Comparative assessment of genotyping-by-sequencing and whole-exome sequencing for estimating genetic diversity and geographic structure in small sample sizes: insights from wild jaguar populations.

Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.

Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats.

Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here, we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological, and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that divergent ecological strategies are reflected in genomic features, for example a generalist species shows historically larger effective population size and higher heterozygosity than habitat specialists. The demographic history of these cats seems to have been jointly driven by climate fluctuations and habitat specialization, with different ecological adaptations leading to distinct trajectories. Finally, a gene involved in vertebrate retinal neurogenesis (POU4F2) was found to be under positive selection in the margay, a cat with notoriously large eyes that are likely associated with its nocturnal and arboreal specializations.

Introduction of SARS-CoV-2 C.37 (WHO VOI lambda) in the Sao Paulo State, Southeast Brazil.

The Lambda variants of interest (VOI) (C37/GR/452Q.V1/21G) was initially reported in Lima, Peru but has gained rapid dissemination through other Latin American countries. Nevertheless, the dissemination and molecular epidemiology of the Lambda VOI in Brazil is unknown apart from a single case report. In this respect, we characterized the circulation of the SARS-CoV-2 Lambda VOI (C37/GR/452Q.V1/21G) in Sao Paulo State, Brazil. From March to June 2021, we identified seven Lambda isolates in a set of approximately 8000 newly sequenced genomes of the Network for Pandemic Alert of Emerging SARS-CoV-2 variants from Sao Paulo State. Interestingly, in three of the positive patients, the Lambda VOI infection was probably related to a contact transmission. These individuals were fully vaccinated to COVID-19 and presented mild symptoms. The remaining positive for Lambda VOI individuals showed different levels of COVID-19 symptoms and one of them needed hospitalization (score 5, WHO). In our study, we present a low level of Lambda VOI circulation in the Sao Paulo State. This reinforces the essential role of molecular surveillance for the effective SARS-CoV-2 pandemic response, especially in regard to circulating variants.

Immune status, well-being and gut microbiota in military supplemented with synbiotic ice cream and submitted to field training: a randomised clinical trial.

Strenuous physical activity, sleep deprivation and psychological stress are common features of military field training. The present study aimed to evaluate the effects of supplementation with a synbiotic ice cream on salivary IgA, gastrointestinal symptoms, well-being indicators and gut microbiota in young military participants undergoing field training. Sixty-five military completed the study: one group was supplemented for 30 d with synbiotic ice cream containing: 2·1 × 108 CFU/g for Lactobacillus acidophilus LA-5 and 2·7 × 109 CFU/g for Bifidobacterium animalis BB-12 and 2·3 g of inulin in the 60 g of ice cream at manufacture, and the other with a placebo ice cream. Volunteers were evaluated at pre-supplementation (baseline), post-supplementation and after a 5-d military training. Bifidobacterium and Lactobacillus genera were measured in stool samples and both showed a higher differential abundance post-supplementation and training. Salivary IgA and gastrointestinal symptoms decreased at post-training in both groups (P < 0·05; main effect of time); however, supplementation with synbiotic did not mitigate this effect. Tenseness and sleepiness were decreased in the synbiotic-treated group, but not in the placebo group at post-military training (P = 0·01 and 0·009, respectively; group × time effect). The other well-being indicators were not affected by the synbiotic supplementation. In conclusion, 30 d of synbiotic ice cream supplementation containing inulin, L. acidophilus LA-5 and B. animalis BB-12 favourably modulated gut microbiota and improved tenseness and sleepiness in healthy young military undergoing a 5-d field training. These improvements may be relevant to this population as they may influence the decision-making process in an environment of high physical and psychological stress.

Role of neuroendocrine modulation and biochemistry in the sepsis in Piaractus mesopotamicus.

