Resumen en Inglés:

Abstract X-STR analysis offers novel pathways for exploring both paternal and maternal lineages, which is particularly valuable in parenthood testing where standard methods fail. Despite being limited in availability, these markers show promise in improving forensic analyses, especially with emerging technology such as Massively Parallel Sequencing (MPS). This study introduces a new X-STRs multiplex system that could increase discrimination power in complex cases, expanding marker diversity and complementing traditional markers. We selected 12 X-STR loci (DXS61071, DXS97199, DXS12310, DXS14221, DXS33963, DXS39152, DXS44734, DXS54471, DXS68748, DXS70370, DXS13932, and DXS14986) for the assay. Genomic DNA was extracted from 100 unrelated males and 104 females, in a sample population from Rio de Janeiro, amplified with custom-designed primers and subjected to capillary gel electrophoresis and MPS. Forensic efficiency evaluation revealed high values of the combined power of discrimination in males (cPDM ≥ 0.999999997) and females (cPDF ≥ 0.999999999999995), as well as combined paternity exclusion (cPE ≥ 0.99999). Among these markers, two exhibit high polymorphism, with multiple isoalleles distinguishable by their sequences, using MPS technology. The incorporation of these new X-STR markers multiplex system in conjunction with MPS analysis could potentially increase the power of discrimination in forensic analysis for mixtures and complex cases.

Resumen en Inglés:

Abstract This study updates data on the distribution of CCR5Δ32 allele frequency in populations from Brazilian states. CCR5Δ32 is a variant allele of the CCR5 gene, which prevents (in homozygosity) or reduces (in heterozygosity) the expression of the CCR5 protein on the surface of leukocytes, being an important factor in infectious diseases. Also, this study reports the frequency of CCR5Δ32 in women from the state of Acre, located in the Brazilian Amazon, a region where the Δ32 allele and malaria are observed concurrently. We found allele frequencies of 2.88% in Plasmodium-infected women and of 1.04% among uninfected women. The low Δ32 allele frequencies observed in Acre, compared to other Brazilian regions, could be a reflection of the particular ancestry patterns in current Amazonian populations influenced by past European colonization.

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Abstract Satellite DNAs are abundant components of the genomes of many eukaryotic species. They are composed of long and rather homogeneous arrays of tandem repeats that are typically located at the heterochromatin. They may contribute to the structural organization and regulatory dynamics of the genome. However, they evolve rapidly between species and changes in their sequences and abundance may contribute to the process of speciation. Here we used Illumina genomic sequencing raw data and the TAREAN bioinformatic tool to identify and characterize the most abundant satDNAs present in two sister species from the buzzatii cluster (repleta group): D. gouveai and D. borborema. We found five satDNAs, two are reported in these species for the first time (CDSTR138 and CDSTR230), two have already been reported (pBuM and DBC-150) and one is described here for the first time (CDSTR8). These satDNAs differ in both quantitative and qualitative terms between the two species. Most notoriously, the pBuM satDNA was found in D. gouveai, but it is virtually absent in D. borborema, despite their relatively recent divergence (<0.5My). We mapped these satDNAs to the chromosomes and found that most of them are located near or at the centromeres, with overlapping distribution in several locations.

Resumen en Inglés:

Abstract The selection of high feed efficiency (FE) animals impacts sustainability and profitability of beef and dairy cattle production systems. An approach to investigate the mechanisms of FE involves analyzing gene expression profile in liver. This study used residual feed intake as a metric of FE to select 10 Gir x Holstein crossbred cows (Girolando F1) divided into high (HE) and low (LE) FE groups. Hepatic biopsies were used for differential gene expression investigation using RNA-seq analyses which revealed 20,787 known genes mapped accordingly to the bovine reference genome. The comparison of HE and LE revealed 149 significantly differentially expressed genes (DEG), 41 up-regulated, and 108 down-regulated in the LE group. Among DEG, some stood out as potential candidate genes, including DLK1, CACNG4, SLC2A12, SLC26A4, DUOX2, and DUOXA2. Functional enrichment analyses showed pathways that potentially influence FE, such as the negative regulation of leukocyte migration, regulation of calcium channel activity, negative regulation of cell migration and adhesion, extracellular matrix (ECM) organization, and thyroid hormone synthesis. ECM composition and immune system roles were also highlighted. These results could help understanding the mechanisms related to FE in dairy cattle and the development of selection strategies to improve this trait.

