Occurrence, distribution, and genetic diversity of faba bean viruses in China.

With worldwide cultivation, the faba bean (Vicia faba L.) stands as one of the most vital cool-season legume crops, serving as a major component of food security. China leads global faba bean production in terms of both total planting area and yield, with major production hubs in Yunnan, Sichuan, Jiangsu, and Gansu provinces. The faba bean viruses have caused serious yield losses in these production areas, but previous researches have not comprehensively investigated this issue. In this study, we collected 287 faba bean samples over three consecutive years from eight provinces/municipalities of China. We employed small RNA sequencing, RT-PCR, DNA sequencing, and phylogenetic analysis to detect the presence of viruses and examine their incidence, distribution, and genetic diversity. We identified a total of nine distinct viruses: bean yellow mosaic virus (BYMV, Potyvirus), milk vetch dwarf virus (MDV, Nanovirus), vicia cryptic virus (VCV, Alphapartitivirus), bean common mosaic virus (BCMV, Potyvirus), beet western yellows virus (BWYV, Polerovirus), broad bean wilt virus (BBWV, Fabavirus), soybean mosaic virus (SMV, Potyvirus), pea seed-borne mosaic virus (PSbMV, Potyvirus), and cucumber mosaic virus (CMV, Cucumovirus). BYMV was the predominant virus found during our sampling, followed by MDV and VCV. This study marks the first reported detection of BCMV in Chinese faba bean fields. Except for several isolates from Gansu and Yunnan provinces, our sequence analysis revealed that the majority of BYMV isolates contain highly conserved nucleotide sequences of coat protein (CP). Amino acid sequence alignment indicates that there is a conserved NAG motif at the N-terminal region of BYMV CP, which is considered important for aphid transmission. Our findings not only highlight the presence and diversity of pathogenic viruses in Chinese faba bean production, but also provide target pathogens for future antiviral resource screening and a basis for antiviral breeding.

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China.

Introduction: The Wuzhishan ant (MY) chicken exhibits significant differences from other chicken breeds. However, the molecular genetic relationship between the MY breed and other chicken breeds has not been assessed. Methods: Whole-genome resequencing was used to compare genetic diversity, nucleotide diversity, the fixation index, the linkage disequilibrium coefficient, and phylogenetic tree relationships between the MY breed and the Wenchang (WC), Danzhou (DZ), Bawangling (BW), and Longsheng Feng (LF) breeds. Results: A total of 21,586,378 singlenucleotide polymorphisms and 4,253,341 insertions/deletions were screened out among the five breeds. The MY breed had the second highest genomic genetic diversity and nucleotide diversity and the lowest LD coefficient among the five breeds. Moreover, the phylogenetic tree analysis showed that individual birds of each breed clustered together with those of their respective breeds. Discussion: Our data indicated that the MY breed is distinct from the other breeds and can be considered a new genetic resource.

Danzhou chicken: a unique genetic resource revealed by genome-wide resequencing data.

Danzhou chicken (DZ) is a local breed in China noted for its strong adaptability, roughage resistance, strong wildness, and delicious taste, thus containing important genetic resources. In this study, genome re-sequencing data was generated from 200 DZ chickens. Combined with previously generated data from 72 additional chickens across six other exotic and local breeds, these data were used to systematically evaluate the germplasm characteristics of DZ chickens from a genomic perspective. Unlike exotic breeds, both DZ and southern local chicken varieties exhibited high genetic diversity, and the genetic distance between DZ and southern local chickens was smaller than the genetic distance between DZ and exotic chickens. A reconstructed Neighbor-Joining phylogenetic tree indicated that all sampled populations clustered into single independent populations, with DZ chickens showing clear evidence of intra-population differentiation, forming 2 subpopulations. Principal component analysis and ADMIXTURE analysis showed that DZ was significantly different from other breeds. These results indicate that DZ is a unique genetic resource that is different from other southern native and exotic chickens. The results of the study will improve our understanding of the genetic structure and current status of the DZ breed, which is of great significance in promoting the conservation of genetic resources of DZ chickens and fostering breed innovations and genetic improvement.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China.

BACKGROUND: Wheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms. RESULTS: To understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation. CONCLUSIONS: A core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

The Diversity of CYP2C19 Polymorphisms in the Thai Population: Implications for Precision Medicine.

