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1.
Virus Genes ; 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38847934

RESUMO

Since its initial detection in Africa, the West Nile virus has disseminated widely across all continents, becoming endemic in numerous countries, including the Russian Federation. A substantial expansion of the West Nile virus range was observed in the European part of the Russian territory in 1999. In light of this epidemiological trend, research endeavours focusing on monitoring West Nile virus circulation activity in endemic regions of the country have gained paramount significance. A substantial dataset has been accrued from 2007 onwards regarding genomic variability and dissemination dynamics across the country throughout the entire monitoring period for the West Nile fever pathogen. The objective of this study was to characterise West Nile virus isolates that have been circulating in the Russian Federation and identify their molecular and genetic characteristics. A phylogenetic analysis of 55 complete genome sequences revealed that the West Nile virus population within the Russian Federation is genetically heterogeneous and is represented by four major clades. One of these clades is currently exhibiting extensive spread into new regions of the country.

2.
Front Microbiol ; 15: 1379825, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38835487

RESUMO

Fungi are an integral part of the nitrogen and phosphorus cycling in trophic networks, as they participate in biomass decomposition and facilitate plant nutrition through root symbioses. Nutrient content varies considerably between the main fungal habitats, such as soil, plant litter or decomposing dead wood, but there are also large differences within habitats. While some soils are heavily loaded with N, others are limited by N or P. One way in which nutrient availability can be reflected in fungi is their content in biomass. In this study, we determined the C, N, and P content (in dry mass) of fruiting bodies of 214 fungal species to inspect how phylogeny and membership in ecological guilds (soil saprotrophs, wood saprotrophs, and ectomycorrhizal fungi) affect the nutrient content of fungal biomass. The C content of fruiting bodies (415 ± 25 mg g-1) showed little variation (324-494 mg g-1), while the range of N (46 ± 20 mg g-1) and P (5.5 ± 3.0 mg g-1) contents was within one order of magnitude (8-103 mg g-1 and 1.0-18.9 mg g-1, respectively). Importantly, the N and P contents were significantly higher in the biomass of soil saprotrophic fungi compared to wood saprotrophic and ectomycorrhizal fungi. While the average C/N ratio in fungal biomass was 11.2, values exceeding 40 were recorded for some fungi living on dead wood, typically characterized by low N content. The N and P content of fungal mycelium also showed a significant phylogenetic signal, with differences in nutrient content being relatively low within species and genera of fungi. A strong correlation was found between N and P content in fungal biomass, while the correlation of N content and the N-containing fungal cell wall biopolymer-chitin showed only weak significance. The content of macronutrients in fungal biomass is influenced by the fungal life style and nutrient availability and is also limited by phylogeny.

3.
Infect Drug Resist ; 17: 2199-2211, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38835492

RESUMO

Background: Human adenovirus (HAdV) is common pathogens that cause various respiratory diseases. The genetic diversity of viruses caused by recombination is considered to be the main source of emerging outbreaks. The aim of this study is to explore the evolutionary relationship and recombination events of HAdV genome in respiratory tract infections in Jiangsu Province. Methods: Whole-genome sequencing (WGS) technology was used to sequence 66 patients with HAdV infection (37 patients with influenza-like illness (ILI) and 29 hospitalized patients with pneumonia) from Jiangsu Province. Epidemiological analysis was performed on hospitalized pneumonia and ILI patients infected with HAdV. Subsequently, phylogenetic, recombination, and nucleotide and amino acid identity analyses were performed. Results: Epidemiological analysis of patients undergoing WGS showed that 75.7% of ILI patients were infected with the HAdVB strain and 69.0% of hospitalized pneumonia patients were infected with the HAdVC strain. Moreover, the hospitalized pneumonia and ILI patients infected with HAdV were different in region and time. The strains of HAdVB3 and HAdVB7 genotypes were mainly infected in 2015 and 2017, and the strains of HAdVC1 and HAdVC2 genotypes were mainly infected in 2020. The results of histogram analysis showed that the HAdV strain mainly infected children under 5 years old. In addition, 36 novel recombinant strains were identified. The discovery of these recombinant strains may contribute to understanding the epidemiology of HAdV and research on related vaccines. Furthermore, the percentage of nucleotide and amino acid identities revealed a high level of genetic conservation within isolates from HAdVB3, HAdVB7, HAdVC1, HAdVC2 and HAdVC5 genotypes. Conclusion: The WGS analysis reveals the evolutionary relationships and recombination events of HAdV strains in Jiangsu Province, which is helpful to deepen the understanding of HAdV epidemiology and evolution. In addition, it provides a basis for the formulation of public health strategies in Jiangsu Province.

