata)

description: Abstract The hawksbill turtle is a broadly distributed, highly migratory and critically endangered sea turtle species. The paucity of studies restricts the comprehension of its behavior and life history. In this work, we performed a global phylogeographic analysis using a compilation of previously published mitochondrial haplotype data to understand the dynamics and diversity of hawksbill populations worldwide. Our results revealed a complex demographic pattern associated to hawksbill phylogeography since the Pliocene. Isolation by distance is not enough to explain distinct demographic units of hawksbill turtles, which are also influenced by other factors as oceanic currents, coral reef distribution and nesting timing. The foraging aggregations are typically mixed stocks of individuals originating from multiple nesting areas, but there is also a trend of foragers coming from nearby natal beaches. Phylogenetic analysis indicates two highly divergent major lineages split between Atlantic and Indo-Pacific rookeries, but there is also a more recent Atlantic Ocean colonization from the Indo-Pacific Ocean. Long-distance dispersal events are likely responsible for homogenization between distant populations within oceans. Our findings provided new insights about population connectivity, identified gaps that should be prioritized in future research and highlighted the need for international efforts aiming at hawksbill's conservation.
DOI: 10.6084/m9.figshare.14320410.v1
title: Global phylogeography of the critically endangered hawksbill turtle (Eretmochelys imbricata)

description: Abstract The hawksbill turtle is a broadly distributed, highly migratory and critically endangered sea turtle species. The paucity of studies restricts the comprehension of its behavior and life history. In this work, we performed a global phylogeographic analysis using a compilation of previously published mitochondrial haplotype data to understand the dynamics and diversity of hawksbill populations worldwide. Our results revealed a complex demographic pattern associated to hawksbill phylogeography since the Pliocene. Isolation by distance is not enough to explain distinct demographic units of hawksbill turtles, which are also influenced by other factors as oceanic currents, coral reef distribution and nesting timing. The foraging aggregations are typically mixed stocks of individuals originating from multiple nesting areas, but there is also a trend of foragers coming from nearby natal beaches. Phylogenetic analysis indicates two highly divergent major lineages split between Atlantic and Indo-Pacific rookeries, but there is also a more recent Atlantic Ocean colonization from the Indo-Pacific Ocean. Long-distance dispersal events are likely responsible for homogenization between distant populations within oceans. Our findings provided new insights about population connectivity, identified gaps that should be prioritized in future research and highlighted the need for international efforts aiming at hawksbill's conservation.
DOI: 10.25678/00035v
title: Data for: Non‐Gaussian parameter inference for hydrogeological models using Stein Variational Gradient Descent

description: This package includes the data and Python files for the publication "Non‐Gaussian parameter inference for hydrogeological models using Stein Variational Gradient Descent".
DOI: 10.6084/m9.figshare.14320411
title: BAP1 functions as a tumor promoter in prostate cancer cells through EMT regulation

description: Abstract BRCA1-associated protein 1 (BAP1) is a deubiquitinating enzyme that has long been considered to be a tumor suppressor in various tumors, including renal cell carcinoma, uveal melanoma, mesothelioma, and cutaneous melanoma. However, the involvement of BAP1 in the progression of prostate cancer has not been studied until recently. Herein, we investigated the tumor promoting function of BAP1 in the context of prostate cancer. Analysis of The Cancer Genome Atlas (TCGA) data set showed that prostate cancer patients express high levels of BAP1 mRNA. High BAP1 expression is inversely correlated with disease-free survival in patients with prostate cancer. Among the prostate cell lines tested, BAP1 expression was high in tumorigenic and metastatic cell lines, but was low in normal prostate cell line. Knockdown of BAP1 in PC3 or DU145 cells induced mesenchymal-to-epithelial transition (MET). Further, BAP1-knockdown resulted in decreased migration and invasion of PC3 and DU145 cells. Conversely, overexpression of BAP1 in RWPE1, a normal prostate cell line, induced the migratory and invasive properties. Collectively, our findings identified that BAP1 has a tumor promoting function in prostate cancer cells, and suggest that BAP1 can serve as a potential therapeutic target for prostate cancer.
DOI: 10.6084/m9.figshare.14320411.v1
title: BAP1 functions as a tumor promoter in prostate cancer cells through EMT regulation