Introduction: CYP2C19 plays a major role in the metabolism of various drugs. The most common genetic variants were the CYP2C19*2 and *3 alleles (rs4244285 and rs4986893, non-functional variants). In previous studies, we found that genetic polymorphisms in CYP2C19 variants influenced the active metabolites of clopidogrel and caused major adverse cardiovascular and cerebrovascular effects. However, the distribution of CYP2C19 varies among ethnic groups and according to adverse drug reactions. This study aimed to investigate the frequency of CYP2C19 genetic polymorphisms in the Thai population and analyze the differences in the frequency of CYP2C19 genetic polymorphisms between Thai and other populations. Methods: This study enrolled 211 unrelated healthy Thai individuals in total. We performed a real-time polymerase chain reaction to genotype CYP2C19*2 (681G > A) and CYP2C19*3 (636G > A). Results: In the Thai population, the CYP2C19*1 allele was the most prevalent at 70.14%, while the CYP2C19*2 and *3 alleles were found at frequencies of 25.36% and 4.50%, respectively. Conversely, the CYP2C19*3 allele was not detected in Caucasian, Hispanic, African, Italian, Macedonian, Tanzanian, or North Indian populations. The phenotypic profile of this gene revealed that the frequency of intermediate metabolizers (IMs) is nearly equal to that of extensive metabolizers (EMs), at 42.65% and 48.82% respectively, with genotypes *1/*2 (36.02%) and *1/*3 (6.63%). Likewise, poor metabolizers (PMs) with genotypes *2/*2 (6.16%), *2/*3 (2.37%), and *3/*3 (<1%) are more prevalent in our population as well. Conclusion: The distribution of CYP2C19 genotype and phenotype influenced by non-functional alleles has potential as a pharmacogenomics biomarker for precision medicine and is dependent on an ethnic-specific genetic variation database.

Emergence of genetic diversity and multi-drug resistant Clostridium perfringens from wild birds.

BACKGROUND: Clostridium perfringens (C. perfringens) is an important zoonotic microorganism that can cause animal and human infections, however information about the prevalence status in wild birds of this pathogenic bacterium is currently limited. RESULT: In this study, 57 strains of C. perfringens were isolated from 328 fecal samples of wild birds. All the isolates were identified as type A and 70.18% of the isolates carried the cpb2 gene. Antimicrobial susceptibility testing showed that and 22.80% of the isolates were classified as multidrug-resistant strains. The MLST analysis of the 57 isolates from wild birds was categorized into 55 different sequence types (STs) and clustered into eight clonal complexes (CCs) with an average of 20.1 alleles and the Simpson Diversity index (Ds) of 0.9812, and revealed a high level of genetic diversity within the C. perfringens populations. Interestingly, the isolates from swan goose were clustered in the same CC while isolates from other bird species were more scattered suggesting that a potential difference in genetic diversity among the C. perfringens populations associated with different bird species. CONCLUSION: C. perfringens exhibits a wide range of host adaptations, varying degrees of antimicrobial resistance, and a high degree of genetic diversity in wild birds. Understanding the prevalence, toxin type, antimicrobial resistance, and genetic diversity of C. perfringens in wildlife populations is essential for developing effective strategies for disease control and management.

Population dynamics and genetic isolation in the Central Himalayan region: insights from Sikkim population, India.

India's rich diversity encompasses individuals from varied geographical, cultural, and ethnic backgrounds. In the field of population genetics, comprehending the genetic diversity across distinct populations plays a crucial role. This study presents significant findings from genetic data obtained from the Sikkimese population of India. Autosomal markers were crucial for evaluating forensic parameters, with a combined paternity index of 1 × 109. Notably, Penta E emerged as a distinguishing marker for individual identification in the Sikkim population. Fst genetic distance values revealed insights into genetic isolation among different groups, enhancing our understanding of population dynamics in the central Himalayan region. The NJ-based phylogenetic tree highlighted close genetic relationships, of the Sikkim population with the Nepalese population surrounding neighbouring Himalayan populations providing glimpses into common ancestry. In summary, this study contributes valuable data to population genetics and underscores the importance of genetic variation in comprehending population dynamics and forensic applications.

Population genetic structure of Culex tritaeniorhynchus in different types of climatic zones in China.