4.
Mitochondrial DNA B Resour ; 9(6): 687-691, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38835639

RESUMO

Arachis lutescens Krapov. & Rigoni 1958 is an important species due to their potentially extensive applications for cultivated peanut breeding. The whole chloroplast genome of A. lutescens was successfully assembled and annotated for the first time. The complete chloroplast genome of A. lutescens is a typically circular structure of 156,398 bp with a GC content of 36.3%. It comprises a large single-copy (LSC) region of 85,950 bp, a small single-copy (SSC) region of 18,800 bp, and two inverted repeat regions (IRs) of 25,824 bp, each. The plastome of A. lutescens contains a total of 125 genes, including 81 protein-coding genes, 36 tRNAs, and eight rRNAs. The phylogenetic analysis strongly supports the close relationship between A. lutescens and cultivated peanut clades. This study contributes to our understanding of the molecular characteristics and evolutionary relationships of this plant species.

5.
Mitochondrial DNA B Resour ; 9(6): 701-706, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38835641

RESUMO

The striped notothen Trematomus hansoni is an Antarctic fish species belonging to the family Nototheniidae (cod icefishes) that is distributed throughout the Southern Ocean. In this study, the complete mitochondrial genome of T. hansoni was sequenced using an Illumina MiSeq platform. The circular mitochondrial genome is 19,218 bp long and contains 13 protein-coding genes, 23 tRNA genes, two rRNA genes, and one control region. Notably, there are two trnG-UCC genes and the second gene, located between trnE-UUC and trnI-GAU, has no D-arm structure. The base composition is 56.18% of A + T and 43.82% of G + C. The phylogenetic analysis supports that T. hansoni is grouped into a single clade with T. bernacchii. This study will be a valuable resource for further research on the phylogeny and evolution of the genus Trematomus.

6.
BMC Ecol Evol ; 24(1): 74, 2024 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-38831426

RESUMO

BACKGROUND: The geographic patterns of plant diversity in the Qinghai-Tibet Plateau (QTP) have been widely studied, but few studies have focused on wetland plants. This study quantified the geographic patterns of wetland plant diversity in the QTP through a comprehensive analysis of taxonomic, phylogenetic and functional indices. METHODS: Based on a large number of floras, monographs, specimens and field survey data, we constructed a comprehensive dataset of 1,958 wetland plant species in the QTP. Species richness (SR), phylogenetic diversity (PD), functional diversity (FD), net relatedness index (NRI) and net functional relatedness index (NFRI) were used to assess the taxonomic, phylogenetic and functional diversity of wetland plants. We explored the relationships between the diversity indices and four categories of environmental variables (i.e. energy-water, climate seasonality, topography and human activities). We used four diversity indices, namely endemic species richness, weighted endemism, phylogenetic endemism and functional endemism, together with the categorical analysis of neo- and paleo-endemism (CANAPE), to identify the endemic centers of wetland plants in the QTP. RESULTS: SR, PD and FD were highly consistent and showed a decreasing trend from southeast to northwest, decreasing with increasing elevation. The phylogenetic structure of wetland plant assemblages in most parts of the plateau is mainly clustered. The functional structure of wetland plant assemblages in the southeast of the plateau is overdispersed, while the functional structure of wetland plant assemblages in other areas is clustered. Energy-water and climate seasonality were the two most important categories of variables affecting wetland plant diversity. Environmental variables had a greater effect on the functional structure of wetland plants than on the phylogenetic structure. This study identified seven endemic centres, mainly in the Himalayas and Hengduan Mountains. CONCLUSIONS: Climate and topography are the main factors determining the geographic distribution of wetland plant diversity at large scales. The majority of grid cells in the QTP with significant phylogenetic endemism were mixed and super-endemism. At large scales, compared to climate and topography, human activities may not have a negative impact on wetland plant diversity in the QTP.