description: Abstract BRCA1-associated protein 1 (BAP1) is a deubiquitinating enzyme that has long been considered to be a tumor suppressor in various tumors, including renal cell carcinoma, uveal melanoma, mesothelioma, and cutaneous melanoma. However, the involvement of BAP1 in the progression of prostate cancer has not been studied until recently. Herein, we investigated the tumor promoting function of BAP1 in the context of prostate cancer. Analysis of The Cancer Genome Atlas (TCGA) data set showed that prostate cancer patients express high levels of BAP1 mRNA. High BAP1 expression is inversely correlated with disease-free survival in patients with prostate cancer. Among the prostate cell lines tested, BAP1 expression was high in tumorigenic and metastatic cell lines, but was low in normal prostate cell line. Knockdown of BAP1 in PC3 or DU145 cells induced mesenchymal-to-epithelial transition (MET). Further, BAP1-knockdown resulted in decreased migration and invasion of PC3 and DU145 cells. Conversely, overexpression of BAP1 in RWPE1, a normal prostate cell line, induced the migratory and invasive properties. Collectively, our findings identified that BAP1 has a tumor promoting function in prostate cancer cells, and suggest that BAP1 can serve as a potential therapeutic target for prostate cancer.
DOI: 10.6084/m9.figshare.14320413
title: USP7 deubiquitinates and stabilizes EZH2 in prostate cancer cells

description: Abstract Regulation of target proteins by the ubiquitin-proteasome system (UPS) is common in a wide range of cellular events, including transcriptional regulation, cell cycle progression, differentiation, and tumorigenesis. Ubiquitin-specific protease 7 (USP7) has been implicated in tumor development and metastasis in various malignancies through the regulation of target protein stability. In this study, we found that the enhancer of zeste homolog 2 (EZH2), which catalyzes the methylation at lysine 27 of histone H3, is a target of USP7 and is stabilized by USP7-mediated deubiquitination. In prostate cancer cells, the transcriptional repression function of EZH2 was inhibited by USP7-knockdown. Furthermore, ectopic introduction of EZH2 restored the cell migration, invasion, and sphere-forming potential of prostate cancer cells, which had been decreased by USP7-knockdown. Moreover, combined treatment with the USP7-specific inhibitor P5091 and EZH2 inhibitors, such as GSK126, EPZ6438, and DZNep, induced synergistic inhibitory effects on cell migration, invasion, and sphere-forming potential in prostate cancer cells. Collectively, our findings revealed that the promotion of the malignancy-associated characteristics of prostate cancer cells by USP7 was in part due to EZH2 stabilization. Thus, we suggest that simultaneous treatment with a USP7 inhibitor and an EZH2 inhibitor could be a rational strategy for treating EZH2-dependent cancers.
DOI: 10.6084/m9.figshare.14320413.v1
title: USP7 deubiquitinates and stabilizes EZH2 in prostate cancer cells

description: Abstract Regulation of target proteins by the ubiquitin-proteasome system (UPS) is common in a wide range of cellular events, including transcriptional regulation, cell cycle progression, differentiation, and tumorigenesis. Ubiquitin-specific protease 7 (USP7) has been implicated in tumor development and metastasis in various malignancies through the regulation of target protein stability. In this study, we found that the enhancer of zeste homolog 2 (EZH2), which catalyzes the methylation at lysine 27 of histone H3, is a target of USP7 and is stabilized by USP7-mediated deubiquitination. In prostate cancer cells, the transcriptional repression function of EZH2 was inhibited by USP7-knockdown. Furthermore, ectopic introduction of EZH2 restored the cell migration, invasion, and sphere-forming potential of prostate cancer cells, which had been decreased by USP7-knockdown. Moreover, combined treatment with the USP7-specific inhibitor P5091 and EZH2 inhibitors, such as GSK126, EPZ6438, and DZNep, induced synergistic inhibitory effects on cell migration, invasion, and sphere-forming potential in prostate cancer cells. Collectively, our findings revealed that the promotion of the malignancy-associated characteristics of prostate cancer cells by USP7 was in part due to EZH2 stabilization. Thus, we suggest that simultaneous treatment with a USP7 inhibitor and an EZH2 inhibitor could be a rational strategy for treating EZH2-dependent cancers.
DOI: 10.6084/m9.figshare.12210611
title: Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae)

description: Abstract Myrteae is the largest and most diverse tribe within Myrtaceae and represents the majority of its diversity in the Neotropics. Members of Myrteae hold ecological importance in tropical biomes for the provision of food sources for many animal species. Thus, due to its several roles, a growing interest has been addressed to this group. In this study, we report the sequencing and de novo assembly of the complete chloroplast (cp) genomes of six Myrteae species: Eugenia brasiliensis, E. pyriformis, E. nitida, Myrcianthes pungens, Plinia edulis and Psidium cattleianum. We characterized genome structure, gene content, and identified SSRs to detect variation within Neotropical Myrteae. The six newly sequenced plastomes exhibit a typical quadripartite structure, gene content and organization highly conserved among Myrtaceae species. Some differences in genome length, protein-coding genes and non-coding regions were found. Besides, IR boundaries present structural changes among species. Increased sequence diversity was observed in some intergenic regions, suggesting their suitability for investigating intraand interspecific genetic diversity in populational studies. These data also contribute to the improvement of taxa sampling in further phylogenetic investigations to understand Myrtaceae evolution.