Sepsis is a systemic process with multifactorial pathophysiology that affects most animal species. It is responsible for high rates of morbidity and mortality. This work aimed to study the biochemical and neuroendocrine changes of the sepsis process in Piaractus mesopotamicus after Aeromonas hydrophila inoculation analyzing changes in blood leukocyte and differences in neuroendocrine-biochemical modulation using RNA-seq. Fish showed hypercortisolemia, inhibition of glucose absorption, followed by hypocortisolemia and then hyperglycemia. Thyroid hormones (T3 and T4) showed immediate decrease in serum and T4 increased 6 h post-inoculation (HPI). Sepsis-induced hormonal alterations triggered changes in the metabolic pathways increasing protein and lipid catabolism, use of transient anaerobic glycolysis and liver injury. A reference transcriptome was constructed based on blood leukocytes from P. mesopotamicus. The assembly resulted in total 266,272 contigs with a N50 of 2786 bp. There was a reorganization of plasma membrane of leukocytes at the beginning of the septic process with increased expression of neuroendocrine receptors and with continuous flow of neurotransmitters, hormones and solutes with compensatory regulation at 6 HPI. Three and nine HPI seemed to be critical, the expression of a number of transcription factors was increased, including the modulatory DEGs related to glucocorticoid and thyroid hormones induced and suppressed (FDR < 0.05). Neuroendocrine modulation can regulate leukocytes and biochemical parameters of peripheral blood, being important sources for the study of the pathophysiology of sepsis. These finding highlights the importance of further studies focusing on biochemical-neuroendocrine changes in blood leukocytes and systemic sepsis.

Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens.

BACKGROUND: Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs. RESULTS: Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes. CONCLUSIONS: The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.

Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin.

BACKGROUND: Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation. Skin biopsies from four-times-artificially infested R (n = 20) and S (n = 19) hosts, obtained before the first and 24 h after the fourth tick infestation were submitted to RNA-Sequencing. Differential gene expression, functional enrichment, and network analysis were performed to identify genetic pathways and transcription factors (TFs) affecting host resistance. RESULTS: Intergroup comparisons of hosts before (Rpre vs. Spre) and after (Rpost vs. Spost) tick infestation found 51 differentially expressed genes (DEGs), of which almost all presented high variation (TopDEGs), and 38 were redundant genes. Gene expression was consistently different between R and S hosts, suggesting the existence of specific anti-tick mechanisms. In the intragroup comparisons, Rpost vs. Rpre and Spost vs. Spre, we found more than two thousand DEGs in response to tick infestation in both resistance groups. Redundant and non-redundant TopDEGs with potential anti-tick functions suggested a role in the development of different levels of resistance within the same breed. Leukocyte chemotaxis was over-represented in both hosts, whereas skin degradation and remodeling were only found in TopDEGs from R hosts. Also, these genes indicated the participation of cytokines, such as IL6 and IL22, and the activation of Wingless (WNT)-signaling pathway. A central gene of this pathway, WNT7A, was consistently modulated when hosts were compared. Moreover, the findings based on a genome-wide association study (GWAS) corroborate the prediction of the WNT-signaling pathway as a candidate mechanism of resistance. The regulation of immune response was the most relevant pathway predicted for S hosts. Members of Ap1 and NF-kB families were the most relevant TFs predicted for R and S, respectively. CONCLUSION: This work provides indications of genetic mechanisms presented by Braford cattle with different levels of resistance in response to tick infestation, contributing to the search of candidate genes for tick resistance in bovine.

Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle.