Assuntos
Biodiversidade , Plantas , Áreas Alagadas , Plantas/classificação , Tibet , Filogenia , China
7.
Mol Biol Evol ; 2024 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-38860506

RESUMO

MOTIVATION: Phylogenetic inference based on protein sequence alignment is a widely used procedure. Numerous phylogenetic algorithms have been developed, most of which have many parameters and options. Choosing a program, options, and parameters can be a nontrivial task. No benchmark for comparison of phylogenetic programs on real protein sequences is publicly available. RESULTS: We have developed PhyloBench, a benchmark for evaluating the quality of phylogenetic inference, and used it to test a number of popular phylogenetic programs. PhyloBench is based on natural, not simulated, protein sequences of orthologous evolutionary domains. The measure of accuracy of an inferred tree is its distance to the corresponding species tree. A number of tree-to-tree distance measures were tested. The most reliable results were obtained using the Robinson-Foulds distance. Our results confirmed recent findings that distance methods are more accurate than maximum likelihood and maximum parsimony. We tested the bayesian program MrBayes on natural protein sequences and found that, on our datasets, it performs better than maximum likelihood, but worse than distance methods. Of the methods we tested, the Balanced Minimum Evolution method implemented in FastME yielded the best results on our material. AVAILABILITY: Alignments and reference species trees are available at https://mouse.belozersky.msu.ru/tools/phylobench/together with a web-interface that allows for a semi-automatic comparison of a user's method with a number of popular programs.

8.
Microbiol Resour Announc ; : e0015824, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38860813

RESUMO

The whole genome sequence of a low pathogenicity avian influenza virus (H6N2) was sequenced from a Brazilian teal (Amazonetta brasiliensis) in Brazil, 2023. Phylogenetic analysis of the whole genome revealed a distinct genome pertaining to South American LPAIV from 2014 to 2016, indicating extensive circulation among South American wild birds.

9.
Mitochondrial DNA B Resour ; 9(6): 729-733, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38859914

RESUMO

The Sigara lateralis (Leach, 1817) is a small aquatic insect belonging to the family Corixidae. The study aims to reveal the genomic data of the mitochondrial genome of S. lateralis. The length of its circular mitochondrial genome is 15,725 bp long with an A + T bias (75.96%). The mitogenome comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two rRNA genes. The phylogenetic analyses showed that the S. lateralis is the closest to S. septemlineata. These findings will help the conservation of Corixidae from the perspective of genetic evolution.

10.
Bioinform Biol Insights ; 18: 11779322241257991, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38860163

RESUMO

Nucleotide base composition plays an influential role in the molecular mechanisms involved in gene function, phenotype, and amino acid composition. GC content (proportion of guanine and cytosine in DNA sequences) shows a high level of variation within and among species. Many studies measure GC content in a small number of genes, which may not be representative of genome-wide GC variation. One challenge when assembling extensive genomic data sets for these studies is the significant amount of resources (monetary and computational) associated with data processing, and many bioinformatic tools have not been optimized for resource efficiency. Using a high-performance computing (HPC) cluster, we manipulated resources provided to the targeted gene assembly program, automated target restricted assembly method (aTRAM), to determine an optimum way to run the program to maximize resource use. Using our optimum assembly approach, we assembled and measured GC content of all of the protein-coding genes of a diverse group of parasitic feather lice. Of the 499 426 genes assembled across 57 species, feather lice were GC-poor (mean GC = 42.96%) with a significant amount of variation within and between species (GC range = 19.57%-73.33%). We found a significant correlation between GC content and standard deviation per taxon for overall GC and GC3, which could indicate selection for G and C nucleotides in some species. Phylogenetic signal of GC content was detected in both GC and GC3. This research provides a large-scale investigation of GC content in parasitic lice laying the foundation for understanding the basis of variation in base composition across species.