BACKGROUND: Culex tritaeniorhynchus is widely distributed in China, from Hainan Island in the south to Heilongjiang in the north, covering tropical, subtropical, and temperate climate zones. Culex tritaeniorhynchus carries 19 types of arboviruses. It is the main vector of the Japanese encephalitis virus (JEV), posing a serious threat to human health. Understanding the effects of environmental factors on Culex tritaeniorhynchus can provide important insights into its population structure or isolation patterns, which is currently unclear. RESULTS: In total, 138 COI haplotypes were detected in the 552 amplified sequences, and the haplotype diversity (Hd) value increased from temperate (0.534) to tropical (0.979) regions. The haplotype phylogeny analysis revealed that the haplotypes were divided into two high-support evolutionary branches. Temperate populations were predominantly distributed in evolutionary branch II, showing some genetic isolation from tropical/subtropical populations and less gene flow between groups. The neutral test results of HNQH (Qionghai) and HNHK(Haikou) populations were negative (P < 0.05), indicating many low-frequency mutations in the populations and that the populations might be in the process of expansion. Moreover, Wolbachia infection was detected only in SDJN (Jining) (2.24%), and all Wolbachia genotypes belonged to supergroup B. To understand the influence of environmental factors on mosquito-borne viruses, we examined the prevalence of Culex tritaeniorhynchus infection in three ecological environments in Shandong Province. We discovered that the incidence of JEV infection was notably greater in Culex tritaeniorhynchus from lotus ponds compared to those from irrigation canal regions. In this study, the overall JEV infection rate was 15.27 per 1000, suggesting the current risk of Japanese encephalitis outbreaks in Shandong Province. CONCLUSIONS: Tropical and subtropical populations of Culex tritaeniorhynchus showed higher genetic diversity and those climatic conditions provide great advantages for the establishment and expansion of Culex tritaeniorhynchus. There are differences in JEV infection rates in wild populations of Culex tritaeniorhynchus under different ecological conditions. Our results suggest a complex interplay of genetic differentiation, population structure, and environmental factors in shaping the dynamics of Culex tritaeniorhynchus. The low prevalence of Wolbachia in wild populations may reflect the recent presence of Wolbachia invasion in Culex tritaeniorhynchus.

Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis.

In uncertain environments, phenotypic diversity can be advantageous for survival. However, as the environmental uncertainty decreases, the relative advantage of having diverse phenotypes decreases. Here, we show how populations of E. coli integrate multiple chemical signals to adjust sensory diversity in response to changes in the prevalence of each ligand in the environment. Measuring kinase activity in single cells, we quantified the sensitivity distribution to various chemoattractants in different mixtures of background stimuli. We found that when ligands bind uncompetitively, the population tunes sensory diversity to each signal independently, decreasing diversity when the signal's ambient concentration increases. However, among competitive ligands, the population can only decrease sensory diversity one ligand at a time. Mathematical modeling suggests that sensory diversity tuning benefits E. coli populations by modulating how many cells are committed to tracking each signal proportionally as their prevalence changes.

Multi-biomarker approach reveals the effects of heavy metal bioaccumulation in the foundation species Prosopis laevigata (Fabaceae).

Mining is a major economic activity in many developing countries. However, it disturbs the environment, producing enormous quantities of waste, known as mine tailings, which can have deleterious environmental impact, due to their high heavy metals (HM) content. Often, foundation species that establish on mine tailings are good candidates to study the effects of HM bioaccumulation at different levels of biological organization. Prosopis laevigata is considered a HM hyperaccumulator which presents attributes of a foundation species (FS) and establishes naturally on mine tailings. We evaluated the bioaccumulation of Cu, Pb, and Zn in P. laevigata foliar tissue, the leaf micro- and macro-morphological characters, DNA damage, and population genetic effects. In total, 80 P. laevigata individuals (20/site) belonging to four populations: The individuals from both sites (exposed and reference) bioaccumulated HMs (Pb > Cu > Zn). However, in the exposed individuals, Pb and Cu bioaccumulation was significantly higher. Also, a significant effect of macro- and micro-morphological characters was registered, showing significantly lower values in individuals from the exposed sites. In addition, we found significant differences in genotoxic damage in P. laevigata individuals, between the exposed and reference sites. In contrast, for the micro-morphological characters, none of the analyzed metals had any influence. P. laevigata did not show significant differences in the genetic structure and diversity between exposed and reference populations. However, four haplotypes and four private alleles were found in the exposed populations. Since P. laevigata is a species that establishes naturally in polluted sites and bioaccumulates HM in its foliar tissues, the resulting genetic, individual and population effects have not been severe enough to show detrimental effects; hence, P. laevigata can be a useful tool in phytoremediation strategies for soils polluted with Pb and Cu, maintaining its important ecological functions.

