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African swine fever is a viral disease that causes hemorrhagic fever in domestic pigs and wild swine worldwide. The first case of ASF in Indonesia was reported in North Sumatra Province in September 2019. A total of 20 archival samples of positive ASF collected from the Animal Disease Investigation Center of Medan during the outbreak investigation took place from 2019 to 2023, were used in this study. The partial B646L gene (p72), the full sequence of the E183L gene (p54) and the central variable region (CVR) of the B602L gene were amplified, purified, then sequenced. Web-based BLAST program and MEGA XI software were used to analyze the nucleotide sequencing results. The results of molecular and phylogenetic characterization analysis revealed that the ASF virus that infected pigs in North Sumatra Province in 2019-2023 was belonged to genotype II. Analysis of the three genes (B646L, E183L and B602L) did not show changes in the nucleotide and amino acid sequences in the isolates in the last 5 years. No novel variants were found in the CVR gene B602L. CVR analysis showed that these ASF virus strain belonged to subgroup XXXII. The results of this study revealed that the ASF virus in North Sumatra Province has high homology with ASF virus isolates previously detected in China, Vietnam and East Leste in 2019.

The newly described chrysophyte, Mallomonas vietnamica, is reported for the first time in China from specimens collected in Guizhou Province, SW China. The morphological characteristics were studied using light and scanning electron microscopy. The species was described based on morphological characteristics, including cell size, scale size, dome, V-rib, and bristles. Subsequently, molecular sequencing of M. vietnamica was conducted and a phylogenetic tree was constructed based on concatenated SSU, LSU, and rbcL sequences. The phylogenetic tree led us to suggest raising a new section named Uncatusipedae for this species. This study provides new molecular data from the genus Mallomonas and enriches our understanding of the species diversity and geographical distribution of the genus Mallomonas in China. [ABSTRACT FROM AUTHOR]

Summary: Three populations of Pauronemoides siddiqii n. gen., n. sp. were recovered from three different locations in northwestern and northern Iran from bark and soil samples. The new genus was described and illustrated based upon morphological and molecular characteristics. Pauronemoides n. gen. belongs to the family Paurodontidae and is characterised by the medium-sized body, asymmetrical knobs in stylet base, stem-like extension into intestine, post-vulval uterine sac (PUS) absent or rudimentary, different tail tip shape between sexes, and bursa enveloping tail or reaching to the tail end. The type species, Pauronemoides siddiqii n. gen., n. sp., is mainly characterised by 752-1281 μ m body length in females and 660-1085 μ m in males, six equally-sized lips, stylet 9-11 μ m long with asymmetrical knobs, six incisures in lateral fields forming five bands, three of which (two outers and one central) are wider, and variably lengthened stem-like extension projecting into the intestine. Vulva situated posteriorly (V = 87.7-91.7%), PUS absent. Conical tail with widely rounded end, having a small mucron at tip in females, males with conical tail ending to a narrower tip and bursa enveloping tail completely. The type species of the new genus was compared with all known species of the genera Prothallonema , Paurodontus , Paurodontoides and Paurodontella. Pauronemoides siddiqii n. gen., n. sp. resembles Prothallonema macrocellum and P. mucronatum by having the bulb extension penetrating into the intestine, dimorphism in tail shape of both sexes and bursa enveloping tail, and Paurodontella iranica by tail shape dimorphism between sexes and bursa ending near tail tip. Therefore, the above-mentioned species are transferred to the new genus as Pauronemoides macrocellus n. gen., n. comb. (= Prothallonema macrocellum), P. mucronatus n. gen., n. comb. (= Prothallonema mucronatum) and P. iranicus n. gen., n. comb. (= Paurodontella iranica). In addition to morphological comparisons, molecular phylogenetic analyses were performed using two sequences of small subunit (SSU), and three partial sequences of D2-D3 expansion segments of the large subunit (LSU) rDNA, and the resulting topologies were discussed. [ABSTRACT FROM AUTHOR]

