Pipa carvalhoi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA68373 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pipa carvalhoi mitochondrial genome sequencing project
| PRJNA50481 | ENA
Project description:Pipa carvalhoi Transcriptome or Gene expression
| PRJNA73173 | ENA
Project description:Pipidae is a clade of Anura that diverged relatively early from other frogs in the phylogeny of the group. Pipids have a unique combination of morphological features, some of which appear to represent a mix of adaptations to aquatic life and plesiomorphic characters of Anura. The present study describes the karyotype of Pipa carvalhoi Miranda-Ribeiro, 1937, including morphology, heterochromatin distribution, and location of the NOR site. The diploid number of P. carvalhoi is 2n=20, including three metacentric pairs (1, 4, 8), two submetacentric (2 and 7), three subtelocentric (3, 5, 6), and two telocentric pairs (9 and 10). C-banding detected centromeric blocks of heterochromatin in all chromosome pairs and the NOR detected in chromosome pair 9, as confirmed by FISH using the rDNA 28S probe. The telomeric probes indicated the presence of interstitial telomeric sequences (ITSs), primarily in the centromeric region of the chromosomes, frequently associated with heterochromatin, suggesting that these repeats are a significant component of this region. The findings of the present study provide important insights for the understanding of the mechanisms of chromosomal evolution in the genus Pipa, and the diversification of the Pipidae as a whole.
| S-EPMC6803351 | biostudies-literature
Project description:The large amphibian genomes contain numerous repetitive DNA components that have played an important role in the karyotypic diversification of this vertebrate group. Hypotheses based on the presumable primitive karyotype (2n = 20) of the anurans of the family Pipidae suggest that they have evolved principally through intrachromosomal rearrangements. Pipa is the only South American pipid, while all the other genera are found in Africa. The divergence of the South American lineages from the African ones occurred at least 136 million years ago and is thought to have had a strong biogeographic component. Here, we tested the potential of the repetitive DNA to enable a better understanding of the differentiation of the karyotype among the family Pipidae and to expand our capacity to interpret the chromosomal evolution in this frog family. Our results indicate a long history of conservation in the chromosome bearing the H3 histone locus, corroborating inferences on the chromosomal homologies between the species in pairs 6, 8, and 9. The chromosomal distribution of the microsatellite motifs also provides useful markers for comparative genomics at the chromosome level between Pipa carvalhoi and Xenopus tropicalis, contributing new insights into the evolution of the karyotypes of these species. We detected similar patterns in the distribution and abundance of the microsatellite arrangements, which reflect the shared organization in the terminal/subterminal region of the chromosomes between these two species. By contrast, the microsatellite probes detected a differential arrangement of the repetitive DNA among the chromosomes of the two species, allowing longitudinal differentiation of pairs that are identical in size and morphology, such as pairs 1, 2, 4, and 5. We also found evidence of the distinctive composition of the repetitive motifs of the centromeric region between the species analyzed in the present study, with a clear enrichment of the (CA) and (GA) microsatellite motifs in P. carvalhoi. Finally, microsatellite enrichment in the pericentromeric region of chromosome pairs 6, 8, and 9 in the P. carvalhoi karyotype, together with interstitial telomeric sequences (ITS), validate the hypothesis that pericentromeric inversions occurred during the chromosomal evolution of P. carvalhoi and reinforce the role of the repetitive DNA in the remodeling of the karyotype architecture of the Pipidae.
| S-EPMC7385237 | biostudies-literature
Project description:Pipa carvalhoi isolate:CFBHT 2225 Genome sequencing and assembly
| PRJNA778705 | ENA
Project description:Nuclear factor-kappa B (NF-κB) plays a critical role in the host defense against microbial pathogens. Many pathogens modulate NF-κB signaling to establish infection in their host. Salmonella enterica serovar Typhimurium (S. Typhimurium) possesses two type III secretion systems (T3SS-1 and T3SS-2) and directly injects many effector proteins into host cells. It has been reported that some effectors block NF-κB signaling, but the molecular mechanism of the inactivation of NF-κB signaling in S. Typhimurium is poorly understood. Here, we identified seven type III effectors-GogA, GtgA, PipA, SseK1, SseK2, SseK3, and SteE-that inhibited NF-κB activation in HeLa cells stimulated with TNF-α. We also determined that only GogA and GtgA are involved in regulation of the activation of NF-κB in HeLa cells infected with S. Typhimurium. GogA, GtgA, and PipA are highly homologous to one another and have the consensus zinc metalloprotease HEXXH motif. Our experiments demonstrated that GogA, GtgA, and PipA each directly cleaved NF-κB p65, whereas GogA and GtgA, but not PipA, inhibited the NF-κB activation in HeLa cells infected with S. Typhimurium. Further, expressions of the gogA or gtgA gene were induced under the SPI-1-and SPI-2-inducing conditions, but expression of the pipA gene was induced only under the SPI-2-inducing condition. We also showed that PipA was secreted into RAW264.7 cells through T3SS-2. Finally, we indicated that PipA elicits bacterial dissemination in the systemic stage of infection of S. Typhimurium via a T3SS-1-independent mechanism. Collectively, our results suggest that PipA, GogA and GtgA contribute to S. Typhimurium pathogenesis in different ways.
| S-EPMC7971870 | biostudies-literature
Project description:Bokermannohyla carvalhoi Genome sequencing and assembly
| PRJNA487010 | ENA
Project description:This project generated a high-coverage WGS dataset of 1,000+ highly admixed elderly from a census-based cohort from São Paulo, Brazil (SABE Study). Current Brazilian population results from admixture of Iberian Europeans, West and East Africans and Native Americans, and from 19th century onwards other groups from Europe, Asian and Middle East arrived in Brazil. The phase 1 includes BAM files from 1,171 individuals, described in pre-print "Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil)" (DOI: 10.1101/2020.09.15.298026).
| EGAS00001005052 | EGA
Project description:In the 15th century, approximately 900,000 Native Americans, mostly TupÃÂ-speakers, lived on the Brazilian coast. By the end of the 18th century, the coastal native populations were declared extinct. The Tupàarrived on the east coast after leaving the Amazonian basin approximately 2,000 years before present; however, there is no consensus on how this migration occurred - toward the northern Amazon and then directly to the Atlantic coast, or heading south into the continent, and then migrating to the coast. Here we leveraged genomic data from one of the last remaining putative representatives of the Tupàcoastal branch, a small, admixed, self-reported Tupiniquim community, as well as data of a GuaranàMbyá native population from Southern Brazil and of three other native populations from the Amazonian region. We demonstrated that the Tupiniquim Native American ancestry is not related to any extant Brazilian Native American population already studied and thus they could be considered the only living representatives of the extinct Tupàbranch that used to settle the Atlantic Coast of Brazil. Furthermore, these data show evidence of a direct migration from Amazon to the Northeast Coast in pre-Columbian time, giving rise to the TupàCoastal populations, and a single distinct migration southward that originated the Guaranàpeople from Brazil and Paraguay. This is the first study to elucidate the population dynamics and diversification of the Brazilian Natives at a genomic level, which was made possible by recovering data from the Brazilian coastal population through the genomes of mestizo individuals.
| EGAS00001004036 | EGA