Assessment of the genetic diversity of the alleles of gliadin-coding loci in common wheat (Triticum aestivum L.) collections in Kazakhstan and Russia.

The study of genetic resources using prolamin polymorphism in wheat cultivars from countries with different climatic conditions makes it possible to identify and trace the preference for the selection of the alleles of gliadine-coding loci characteristic of specific conditions. The aim of the study was to determine the "gliadin profile" of the collection of common wheat (Triticum aestivum L.) from breeding centers in Russia and Kazakhstan by studying the genetic diversity of allelic variants of gliadin-coding loci. Intrapopulation (µ ± Sµ) and genetic (H) diversity, the proportion of rare alleles (h ± Sh), identity criterion (I) and genetic similarity (r) of common wheat from eight breeding centers in Russia and Kazakhstan have been calculated. It has been ascertained that the samples of common wheat bred in Kostanay region (Karabalyk Agricultural Experimental Station, Kazakhstan) and Chelyabinsk region (Chelyabinsk Research Institute of Agriculture, Russia) had the highest intrapopulation diversity of gliadin alleles. The proportion of rare alleles (h) at Gli-B1 and Gli-D1 loci was the highest in the wheat cultivars bred by the Federal Center of Agriculture Research of the South-East Region (Saratov region, Russia), which is explained by a high frequency of occurrence of Gli-B1e (86 %) and Gli-D1a (89.9 %) alleles. Based on identity criterion (I), the studied samples of common wheat from different regions of Kazakhstan and Russia have differences in gliadin-coding loci. The highest value of I = 619.0 was found when comparing wheat samples originated from Kostanay and Saratov regions, and the lowest I = 114.4, for wheat cultivars from Tyumen and Chelyabinsk regions. Some region-specific gliadin alleles in wheat samples have been identified. A combination of Gli-A1f, Gli-B1e and Gli-Da alleles has been identified in the majority of wheat samples from Kazakhstan and Russia. Alleles (Gli-A1f, Gli-A1i, Gli-A1m, Gli-A1o, Gli-B1e, Gli-D1a, Gli-D1f, Gli-A2q, Gli-B2o, and Gli-D2a) turned out to be characteristic and were found with varying frequency in wheat cultivars in eight regions of Russia and Kazakhstan. The highest intravarietal polymorphism (51.1 %) was observed in wheat cultivars bred in Omsk region (Russia) and the lowest (16.6 %), in Pavlodar region (Kazakhstan). On the basis of the allele frequencies, a "gliadin profile" of wheat from various regions and breeding institutions of Russia and Kazakhstan was compiled, which can be used for the selection of parent pairs in the breeding process, the control of cultivars during reproduction, as well as for assessing varietal purity.

HIV-1 diversity and pre-treatment drug resistance in the era of integrase inhibitor among newly diagnosed ART-naïve adult patients in Luanda, Angola.

The surveillance of drug resistance in the HIV-1 naïve population remains critical to optimizing the effectiveness of antiretroviral therapy (ART), mainly in the era of integrase strand transfer inhibitor (INSTI) regimens. Currently, there is no data regarding resistance to INSTI in Angola since Dolutegravir-DTG was included in the first-line ART regimen. Herein, we investigated the HIV-1 genetic diversity and pretreatment drug resistance (PDR) profile against nucleoside/tide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), and INSTIs, using a next-generation sequencing (NGS) approach with MinION, established to track and survey DRMs in Angola. This was a cross-sectional study comprising 48 newly HIV-diagnosed patients from Luanda, Angola, screened between March 2022 and May 2023. PR, RT, and IN fragments were sequenced for drug resistance and molecular transmission cluster analysis. A total of 45 out of the 48 plasma samples were successfully sequenced. Of these, 10/45 (22.2%) presented PDR to PIs/NRTIs/NNRTIs. Major mutations for NRTIs (2.2%), NNRTIs (20%), PIs (2.2%), and accessory mutations against INSTIs (13.3%) were detected. No major mutations against INSTIs were detected. M41L (2%) and I85V (2%) mutations were detected for NRTI and PI, respectively. K103N (7%), Y181C (7%), and K101E (7%) mutations were frequently observed in NNRTI. The L74M (9%) accessory mutation was frequently observed in the INSTI class. HIV-1 pure subtypes C (33%), F1 (17%), G (15%), A1 (10%), H (6%), and D (4%), CRF01_AG (4%) were observed, while about 10% were recombinant strains. About 31% of detected HIV-1C sequences were in clusters, suggesting small-scale local transmission chains. No major mutations against integrase inhibitors were detected, supporting the continued use of INSTI in the country. Further studies assessing the HIV-1 epidemiology in the era of INSTI-based ART regimens are needed in Angola.

