Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology.

During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.

Performance of intron 7 of the ß-fibrinogen gene for phylogenetic analysis: An example using gladiator frogs, Boana Gray, 1825 (Anura, Hylidae, Cophomantinae).

Boana, the third largest genus of Hylinae, has cryptic morphological species. The potential applicability of b-fibrinogen intron 7 - FGBI7 is explored to propose a robust phylogeny of Boana. The phylogenetic potential of FGBI7 was evaluated using maximum parsimony, MrBayes, and maximum likelihood analysis. Comparison of polymorphic sites and topologies obtained with concatenated analysis of FGBI7 and other nuclear genes (CXCR4, CXCR4, RHO, SIAH1, TYR, and 28S) allowed evaluation of the phylogenetic signal of FGBI7. Mean evolutionary rates were calculated using the sequences of the mitochondrial genes ND1 and CYTB available for Boana in GenBank. Dating of Boana and some of its groups was performed using the RelTime method with secondary calibration. FGBI7 analysis revealed high values at informative sites for parsimony. The absolute values of the mean evolutionary rate were higher for mitochondrial genes than for FGBI7. Dating of congruent Boana groups for ND1, CYTB, and FGBI7 revealed closer values between mitochondrial genes and slightly different values from those of FGBI7. Divergence times of basal groups tended to be overestimated when mtDNA was used and were more accurate when nDNA was used. Although there is evidence of phylogenetic potential arising from concatenation of specific genes, FGBI7 provides well-resolved independent gene trees. These results lead to a paradigm for linking data in phylogenomics that focuses on the uniqueness of species histories and ignores the multiplicities of individual gene histories.

Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae.

MAIN CONCLUSION: Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.

Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita.

Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.

Role of viral load in Hepatitis B virus evolution in persistently normal ALT chronically infected patients.

Chronic HBV infection has been associated with severe liver disease although most of them do not progress to this stage. Even though low replicative carriers form the largest group of HBV chronically infected patients, there is a paucity of longitudinal studies to evaluate the molecular evolution of the whole genome in this subset of patients. In this study, longitudinal samples from 10 patients with persistently normal ALT levels were collected. HBV full-length genome sequences were obtained from 3 samples per patient (baseline, 5 and 10-years of follow-up). Patients were grouped according to HBV-DNA level into <103 IU/ml (group A) or > 103 IU/ml (group B). The substitution rate was inversely related with HBV-DNA levels. Moreover, the rate in the 10-year follow-up was significantly higher in group A (6.9 × 10-4 ±â€¯1.3 × 10-4) than group B (2.7 × 10-4 ±â€¯7.4 × 10-5 substitution/site/year, p < .001). Most of the substitutions were in the Core region and the majority were non-synonymous changes. The rate of nucleotide substitution was inversely related to HBV-DNA levels, highlighting the role of viral load in the HBV intra-host dynamics, even in low replicative state patients. Moreover, the difference in the substitution rate between the analysed groups was mainly consequence of substitutions restricted to the Core region, particularly in the simple coding region and antigenic epitopes, which suggest that the immune pressure drives the different evolutionary behaviour of groups.

Corn silage supplementation for sheep eating annual ryegrass / Suplementação com silagem de milho para ovinos ingerindo azevém anual