Three new species Buellia darelensis, B. densitheca, B. kashmirensis and two new records B. elegans and B. taishanensis are added to the lichen biota of Pakistan. Buellia darelensis and B. kashmirensis share the same habitats found on the rock while B. densitheca colonized on bark of Pinus hardwoods in the Himalayan forest, Pakistan. Morphological, chemical, and phylogenetic analyses were carried out to elucidate the placement of these species and to support the delimitation of the new taxa. Detailed descriptions and figures for the species are given, and a key to all known buellioid species from Pakistan is provided. Research Highlights: During recent explorations of lichens from different regions of Pakistan, we observed specimens that could not be readily assigned to any known species. A phylogenetic analysis of the internal transcribed spacer nrDNA region confirms their position within the genus Buellia, and morphological data showed distinctiveness of three species from other known species of the genus. We therefore describe these specimens as new species to science, and two species are as new records for the country. Pakistan exhibits a large altitudinal variation, with climatic conditions and a diverse vegetation that supports a diverse and conspicuous lichen biota. The nature reserves have abundant biological resources, and it is expected that more new species of lichen may be discovered in the future. [ABSTRACT FROM AUTHOR]

Piroplasmosis is a zoonotic disease mainly caused by the Babesia and Theileria parasites. Piroplasmosis is often a subclinical infection in dogs and cats that is difficult to detect and is often suspected when clinical signs such as anemia are present. It has been reported to be prevalent in China. However, molecular evidence of the disease has not been reported in pet dogs and cats in Guiyang. In this study, we collected 307 anticoagulated blood samples from an animal hospital in the Wudang District of Guiyang during the period March 2021 to November 2021 and extracted DNA from the samples. The 18S rDNA gene was amplified using PCR, and the positive amplification product was sequenced. The sequences were then analyzed for homology and phylogeny. Of the 307 samples collected, 164 were feline and 143 were canine, with a total of 23 amplifying a target band of approximately 400 bp. The percentage of positives of piroplasms infection in pet cats was 4.27% (7/164), with the pathogens being T. uilenbergi (3) and T. luwenshuni (4). One Colpodella sp. and two undetermined species were also detected in the cat samples. The percentage of positives of piroplasms infection in pet dogs was 7.69% (11/143), with the pathogen being T. uilenbergi (11). One Colpodella sp. was also detected in the dog samples. The results confirmed that T. uilenbergi and T. luwenshuni are prevalent in pet cats and dogs in this area. In addition, the study found a rare zoonotic pathogen, Colpodella sp., in cats and dogs. Therefore, this study is expected to serve as a valuable reference for decision-making regarding animal health management and public health work. [ABSTRACT FROM AUTHOR]

Background: DNA barcoding is a powerful method for phylogenetic mapping and species identification. However, recent research has come to a consistent conclusion about the universality of DNA barcoding. We used matK and rbcL markers to test the universality of twelve accessions from different locations belonging to two Selinum species, Selinum tenuifolium Wall. C. B. Clarke and Selinum vaginatum C. B. Clarke, keeping in mind their ability to identify species and establish phylogenetic relationships within and between the accessions. Results: The success rates of PCR amplification using matK and rbcL were 75.26% ± 3.65% and 57.24% ± 4.42%, and the rate of DNA sequencing was 63.84% ± 4.32% and 50.82% ± 4.36%, respectively, suggesting that success rates of species identification of the two fragments were higher than 41.00% (matK, 41.50% ± 2.81%; rbcL, 42.88% ± 2.59%), proving that these fragments might be used to identify species. The best evolutionary tree with good supporting values was produced utilizing combinations of matK + rbcL markers when phylogenetic relationships were built with random fragment combinations. The twelve accessions of Selinum collected from different locations and their molecular sequences of matK and rbcL markers were blasted with other genera of Apiaceae family, and it was found that Selinum is most closely related to Angelica species of Apiaceae family. Conclusion: The present study has grouped twelve accessions of Selinum species using molecular markers into phylogenies, which is first-of-its-kind report that established interrelationships within different species of Apiaceae with respect to Selinum. [ABSTRACT FROM AUTHOR]