BACKGROUND: Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer's payment. The selection of these traits has not been satisfactory since they are expressed later in the animal's life and multigene regulated. So, next-generation technologies have been applied in this area to improve animal's selection and better understand the molecular mechanisms involved in the development of these traits. Correlation network analysis, performed by tools like WGCNA (Weighted Correlation Network Analysis), has been used to explore gene-gene interactions and gene-phenotype correlations. Thus, this study aimed to identify putative candidate genes and metabolic pathways that regulate REA and BFT by constructing a gene co-expression network using WGCNA and RNA sequencing data, to better understand genetic and molecular variations behind these complex traits in Nelore cattle. RESULTS: The gene co-expression network analysis, using WGCNA, were built using RNA-sequencing data normalized by transcript per million (TPM) from 43 Nelore steers. Forty-six gene clusters were constructed, between them, three were positively correlated (p-value< 0.1) to the BFT (Green Yellow, Ivory, and Light Yellow modules) and, one cluster was negatively correlated (p-value< 0.1) with REA (Salmon module). The enrichment analysis performed by DAVID and WebGestalt (FDR 5%) identified eight Gene Ontology (GO) terms and three KEGG pathways in the Green Yellow module, mostly associated with immune response and inflammatory mechanisms. The enrichment of the Salmon module demonstrated 19 GO terms and 21 KEGG pathways, related to muscle energy metabolism, lipid metabolism, muscle degradation, and oxidative stress diseases. The Ivory and Light yellow modules have not shown significant results in the enrichment analysis. CONCLUSION: With this study, we verified that inflammation and immune response pathways modulate the BFT trait. Energy and lipid metabolism pathways, highlighting fatty acid metabolism, were the central pathways associated with REA. Some genes, as RSAD2, EIF2AK2, ACAT1, and ACSL1 were considered as putative candidate related to these traits. Altogether these results allow us to a better comprehension of the molecular mechanisms that lead to muscle and fat deposition in bovine.

MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness.

BACKGROUND: MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs are involved in the regulation of many processes including cell proliferation, differentiation, neurogenesis, angiogenesis, and apoptosis. Beef tenderness is an organoleptic characteristic of great influence in the acceptance of meat by consumers. Previous studies have shown that collagen level, marbling, apoptosis and proteolysis are among the many factors that affect beef tenderness. Considering that miRNAs can modulate gene expression, this study was designed to identify differentially expressed miRNAs that could be modulating biological processes involved with beef tenderness. RESULTS: Deep sequence analysis of miRNA libraries from longissimus thoracis muscle allowed the identification of 42 novel and 308 known miRNAs. Among the known miRNAs, seven were specifically expressed in skeletal muscle. Differential expression analysis between animals with high (H) and low (L) estimated breeding values for shear force (EBVSF) revealed bta-mir-182 and bta-mir-183 are up-regulated (q value < 0.05) in animals with L EBVSF, and bta-mir-338 is up-regulated in animals with H EBVSF. The number of bovine predicted targets for bta-mir-182, bta-mir-183 and bta-mir-338 were 811, 281 and 222, respectively, which correspond to 1204 unique target genes. Among these, four of them, MEF2C, MAP3K2, MTDH and TNRC6B were common targets of the three differentially expressed miRNAs. The functional analysis identified important pathways related to tenderness such as apoptosis and the calpain-calpastatin system. CONCLUSION: The results obtained indicate the importance of miRNAs in the regulatory mechanisms that influence muscle proteolysis and meat tenderness and contribute to our better understanding of the role of miRNAs in biological processes associated with beef tenderness.

Impact of exposure time to harsh environments on physiology, mortality, and thermal comfort of day-old chickens in a simulated condition of transport.

The aim of this study was to assess the variation of physiological responses and mortality of day-old chicks subjected to different thermal conditions and exposure times during simulated transport. For this purpose, day-old chicks (n = 900) were used and subjected to simulated conditions of transport in a climate chamber. The experimental design was a completely randomized block design, with the structure of the treatments in a 3 × 3 factorial scheme (thermal ranges and time intervals) and each level of containers considered a block. The physiological variables used in this trial were body weight, respiratory rate, cloacal temperature, average surface temperature, and gene expression of heat shock protein (HSP70). Regarding body weight, a small variation was observed between treatments (P > 0.05). The animals subjected to the heat treatment exhibited respiratory rates above 100 movements per minute (P < 0.05), average cloacal temperatures above 44.7 °C, surface temperatures above the comfort zone (greater than 39.6 °C; P < 0.05), and increased gene expression of HSP70 (P < 0.001), especially after 3 initial hours of exposure. In addition, the heat treatment lead to increased mortality of the animals (over 6%). Also in the cold treatment, despite the absence of mortality, the animals showed hypothermia from 3 h of exposure, based on the results of the average surface (28 °C) and cloacal temperatures (39.6 °C; P < 0.05). In this way, the results imply that the effects of thermal stress caused by heat as well as by cold in a simulated transport condition are increased when traveling for more than 3 h, indicating a trend of rising mortality after long-term transportation of day-old chickens.