Resumen en Inglés:

Abstract Evolutionary analyses of mitogenomes have provided insights into species evolution and conservation. Studies on snakes revealed a higher diversity especially involving variation in tRNA clusters. However, despite the increase in assemblies in databases, the available information for Brazilian species remains scarce in mitogenomic surveys. Based on this, we sequenced and provided the first description of the mitogenome of Bothrops insularis, a critically endangered taxon. We also used the B. insularis assembly and 128 molecules available in databases up to March 2022 to explore rearrangements and evolution of the mtDNA under a phylogenomic perspective. Comparative analyses revealed 24 mitotypes due to rearrangements within four tRNA clusters and within control regions. Mitotype 1 (M1) and Mitotype 2 (M2) are restricted to Scolecophidia and M3 is highly distributed within Alethinophidia. In addition, the M3 is suggested as the most likely ancestral mitotype during the mitogenome evolution. Regarding Bothrops, we recovered the same mitotype for B. jararaca and B. insularis, which structure differs from other Bothrops species. Nucleotide variation suggests 1.5% divergence between B. jararaca and B. insularis. Therefore, we suggest that B. insularis can be considered an evolutionary significant unit, and the data generated herein can be valuable for insights into genome evolution and conservation.

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Abstract Stingless bees like Melipona interrupta play vital ecological roles and rely on diverse microbial communities in their larval food. This study investigated the impact of fungal diversity on larval development and caste differentiation. Fungi isolated from brood cell food were identified morphologically and molecularly, with Fomitopsis sp. and Zygosaccharomyces sp. showing high prevalence. Artificial larval rearing was conducted using sterilized and non-sterilized food inoculated with these fungi. Zygosaccharomyces sp. significantly enhanced survival rates and queen production, achieving results comparable to natural conditions, while Fomitopsis sp. had a modest effect. Statistical analyses confirmed significant associations between fungal treatments and larval outcomes. These findings underscore the functional role of fungi in M. interrupta larval nutrition and offer potential applications in sustainable meliponiculture.

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Abstract Paracidovorax citrulli is the causative agent of bacterial fruit blotch in melons and watermelons. This study used comparative genomic approaches of 17 Brazilian P. citrulli strains obtained from melons and watermelons to classify them into groups I and II and try to understand their genomic differences. The genomes of P. citrulli presented general characteristics similar to those shown for the genomes of the type strain of P. citrulli and reference strains of groups I and II. A phylogenomic analysis revealed two distinct groups of P. citrulli, in which most Brazilian P. citrulli strains were grouped with the strain representing group I. CRISPR-Cas analysis revealed the presence of two proteins, Cas3 and Cas10, in all Brazilian P. citrulli genomes. In addition, we observed the presence of two plasmids (pAMC6 and pAC53) in three Brazilian P. citrulli strains, all closely related to group I. The prediction of effector proteins revealed the XopE/AvrPphe protein as a differential between the strains of groups I and II. The present study will contribute to a more detailed understanding of aspects of host-pathogen interactions and will help improve the detection of strains from these groups, thus elucidating the population dynamics of Brazilian strains of P. citrulli.

Resumen en Inglés:

Abstract Bees are fundamental factors in ecology and agriculture due to their ecosystem services as pollinators, including many important crops. Because of its ecological significance and value to humans, the honey bee, Apis mellifera, was one of the earliest insect species targeted for genome sequencing, and over the last decades, many other species of social bees, including practically all species comprising the genus Apis and dozens of bumble bee species (Bombini) have complete genome assemblies deposited in public databases. The largest clade of the social bees, the stingless bees (Meliponini), is, however, strongly underrepresented. To date, only five genomes for species of three genera have been released for the New World stingless bees, which comprise over 400 species distributed in 32 genera. Different from the honey bee, these species are native to the Neotropics, being important pollinators of many native plants and cultivars, including greenhouse cultures. We present here the genome assemblies for two species of the genus Scaptotrigona, one of the largest genera among the stingless bees in Brazil. The new datasets are highly complete and, as shown in our phylogenomics analysis, these genomes provide robust support for the clades of the corbiculate bees and their evolutionary history.

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Abstract The oxytocinergic system plays a crucial role in regulating physiological and behavioral processes, making it a key component of neurobiology in both humans and animals. This study utilizes computational modeling to explore the interaction between G protein-coupled receptors (GPCRs) and the Homo sapiens neurohormone oxytocin (Leu8OT), as well as, for the first time, the Pro8OT variant found in Callithrix jacchus and other New World monkeys. Pro8OT has been previously recognized for its functional and evolutionary significance. We performed homology modeling of receptors (OTR, VTR1a, and VTR1b) in both human and marmoset species. Additionally, cholesterol’s role in modulating receptor binding and stability was evaluated in our simulations. Our findings suggest a general pattern across primates, preserving the essential pleiotropic functions of the oxytocinergic system in regulating physiology and behavior, which align with the shared evolutionary framework of species within this order. However, some specific variations were observed, as Pro8OT exhibits distinct binding affinities and unique receptor interactions. Comparative analysis of human and marmoset OT-OTR complexes indicate a more stable and favorable binding environment in marmoset systems, suggesting species-specific adaptations. These results enhance our understanding of the oxytocinergic system, bridging computational models with evolutionary neurobiology and providing insights for future functional studies.