Abstract Background DNA barcoding is a powerful method for phylogenetic mapping and species identification. However, recent research has come to a consistent conclusion about the universality of DNA barcoding. We used matK and rbcL markers to test the universality of twelve accessions from different locations belonging to two Selinum species, Selinum tenuifolium Wall. C. B. Clarke and Selinum vaginatum C. B. Clarke, keeping in mind their ability to identify species and establish phylogenetic relationships within and between the accessions. Results The success rates of PCR amplification using matK and rbcL were 75.26% ± 3.65% and 57.24% ± 4.42%, and the rate of DNA sequencing was 63.84% ± 4.32% and 50.82% ± 4.36%, respectively, suggesting that success rates of species identification of the two fragments were higher than 41.00% (matK, 41.50% ± 2.81%; rbcL, 42.88% ± 2.59%), proving that these fragments might be used to identify species. The best evolutionary tree with good supporting values was produced utilizing combinations of matK + rbcL markers when phylogenetic relationships were built with random fragment combinations. The twelve accessions of Selinum collected from different locations and their molecular sequences of matK and rbcL markers were blasted with other genera of Apiaceae family, and it was found that Selinum is most closely related to Angelica species of Apiaceae family. Conclusion The present study has grouped twelve accessions of Selinum species using molecular markers into phylogenies, which is first-of-its-kind report that established interrelationships within different species of Apiaceae with respect to Selinum. Graphical abstract

This study investigated the prevalence, distribution, and genotypes of adenoviruses (AdVs) and noroviruses (NoVs) in the Puzi River and surrounding areas in Taiwan. The viruses in the water samples were isolated using the membrane filtration method and the viral nucleic acids were extracted. The RNA of NoVs was reverse‐transcribed into complementary DNA using reverse transcriptase‐polymerase chain reaction. AdVs and NoVs were detected using nested PCR. Genotyping and phylogenetic analyses were performed to identify the various viral genotypes in the water samples. Human adenovirus (HAdVs) and porcine adenovirus (PAdVs) were the predominant genotypes in the water samples. The prevalence of F species HAdVs serotype 41 (79.2%) and C species PAdVs serotype 5 (18.1%) was higher than that of other serotypes. Among NoVs, genogroup GII was more prevalent than GI. In particular, GII.4 (21.2%) and GII.17 (18.2%) were the predominant genotypes, which was consistent with the clinical findings. The prevalence of both AdVs and NoVs was higher in the winter than spring, summer and autumn seasons. AdVs and NoVs detection results were statistically analyzed by investigating their association with water quality indicators. The results revealed that the presence of AdVs was significantly correlated with the heterotrophic bacterial count, total coliform Escherichia coli, turbidity, salinity, and dissolved oxygen. Meanwhile, the presence of NoVs was only significantly correlated with temperature, pH, and dissolved oxygen. Microbial pollution sources may include urban runoff and discharge of water from livestock farms situated near the river and tributaries within this region of Taiwan. Future studies should include comparisons of the presence of AdVs and NoVs in these known pollution sources and water quality monitoring of these watersheds, as this will allow potential identification of pollution sources. Additionally, remediation strategies must be developed to minimize viral contamination in the river ecosystem. Plain Language Summary: Adenovirus and norovirus contamination in the river and coastal ecosystem were associated with several infections and health risks such as gastrointestinal and respiratory diseases in humans and animals. In this work, we have investigated the occurrence, distribution and genotypes of adenovirus and norovirus in the Puzi River, its tributaries, Dongshi fishing port and nearby coastal oyster breeding area in four seasons. We have found that the Puzi River has shown a higher prevalence of adenovirus and norovirus than other study sites and the incidence of both viruses was high in the winter season. Human adenovirus 41, porcine adenovirus 5, norovirus GII.4 and GII.17 were the predominant in the water samples. The outflow from the nearby livestock wastewater channels and urban runoff into the river and coastal ecosystem may be a source of contamination of the study sites. The occurrence of both the viruses is significantly correlated with the water quality parameters, which suggested that adenovirus and norovirus are some of the potential water quality indicators. Further, identifying the natural and anthropogenic activities in the contaminated sites can aid in framing the risk management strategies of the related river and coastal ecosystem. Key Points: AdVs prevalence is higher in the river than in other sitesHAdV 41 and PAdV 5 are the dominant genotypes over all sample sitesDominant NoVs genotypes are GII.4 and GII.17, they were associated with clinical cases [ABSTRACT FROM AUTHOR]