11.
Virus Evol ; 10(1): veae024, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38827419

RESUMO

Venom is known as the source of natural antimicrobial products. Previous studies have largely focused on the expression of venom-related genes and the biochemical components of venom. With the advent of metagenomic sequencing, many more microorganisms, especially viruses, have been identified in highly diverse environments. Herein, we investigated the RNA virome in the venom-related microenvironment through analysis of a large volume of venom-related RNA-sequencing data mined from public databases. From this, we identified viral sequences belonging to thirty-six different viruses, of which twenty-two were classified as 'novel' as they exhibited less than 90 per cent amino acid identity to known viruses in the RNA-dependent RNA polymerase. Most of these novel viruses possessed genome structures similar to their closest relatives, with specific alterations in some cases. Phylogenetic analyses revealed that these viruses belonged to at least twenty-two viral families or unclassified groups, some of which were highly divergent from known taxa. Although further analysis failed to find venom-specific viruses, some viruses seemingly had much higher abundance in the venom-related microenvironment than in other tissues. In sum, our study provides insights into the RNA virome of the venom-related microenvironment from diverse animal phyla.

12.
BMC Infect Dis ; 24(1): 550, 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38824508

RESUMO

BACKGROUND: Influenza A virus infections can occur in multiple species. Eurasian avian-like swine influenza A (H1N1) viruses (EAS-H1N1) are predominant in swine and occasionally infect humans. A Eurasian avian-like swine influenza A (H1N1) virus was isolated from a boy who was suffering from fever; this strain was designated A/Shandong-binzhou/01/2021 (H1N1). The aims of this study were to investigate the characteristics of this virus and to draw attention to the need for surveillance of influenza virus infection in swine and humans. METHODS: Throat-swab specimens were collected and subjected to real-time fluorescent quantitative polymerase chain reaction (RT‒PCR). Positive clinical specimens were inoculated onto Madin-Darby canine kidney (MDCK) cells to isolate the virus, which was confirmed by a haemagglutination assay. Then, whole-genome sequencing was carried out using an Illumina MiSeq platform, and phylogenetic analysis was performed with MEGA X software. RESULTS: RT‒PCR revealed that the throat-swab specimens were positive for EAS-H1N1, and the virus was subsequently successfully isolated from MDCK cells; this strain was named A/Shandong-binzhou/01/2021 (H1N1). Whole-genome sequencing and phylogenetic analysis revealed that A/Shandong-binzhou/01/2021 (H1N1) is a novel triple-reassortant EAS-H1N1 lineage that contains gene segments from EAS-H1N1 (HA and NA), triple-reassortant swine influenza H1N2 virus (NS) and A(H1N1) pdm09 viruses (PB2, PB1, PA, NP and MP). CONCLUSIONS: The isolation and analysis of the A/Shandong-binzhou/01/2021 (H1N1) virus provide further evidence that EAS-H1N1 poses a threat to human health, and greater attention should be given to the surveillance of influenza virus infections in swine and humans.


Assuntos
Vírus da Influenza A Subtipo H1N1 , Influenza Humana , Filogenia , Vírus da Influenza A Subtipo H1N1/genética , Vírus da Influenza A Subtipo H1N1/isolamento & purificação , Vírus da Influenza A Subtipo H1N1/classificação , China/epidemiologia , Humanos , Masculino , Animais , Influenza Humana/virologia , Influenza Humana/epidemiologia , Cães , Células Madin Darby de Rim Canino , Criança , Suínos , Sequenciamento Completo do Genoma , Infecções por Orthomyxoviridae/virologia , Infecções por Orthomyxoviridae/veterinária , Infecções por Orthomyxoviridae/epidemiologia , Genoma Viral
13.
BMC Genomics ; 25(1): 546, 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38824587

RESUMO

BACKGROUND: Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS: The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS: The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.


Assuntos
Brassica rapa , Genoma Mitocondrial , Filogenia , Brassica rapa/genética , Anotação de Sequência Molecular , Genoma de Planta , RNA de Transferência/genética , Composição de Bases
14.
PeerJ ; 12: e17480, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38827288

RESUMO

Background: Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae. Methods: Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method. Results: The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.


