Pterygoplichthys is a genus of related suckermouth armoured catfish native to South America that has invaded tropical and subtropical regions worldwide. Physiological features, including an augmented resistance to organic xenobiotics, may have aided their settlement in foreign habitats. The liver transcriptome of Pterygoplichthys anisitsi was sequenced and used to characterize the diversity of mRNAs potentially involved in the responses to natural and anthropogenic chemicals. In total, 66,642 transcripts were assembled. Among the identified defensome genes, cytochromes P450 (CYP) were the most abundant, followed by nuclear receptors (NR), sulfotransferases (SULT) and ATP binding cassette transporters (ABC). A novel expansion in the CYP2Y subfamily was identified, as well as an independent expansion of the CYP2AAs. Two expansions were also observed among SULT1. Thirty-two transcripts were classified into twelve subfamilies of NR, while 21 encoded ABC transporters. The diversity of defensome transcripts sequenced herein could contribute to this species resistance to organic xenobiotics.
Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.
-Genetic differentiation among nine populations of the endemic lizard Lacerta dugesii Milne-Edwards 1829 (Lacertidae) from four groups of islands constituting the Archipelago of Madeira, was investigated by protein electrophoresis at 23 enzyme loci. Among twenty polymorphic loci, the total genetic diversity was due primarily to intra-population variation. The allele and genotypic frequencies among populations showed some heterogeneity, allowing the species to present a structuring pattern compatible with their geographical clustering. Some evidence suggests that selection acting on some loci in different ecological conditions may be responsible for the clustering of the populations studied. There was no apparent isolation effect expected under an "island" model of population divergence, and no correlation was found between genetic and geographic distances among populations. Morphological variation of the proposed three L. dugesii subspecies is not congruent with the allozyme analysis. This most probably suggests a rapid colonization of the islands followed by a strong effect of selection operating over the morphological characters used to define the subspecies.Lacerta dugesii / allozymes / morphology / geographical population structure * Correspondence and reprints E-mail: brehm@uma.pt 672 A. Brehm et al.
HIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Understanding the distribution of viral variants and their temporal dynamics can help to design vaccines and monitor changes in viral transmission patterns. Brazil has one of the largest HIV-1 epidemics in the western-world and the molecular features of the virus circulating in the country are still not completely known. Over 50,000 partial HIV-1 genomes sampled between 2008 and 2017 by the Brazilian genotyping network (RENAGENO) were analyzed. Sequences were filtered by quality, duplicate sequences per patient were removed and subtyping was performed with online tools and molecular phylogeny. Association between patients’ demographic data and subtypes were performed by calculating the relative risk in a multinomial analysis and trends in subtype prevalence were tested by Pearson correlation. HIV-1B was found to be the most prevalent subtype throughout the country except in the south, where HIV-1C prevails. An increasing trend in the proportion of HIV-1C and F1 was observed in several regions of the country, while HIV-1B tended to decrease. Men and highly educated individuals were more frequently infected by HIV-1B and non-B variants were more prevalent among women with lower education. Our results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks. Historical events could explain a preferential circulation of HIV-1B among men who have sex with men (MSM) and non-B variants among heterosexual individuals. In view of an increasing male/female ratio of AIDS cases in Brazil in the last 10–15 years, the decrease of HIV-1B prevalence is surprising and suggests a greater penetrance of non-B subtypes in MSM transmission chains.
-Genetic differentiation among nine populations of the endemic lizard Lacerta dugesii Milne-Edwards 1829 (Lacertidae) from four groups of islands constituting the Archipelago of Madeira, was investigated by protein electrophoresis at 23 enzyme loci. Among twenty polymorphic loci, the total genetic diversity was due primarily to intra-population variation. The allele and genotypic frequencies among populations showed some heterogeneity, allowing the species to present a structuring pattern compatible with their geographical clustering. Some evidence suggests that selection acting on some loci in different ecological conditions may be responsible for the clustering of the populations studied. There was no apparent isolation effect expected under an "island" model of population divergence, and no correlation was found between genetic and geographic distances among populations. Morphological variation of the proposed three L. dugesii subspecies is not congruent with the allozyme analysis. This most probably suggests a rapid colonization of the islands followed by a strong effect of selection operating over the morphological characters used to define the subspecies.Lacerta dugesii / allozymes / morphology / geographical population structure * Correspondence and reprints E-mail: brehm@uma.pt 672 A. Brehm et al.
The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008–2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15–24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil.
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