Abstract This study investigated the prevalence, distribution, and genotypes of adenoviruses (AdVs) and noroviruses (NoVs) in the Puzi River and surrounding areas in Taiwan. The viruses in the water samples were isolated using the membrane filtration method and the viral nucleic acids were extracted. The RNA of NoVs was reverse‐transcribed into complementary DNA using reverse transcriptase‐polymerase chain reaction. AdVs and NoVs were detected using nested PCR. Genotyping and phylogenetic analyses were performed to identify the various viral genotypes in the water samples. Human adenovirus (HAdVs) and porcine adenovirus (PAdVs) were the predominant genotypes in the water samples. The prevalence of F species HAdVs serotype 41 (79.2%) and C species PAdVs serotype 5 (18.1%) was higher than that of other serotypes. Among NoVs, genogroup GII was more prevalent than GI. In particular, GII.4 (21.2%) and GII.17 (18.2%) were the predominant genotypes, which was consistent with the clinical findings. The prevalence of both AdVs and NoVs was higher in the winter than spring, summer and autumn seasons. AdVs and NoVs detection results were statistically analyzed by investigating their association with water quality indicators. The results revealed that the presence of AdVs was significantly correlated with the heterotrophic bacterial count, total coliform Escherichia coli, turbidity, salinity, and dissolved oxygen. Meanwhile, the presence of NoVs was only significantly correlated with temperature, pH, and dissolved oxygen. Microbial pollution sources may include urban runoff and discharge of water from livestock farms situated near the river and tributaries within this region of Taiwan. Future studies should include comparisons of the presence of AdVs and NoVs in these known pollution sources and water quality monitoring of these watersheds, as this will allow potential identification of pollution sources. Additionally, remediation strategies must be developed to minimize viral contamination in the river ecosystem.

Cucumber mosaic virus (CMV) is one of the most widespread viruses that infects a large number of cultivated crops worldwide and causes severe losses. Besides vegetables and ornamental crops, it is also spreading on medicinal and aromatic plants (MAPs) at an alarming rate. Natural occurrence of green mosaic, leaf curling, necrosis, and distortion were observed on the leaves of Salvia sclarea in the experimental field of CSIR-CIMAP, Lucknow, India. Mechanical transmission assay, morphological features, CP gene, and RNA3-based genomic characterization revealed the association of a new CMV isolate with the present disease. Virus is mechanically sap transmissible to the test plants. Transmission electron microscopy showed the presence of isodiametric particles of ~ 28 nm in diameter. Phylogenetic studies revealed that RNA3 (~ 2.2 kb) belongs to the subgroup IA of CMV. Multiple sequence alignment of amino acid sequences showed that MP possesses two unique changes in the RNA-binding domain and CP was found to be the conserved one with one change only. To the best of our knowledge, this is the first report of a CMV isolate infecting S. sclarea. [ABSTRACT FROM AUTHOR]