Assuntos
Filogenia , Animais , Genoma Mitocondrial/genética , Sanguessugas/genética , Sanguessugas/classificação , Sequenciamento de Nucleotídeos em Larga Escala , RNA Ribossômico 28S/genética
15.
Ann Bot ; 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38822911

RESUMO

Carex breviculmis is a perennial herb with good resistance and is widely used for forage production and turf management. We assembled the genome of 469.01 Mb, revealing 37,372 genes with a BUSCO completeness score of 99.0%. The genome comprises 52.03% repetitive sequences, primarily influenced by recent LTR insertions that have contributed to its expansion. Phylogenetic analysis suggested that C. breviculmis diverged from C. littledalei approximately 6.61 Mya. Investigation into repetitive sequences and expanded gene families (EGFs) highlighted a rapid expansion of tandem duplicate (TD) genes, particularly in areas related to sugar metabolism, various amino acid synthesis, and phenylpropanoid biosynthesis. Additionally, our analysis identified crucial genes involved in secondary metabolic pathways such as glycolysis, phenylpropanoid biosynthesis, and amino acid metabolism, which have undergone positive selection. We reconstructed the sucrose metabolic pathway and identified significant gene expansions, included 16 INV, 9 SPS, and 12 SuSy genes associated with sucrose metabolism, showed varying levels of expansion. In summary, the expansion of these genes, coupled with subsequent positive selection, contributed to C. breviculmis' ability to adapt to environmental stressors. This study lays the foundation for future research on the evolution of Carex plants, their environmental adaptations, and potential genetic breeding.

16.
Braz J Microbiol ; 2024 Jun 04.
Artigo em Inglês | MEDLINE | ID: mdl-38833117

RESUMO

This study aimed to investigate the presence of Mycoplasma spp. and identify the species of mycoplasma isolates obtained from seabirds found on Brazilian coastal beaches. Tracheal and cloacal swab samples were collected from 50 seabirds rescued by three conservation and marine animal rehabilitation centers located in Brazil. The tracheal and cloacal samples were subjected to mycoplasma culture and the isolates were identified through PCR. A "Mollicutes-specific" 16S rRNA PCR reaction was employed for triage. Four species-specific PCR reactions were used to detect Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, or M. gallinarum. The Mollicutes positive and species negative samples were submitted do 16S rRNA sequencing. Eighteen (36%) of 50 seabirds tested positive for mycoplasma by culture. In the PCR for the genus, 28 (56%) of 50 seabirds were positive for Mycoplasma spp., with 13 (26%) detected in the trachea, one (2%) in the cloaca, and 14 (28%) in both sites. In the species-specific PCR, M. gallisepticum was detected in 17.8%, and M. meleagridis in 17.8%. Both species were detected in 14.3%. Of the isolates not characterized at species level, we obtained ten sequences and they were divided into three clusters. The first cluster was closely related to M. meleagridis, the second to M. synoviae, and the third grouped M. tully, M. gallisepticum, and M. imitans. Four and five of nine species of seabirds studied had mycoplasma detected by culture or PCR, respectively. Mycoplasmas were found in the majority of the animals studied, with the highest prevalence proportionally found in Sula leucogaster, and the lowest in Fregata magnificens. The phylogenetic analysis identified Mycoplasma spp. adapted to aquatic birds.

17.
BMC Vet Res ; 20(1): 244, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38849870

RESUMO

BACKGROUND: Fowl adenovirus-4 is a causative agent of hydropericardium hepatitis syndrome (HHS) in chickens and has been frequently reported from many countries. Fowl adenoviruses cause severe disease and mortality in broiler and layer breeders in Azerbaijan. Therefore, in this study, pathological lesions and the dissemination of fowl adenovirus-4 into the visceral organs of infected birds were investigated as well as molecular characterisation of detected strains. For this, liver, heart and spleen from 20 necropsied chickens originated from a broiler breeder flock and a layer breeder flock were embeded on the FTA cards and the samples were analysed for adenovirus-DNA by PCR and sequencing. RESULTS: The findings of necropsy in both broiler and layer breeder chickens were similar, and the liver was severely effected showing hepatitis, and the heart with hydropericardium lesions. The kidneys were swollen with haemorrhages and small white foci on the surface of the spleens were noted. Intestinal congestion and ecchymotic hemorrhages were also observed in some birds. Fowl adenovirus-4-DNA was detected by PCR in all collected organs of 20 birds. The sequence analysis revealed that fowl adenovirus-4 present in Azerbaijan and close similarity of the hexon genes of the adenoviruses existing in the Middle East, North America, far east and Indian subcontinent were determined by phylogenetic analysis. However, sequence diversity was detected from the adenovirus strains circulating in Europe, North and South America. CONCLUSIONS: This study indicates the impact of fowl adenovirus-4 on the poultry health and production, and improved disease control and prevention strategies are necessary to reduce the HHS disease in chickens in Azerbaijan.