Preliminary insights of the genetic diversity and invasion pathways of Cedrela odorata in the Galapagos Islands, Ecuador.

Cedrela odorata is considered the second most invasive tree species of the Galapagos Islands. Although it is listed in CITES Appendix II and there are population losses in mainland Ecuador, in Galapagos it is paradoxically a species of concern due to its invasive potential. Genetic studies can shed light on the invasion history of introduced species causing effects on unique ecosystems like the Galapagos. We analyzed nine microsatellite markers in C. odorata individuals from Galapagos and mainland Ecuador to describe the genetic diversity and population structure of C. odorata in the Galapagos and to explore the origin and invasion history of this species. The genetic diversity found for C. odorata in Galapagos (H e = 0.55) was lower than reported in the mainland (H e = 0.81), but higher than other invasive insular plant species, which could indicate multiple introductions. Our results suggest that Ecuador's northern Coastal region is the most likely origin of the Galapagos C. odorata, although further genomic studies, like Whole Genome Sequencing, Rad-Seq, and/or Whole Genome SNP analyses, are needed to confirm this finding. Moreover, according to our proposed pathway scenarios, C. odorata was first introduced to San Cristobal and/or Santa Cruz from mainland Ecuador. After these initial introductions, C. odorata appears to have arrived to Isabela and Floreana from either San Cristobal or Santa Cruz. Here, we report the first genetic study of C. odorata in the Galapagos and the first attempt to unravel the invasion history of this species. The information obtained in this research could support management and control strategies to lessen the impact that C. odorata has on the islands' local flora and fauna.

Cedrela odorata es considerada la segunda especie más invasora de árboles en las Islas Galápagos. Esta especie está catalogada en el Apéndice II de CITES y sus poblaciones se encuentran amenazadas en Ecuador continental, pero paradójicamente en Galápagos es una especie de preocupación por su potencial invasor. Estudios genéticos pueden ayudar a entender la historia de invasión de especies introducidas que causan efectos en ecosistemas únicos como Galápagos. En este estudio, analizamos 9 marcadores microsatélites en individuos de Galápagos y Ecuador continental para describir la diversidad genética y estructura poblacional de C. odorata en Galápagos y explorar el origen e historia de invasión de esta especie. La diversidad genética encontrada para C. odorata en Galápagos (H e = 0.55) fue menor que la reportada en continente (H e = 0.81), pero mayor que la de otras especies de plantas insulares invasoras, lo que podría sugerir múltiples introducciones de esta especie a Galápagos. Nuestros resultados sugieren que la costa norte ecuatoriana es el origen más probable de C. odorata en Galápagos, aunque más estudios, como secuenciación del genoma completo, Rad­Seq y/o análisis de SNPs, son necesarios para confirmar este hecho. Además, de acuerdo con los escenarios propuestos, es posible que C. odorata haya sido introducida primero a San Cristóbal y/o Santa Cruz desde Ecuador continental. Después de estas introducciones iniciales, parece haber llegado a Isabela y Floreana desde San Cristóbal o Santa Cruz. Este es el primer estudio genético de C. odorata en Galápagos y el primer intento de esclarecer la historia de invasión de esta especie. La información obtenida en esta investigación podría apoyar estrategias de manejo para disminuir el impacto que C. odorata tiene sobre la flora y fauna nativa de estas islas.

Molecular epizootiology of porcine reproductive and respiratory syndrome virus in the Xinjiang Uygur Autonomous Region of China.