Food intake is determinant in the production process and can be modified when more than one type of forage is supplied in the diet. The aim of this study was to evaluate the effects of supplementation with corn silage + soybean meal (9:1 based on DM) in the proportion of 10 g DM kg−1 live weight (LW) for lambs receiving pre-dried ryegrass (Lolium multiflorum Lam) in two forage supply levels: ad libitum or restricted (60% of the consumption ad libitum). Eight castrated male sheep crosses Texel × Criollo (average of 31.5 ± 2.2 kg LW) were used in an experimental design of 4 × 4 Latin square. Each experimental period was performed for 19 days, with 14 days for adaptation and 5 days for collections. Animals were fed three times a day (08h00, 11h30, and 16h30). Supplemented animals received corn silage at 08h00 and ryegrass silage at 11h30 and 16h30. The substitution rates (kg DM consumed forage per kg DM consumed silage) were 0.93 for animals with a supply of ryegrass ad libitum and zero for those receiving the same in a restricted amount. The digestible OM (DOM) intake and nitrogen retention did not vary with supplementation in animals that received ryegrass ad libitum but increased in those with restricted supply. However, animals with restricted supply and supplemented had a less digestible OM intake and nitrogen retention than the average of those that received ryegrass ad libitum. Organic matter digestibility and efficiency of microbial protein synthesis were not affected by treatments, but the digestibility of NDF and ADF was lower in supplemented animals when compared to those non-supplemented and in restricted supply when compared to consumption ad libitum. Even with supplementation, feed restriction of base forage can limit the daily intake of digestible OM and the daily retention of N in sheep.(AU)

O consumo é determinante no processo produtivo e pode ser modificado quando é fornecido mais de um tipo de forragem na dieta. O objetivo deste trabalho foi avaliar os efeitos da suplementação com silagem de milho + farelo de soja (9:1 com base na MS) na proporção de 10 g MS kg-1 PV, para cordeiros recebendo pré-secado de azevém (Lolium multiflorum Lam) em duas ofertas de forragem: à vontade ou restrito (60% do consumo à vontade). Oito ovinos machos castrados cruza Texel × Crioula (média de 31,5 ± 2,2 kg de peso vivo, PV) foram usados em um delineamento experimental em Quadrado Latino 4 × 4. Cada período experimental foi realizado durante 19 dias, com 14 de adaptação e 5 de coletas. Os animais foram alimentados três vezes ao dia (08h00, 11h30 e 16h30). Animais suplementados receberam silagem de milho às 08h00 h e silagem de azevém às 11h30 e as 16h30 . As taxas de substituição (kg MS forragem consumida por kg MS silagem consumida) foram 0,93 nos animais com oferta de azevém à vontade e zero nos que recebiam o mesmo em quantidade restrita. O consumo de MO digestível e a retenção nitrogenada não variaram com a suplementação nos animais que receberam o azevém à vontade, mas aumentaram nos com oferta restrita. Contudo, os animais com oferta restrita e suplementados tiveram menor consumo de MOD e retenção nitrogenada que a média dos que receberam azevém à vontade. A digestibilidade da MO e a eficiência de síntese de proteína microbiana não foram afetadas pelos tratamentos, mas a digestibilidade da FDN e FDA foi menor nos animais suplementados em comparação aos não suplementados e nos de oferta restrita em comparação ao consumo à vontade. Mesmo com a suplementação, a restrição alimentar da forragem de base pode limitar a ingestão diária de MO digestível e a retenção diária de N em ovinos.(AU)

Corn silage supplementation for sheep eating annual ryegrass / Suplementação com silagem de milho para ovinos ingerindo azevém anual

Food intake is determinant in the production process and can be modified when more than one type of forage is supplied in the diet. The aim of this study was to evaluate the effects of supplementation with corn silage + soybean meal (9:1 based on DM) in the proportion of 10 g DM kg−1 live weight (LW) for lambs receiving pre-dried ryegrass (Lolium multiflorum Lam) in two forage supply levels: ad libitum or restricted (60% of the consumption ad libitum). Eight castrated male sheep crosses Texel × Criollo (average of 31.5 ± 2.2 kg LW) were used in an experimental design of 4 × 4 Latin square. Each experimental period was performed for 19 days, with 14 days for adaptation and 5 days for collections. Animals were fed three times a day (08h00, 11h30, and 16h30). Supplemented animals received corn silage at 08h00 and ryegrass silage at 11h30 and 16h30. The substitution rates (kg DM consumed forage per kg DM consumed silage) were 0.93 for animals with a supply of ryegrass ad libitum and zero for those receiving the same in a restricted amount. The digestible OM (DOM) intake and nitrogen retention did not vary with supplementation in animals that received ryegrass ad libitum but increased in those with restricted supply. However, animals with restricted supply and supplemented had a less digestible OM intake and nitrogen retention than the average of those that received ryegrass ad libitum. Organic matter digestibility and efficiency of microbial protein synthesis were not affected by treatments, but the digestibility of NDF and ADF was lower in supplemented animals when compared to those non-supplemented and in restricted supply when compared to consumption ad libitum. Even with supplementation, feed restriction of base forage can limit the daily intake of digestible OM and the daily retention of N in sheep.