Assuntos
Infecções por Adenoviridae , Galinhas , Filogenia , Doenças das Aves Domésticas , Animais , Doenças das Aves Domésticas/virologia , Doenças das Aves Domésticas/epidemiologia , Doenças das Aves Domésticas/patologia , Infecções por Adenoviridae/veterinária , Infecções por Adenoviridae/virologia , Infecções por Adenoviridae/epidemiologia , Azerbaijão/epidemiologia , Aviadenovirus/genética , Aviadenovirus/isolamento & purificação , Aviadenovirus/classificação , Hepatite Viral Animal/virologia , Hepatite Viral Animal/patologia , Hepatite Viral Animal/epidemiologia , DNA Viral/genética , Fígado/patologia , Fígado/virologia , Baço/patologia , Baço/virologia
18.
Mol Biol Evol ; 2024 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-38850168

RESUMO

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (1) species or classification of query sequences and (2) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of non-mitochondrial genes, e.g., ITS or rbcL.

19.
Ecotoxicol Environ Saf ; 280: 116558, 2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38850702

RESUMO

The Multidrug and toxic compound extrusion (MATE) and aluminium activated malate transporter (ALMT) gene families are involved in response to aluminium (Al) stress. In this study, we identified 48 MATE and 14 ALMT gene families in Vigna radiata genome and classified into 5 (MATE) and 3 (ALMT) clades by phylogenetic analysis. All the VrMATE and VrALMT genes were distributed across mungbean chromosomes. Tandem duplication was the main driving force for evolution and expansion of MATE gene family. Collinearity of mungbean with soybean indicated that MATE gene family is closely linked to Glycine max. Eight MATE transporters in clade 2 were found to be associated with previously characterized Al tolerance related MATEs in various plant species. Citrate exuding motif (CEM) was present in seven VrMATEs of clade 2. Promoter analysis revealed abundant plant hormone and stress responsive cis-elements. Results from quantitative real time-polymerase chain reaction (qRT-PCR) revealed that VrMATE19, VrMATE30 and VrALMT13 genes were markedly up-regulated at different time points under Al stress. Overall, this study offers a new direction for further molecular characterization of the MATE and ALMT genes in mungbean for Al tolerance.

20.
Phytomedicine ; 131: 155770, 2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38851103

RESUMO

BACKGROUND: The genus Celastrus is an important medicinal plant resource. The similarity of morphology and the lack of complete chloroplast genome analysis have significantly impeded the exploration of species identification, molecular evolution and phylogeny of Celastrus. PURPOSE: In order to resolve the phylogenic controversy of Celastrus species, the chloroplast genome comparative analysis was performed to provide genetic evidence. METHODS: In this study, we collected and sequenced ten chloroplast genomes of Celastrus species from China and downloaded three chloroplast genomes from the databases. The chloroplast genomes were compared and analyzed to explore their characteristics and evolution. Furthermore, the phylogenetic relationships of Celastrus species were inferred based on the whole chloroplast genomes and protein-coding genes. RESULTS: All the 13 Celastrus species chloroplast genomes showed a typical quadripartite structure with genome sizes ranging from 155,113 to 157,366 bp. The intron loss of the rps16 gene occurred in all the 13 Celastrus species. The GC content, gene sequence, repeat types and codon bias pattern were highly conserved. Ten highly variation regions were identified, which can be used as potential DNA markers in molecular identification of Celastrus species. Eight genes, including accD, atp4, ndhB, rpoC1, rbcL, rpl2, rpl20 and ycf1, were detected to experience positive selection. Phylogenetic analysis showed that Celastrus was a monophyletic group and Tripterygium was the closest sister-group. Noteworthy, C. gemmatus Loes. and C. orbiculatus Thunb. can be discriminated using the chloroplast genome as a super barcode. The comparative and phylogenetic analysis results proposed that C. tonkinensis Pitard. was the synonym of C. hindsii Benth. CONCLUSION: The comparative analysis of the Celastrus chloroplast genomes can provide comprehensive genetic evidence for molecular evolution, species identification and phylogenetic relationships.

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