Rapid evolution of porcine reproductive and respiratory syndrome virus (PRRSV) is the bottleneck for effective prevention and control of PRRS. Thus, understanding the prevalence and genetic background of PRRSV strains in swine-producing regions is important for disease prevention and control. However, there is only limited information about the epizootiological situation of PRRS in the Xinjiang Uygur Autonomous Region, China. In this study, blood or lung tissue samples were collected from 1,411 PRRS-suspected weaned pigs from 9 pig farms in Changji, Shihezi, and Wujiaqu cities between 2020 and 2022. The samples were first tested by RT-quantitative PCR, yielding a PRRSV-2 positive rate of 53.6%. Subsequently, 36 PRRSV strains were isolated through initial adaptation in bone marrow-derived macrophages followed by propagation in grivet monkey Marc-145 cells. Furthermore, 28 PRRSV-positive samples and 20 cell-adapted viruses were selected for high-throughput sequencing (HTS) to obtain the entire PRRSV genome sequences. Phylogenetic analysis based on the nucleotide sequences of the ORF5 gene of the PRRSV strains identified in this study grouped into sub-lineages 1.8 and 8.7 the former being the dominant strain currently circulating in Xinjiang. However, the NSP2 proteins of the Xinjiang PRRSV strains shared the same deletion patterns as sub-lineage 1.8 prototype strain NADC30 with the exception of 4 strains carrying 2-3 additional amino acid deletions. Further analysis confirmed that recombination events had occurred in 27 of 37 PRRSVs obtained here with the parental strains belonging to sub-lineages 1.8 and 8.7, lineages 3 and 5, with the recombination events having occurred most frequently in the 5' and 3' termini of ORF1a and 5' terminus of ORF1b.

Genetic diversity and shallow genetic differentiation of the endangered scaly-sided merganser Mergus squamatus.

Examining patterns of genetic diversity are crucial for conservation planning on endangered species, while inferring the underlying process of recent anthropogenic habitat modifications in the context potential long-term demographic changes remains challenging. The globally endangered scaly-sided merganser (SSME), Mergus squamatus, is endemic to a narrow range in Northeast Asia, and its population has recently been contracted into two main breeding areas. Although low genetic diversity has been suggested in the Russian population, the genetic status and demographic history of these individuals have not been fully elucidated. We therefore examined the genetic diversity and structure of the breeding populations of the SSME and investigated the relative importance of historical and recent demographic changes to the present-day pattern of genetic diversity. Using 10 nuclear microsatellite (SSR) markers and mitochondrial DNA (mtDNA) control region sequences, we found limited female-inherited genetic diversity and a high level of nuclear genetic diversity. In addition, analysis of both markers consistently revealed significant but weak divergence between the breeding populations. Inconsistent demographic history parameters calculated from mtDNA and bottleneck analysis results based on SSR suggested a stable historical effective population size. By applying approximate Bayesian computation, it was estimated that populations started to genetically diverge from each other due to recent fragmentation events caused by anthropogenic effects rather than isolation during Last Glacial Maximum (LGM) and post-LGM recolonization. These results suggest that limited historical population size and shallow evolutionary history may be potential factors contributing to the contemporary genetic diversity pattern of breeding SSME populations. Conservation efforts should focus on protecting the current breeding habitats from further destruction, with priority given to both the Russian and Chinese population, as well as restoring the connected suitable breeding grounds.

Population-specific responses to pollution exposure suggest local adaptation of invasive red swamp crayfish Procambarus clarkii along the Mediterranean French coastline.

Anthropogenic stressors can have an impact in a broad range of physiological processes and can be a major selective force leading to rapid evolution and local population adaptation. In this study, three populations of the invasive crayfish Procambarus clarkii were investigated. They are geographically separated for at least 20 years, and live in different abiotic environments: a freshwater inland lake (Salagou lake) with no major anthropogenic influence and two other coastal wetlands regularly polluted by pesticides along the Mediterranean coast (Camargue region and Bages-Sigean lagoon). Collected adults were genetically characterized using the mitochondrial COI gene and haplotype frequencies were analyzed for genetic variability within and between populations. Results revealed a higher genetic diversity for these invasive populations than any previous report in France, with more than seven different haplotypes in a single population. The contrasting genetic diversity between the Camargue and the other two populations suggest different times and sources of introduction. To identify differences in key physiological responses between these populations, individuals from each population were maintained in controlled conditions. Data on oxygen consumption rates indicate that the Salagou and Bages-Sigean populations possess a high inter-individual variability compared to the Camargue population. The low individual variability of oxygen consumption and low genetic diversity suggest a specific local adaptation for the Camargue population. Population-specific responses were identified when individuals were exposed to a pesticide cocktail containing azoxystrobin and oxadiazon at sublethal concentrations. The Salagou population was the only one with altered hydro-osmotic balance due to pollutant exposure and a change in protease activity in the hepatopancreas. These results revealed different phenotypic responses suggesting local adaptations at the population level.

Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET).

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel.

Genetic Diversity and Population Structure of the Endangered Salamander Hynobius yiwuensis Inferred from Mitochondrial DNA Sequences.

Understanding the genetic diversity patterns of endangered species is crucial for biodiversity conservation. The endangered salamander Hynobius yiwuensis, endemic to the mainland and Zhoushan Island in Zhejiang, China, has suffered from sharp population declines due to habitat loss. However, the levels and patterns of genetic diversity, differentiation, and population structure of H. yiwuensis remain poorly understood. Here, we explored the genetic diversity and phylogeography of H. yiwuensis based on partial mtDNA sequences (Cytb and CO1) through 111 individuals collected from seven localities. Relatively high overall haplotype diversity (h = 0.965) and low nucleotide diversity (π = 0.013) were detected. Our results, through phylogenetic trees and haplotype network analyses, revealed two divergent haplogroups, mainland and island, and the estimated divergence time indicated they diverged ~2.44 million years ago, which coincided with the period when Zhoushan Island became separated from the mainland.

Complexity and Diversity of the Neurological Spectrum of SARS-CoV-2 over Three Waves of COVID-19.

Background/Objectives: SARS-CoV-2 continually mutates, with five identified variants. Many neurological manifestations were observed during the COVID-19 pandemic, with differences between virus variants. The aim of this study is to assess the frequency and characteristics of neurological manifestations during COVID-19 in hospitalized patients over three waves in Poland with comparison and analysis correlation with the course of infection. Methods: This retrospective single-center study included 600 consecutive adults with confirmed COVID-19, hospitalized during 3 waves (pre-Delta, Delta and Omicron) in Poland. Demographic and clinical information and neurological manifestations were collected and compared across three periods. Results: The median age of the study group was 68, lower during the Delta wave. In the Omicron period, the disease severity at admission and inflammatory markers concentration were the lowest. Neurological manifestations were observed in 49%. The most common were altered mentation, headache, myalgia, mood disorder, ischemic stroke and encephalopathy. Smell and taste disturbances (STDs) were less frequent in the Omicron period. Neurological complications were predominant in the pre-Delta and Omicron periods. Ischemic stroke was observed more often in pre-Delta period. Altered mentation was related to higher severity at admission, worse lab test results, higher admission to ICU and mortality, while headache reduced mortality. Pre-existing dementia was related to higher mortality. Conclusions: Neurological manifestations of COVID-19 are frequent, with a lower rate of STDs in the Omicron period and more often cerebrovascular diseases in the pre-Delta period. Headache improves the course of COVID-19, while altered mentation, stroke and neurological comorbidities increase severity and mortality.

Lacticaseibacillus rhamnosus Strains for Alleviation of Irritable Bowel Disease and Chronic Fatigue Syndrome.

Lacticaseibacillus rhamnosus is applied as a probiotic to alleviate various metabolic, gastrointestinal, and psychological symptoms and diseases, and its probiotic effectiveness is strain-specific. In this study, we obtained 21 strains of Ls. rhamnosus, and their genomes were sequenced. We defined the pan- and core-genomes of Ls. rhamnosus. Phenotypes such as the assimilation of carbohydrates and antibiotic resistance were experimentally characterized and associated with genome annotations. Nine strains were selected and tested for growth rates, tolerance to acidity/alkalinity and bile acids, the production of short-chain fatty acids, and competition with pathogenic microbes. Strains WL11 and WL17 were targeted as potential probiotics and were applied in mouse model tests for the alleviation of chronic fatigue syndrome (CFS) and irritable bowel syndrome (IBS). The results showed that WL11 and WL17 effectively alleviated slow body weight gain, anxiety, poor memory, and cognitive impairment in CFS mouse models. They also reduced the expression of pro-inflammatory factors, such as TNF-α and IL-6, and alleviated intestinal peristalsis, visceral hypersensitivity, and anxiety-like behavior in IBS mouse models. This study reports new Ls. rhamnosus strain resources and their effect on alleviation of both IBS and CFS symptoms with mouse models; the probiotic functions of those strains in human patients remain to be further tested.