O consumo é determinante no processo produtivo e pode ser modificado quando é fornecido mais de um tipo de forragem na dieta. O objetivo deste trabalho foi avaliar os efeitos da suplementação com silagem de milho + farelo de soja (9:1 com base na MS) na proporção de 10 g MS kg-1 PV, para cordeiros recebendo pré-secado de azevém (Lolium multiflorum Lam) em duas ofertas de forragem: à vontade ou restrito (60% do consumo à vontade). Oito ovinos machos castrados cruza Texel × Crioula (média de 31,5 ± 2,2 kg de peso vivo, PV) foram usados em um delineamento experimental em Quadrado Latino 4 × 4. Cada período experimental foi realizado durante 19 dias, com 14 de adaptação e 5 de coletas. Os animais foram alimentados três vezes ao dia (08h00, 11h30 e 16h30). Animais suplementados receberam silagem de milho às 08h00 h e silagem de azevém às 11h30 e as 16h30 . As taxas de substituição (kg MS forragem consumida por kg MS silagem consumida) foram 0,93 nos animais com oferta de azevém à vontade e zero nos que recebiam o mesmo em quantidade restrita. O consumo de MO digestível e a retenção nitrogenada não variaram com a suplementação nos animais que receberam o azevém à vontade, mas aumentaram nos com oferta restrita. Contudo, os animais com oferta restrita e suplementados tiveram menor consumo de MOD e retenção nitrogenada que a média dos que receberam azevém à vontade. A digestibilidade da MO e a eficiência de síntese de proteína microbiana não foram afetadas pelos tratamentos, mas a digestibilidade da FDN e FDA foi menor nos animais suplementados em comparação aos não suplementados e nos de oferta restrita em comparação ao consumo à vontade. Mesmo com a suplementação, a restrição alimentar da forragem de base pode limitar a ingestão diária de MO digestível e a retenção diária de N em ovinos.

Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae.

We surveyed the substitution patterns in the ent-kaurenoic acid oxidase (KAO) gene in 11 species of Oryzeae with an outgroup in the Ehrhartoidaea. The synonymous and non-synonymous substitution rates showed a high positive correlation with each other, but were negatively correlated with codon usage bias and GC content at third codon positions. The substitution rate was heterogenous among lineages. Likelihood-ratio tests showed that the non-synonymous/synonymous rate ratio changed significantly among lineages. Site-specific models provided no evidence for positive selection of particular amino acid sites in any codon of the KAO gene. This finding suggested that the significant rate heterogeneity among some lineages may have been caused by variability in the relaxation of the selective constraint among lineages or by neutral processes.

Comparative analysis of human masculinity

To study rapidly evolving male specific Y (MSY) genes we retrieved and analyzed nine such genes. VCY, HSFY and RBMY were found to have functional X gametologs, but the rest did not. Using chimpanzee orthologs for XKRY, CDY, HSFY, PRY, and TSPY, the average silent substitution is estimated as 0.017 +/- 0.006/site and the substitution rate is 1.42 x 10(-9)/site/year. Except for VCY, all other loci possess two or more pseudogenes on the Y chromosome. Sequence differences from functional genes show that BPY2, DAZ, XKRY, and RBMY each have one pseudogene for each one that is human specific, while others were generated well before the human-chimpanzee split, by means of duplication, retro-transposition or translocation. Some functional MSY gene duplication of VCY, CDY and HSFY, as well as X-linked VCX and HSFX duplication, occurred in the lineage leading to humans; these duplicates have accumulated nucleotide substitutions that permit their identification.