Salmonella enterica subspecies enterica serovar Enteritidis is one of the major foodborne zoonotic pathogens globally. It has significantly impacted human health and global trade. In this investigation, whole-genome sequencing was employed to determine the antimicrobial resistance (AMR) pattern of a collection of Salmonella Enteritidis isolated from humans, poultry, and food sources. The study also investigated the virulence genes profile of the isolates as well as the phylogenetic relationships among strains. Illumina NextSeq technology was used to sequence the genome of 82 Salmonella Enteritidis strains isolated over 3 years (2016–2018) in Peninsular Malaysia. The pattern of resistance showed that tetracycline had the highest frequency (37/82, 45.12%), and isolates from food samples showed the highest rate of 9/18 (50.00%), followed by human 17/35 (48.57%) and then poultry 11/29 (37.93%). The second drug with the highest resistance rate is ampicillin with 5/29 (17.24%) for poultry, 4/35 (11.43%) for human, and 0/18 (0.00%) for food isolates respectively. Similarly, a total of 19 antimicrobial resistance (AMR) genes corresponding to the nine drugs used in the disc diffusion assay were evaluated from the whole genome sequence data. The aminoglycoside resistance gene aac(6′)-ly was detected in 79 of the 82 isolates (96.34%). While the phylogenetic analysis revealed distinct lineages isolated, the three sources indicating possible cross-contamination. In conclusion, the results showed that the genomic profile of Salmonella Enteritidis isolated from humans, poultry, and food samples share genetic traits, hence the need to institute measures at controlling the continuous spread of these resistant pathogens.

Salmonella enterica subspecies enterica serovar Enteritidis is one of the major foodborne zoonotic pathogens globally. It has significantly impacted human health and global trade. In this investigation, whole-genome sequencing was employed to determine the antimicrobial resistance (AMR) pattern of a collection of Salmonella Enteritidis isolated from humans, poultry, and food sources. The study also investigated the virulence genes profile of the isolates as well as the phylogenetic relationships among strains. Illumina NextSeq technology was used to sequence the genome of 82 Salmonella Enteritidis strains isolated over 3 years (2016–2018) in Peninsular Malaysia. The pattern of resistance showed that tetracycline had the highest frequency (37/82, 45.12%), and isolates from food samples showed the highest rate of 9/18 (50.00%), followed by human 17/35 (48.57%) and then poultry 11/29 (37.93%). The second drug with the highest resistance rate is ampicillin with 5/29 (17.24%) for poultry, 4/35 (11.43%) for human, and 0/18 (0.00%) for food isolates respectively. Similarly, a total of 19 antimicrobial resistance (AMR) genes corresponding to the nine drugs used in the disc diffusion assay were evaluated from the whole genome sequence data. The aminoglycoside resistance gene aac(6′)-ly was detected in 79 of the 82 isolates (96.34%). While the phylogenetic analysis revealed distinct lineages isolated, the three sources indicating possible cross-contamination. In conclusion, the results showed that the genomic profile of Salmonella Enteritidis isolated from humans, poultry, and food samples share genetic traits, hence the need to institute measures at controlling the continuous spread of these resistant pathogens. [ABSTRACT FROM AUTHOR]

Leucomeris decora is a traditional medicinal plant that is listed as an endangered species in China. Recently, L. decora has become locally rare. Here the complete chloroplast genome of L. decora was assembled and reported for the first time. Its plastome was 151,491 bp in length, including a large single-copy region (LSC; 83,155 bp), a small single-copy region (SSC; 18,216 bp), and a pair of inverted repeated regions (IRa and IRb; 25,060 bp). The overall GC content was 37.8%, and the genome contains 134 genes, including 92 protein-coding genes, 8 rRNA genes, and 34 tRNA genes. Phylogenetic analysis of thirteen representative species from the family of Asteraceae showed that L. decora is clustered into one clade with Gerbera jamesonii with high bootstrap values, indicating a close relationship between these two species.

Luffa plants showing symptoms of begomovirus infection were collected from Vehari, Punjab in 2016. RCA and PCR amplifications of begomovirus genomic components showed the presence of a typical Old World bipartite begomovirus Tomato leaf curl New Delhi virus (ToLCNDV). Interestingly, Ageratum conyzoides symptomless alphasatellite and CLCuMB were also found associated with bipartite begomoviruses in the same host, however, no monopartite begomovirus was detected. To the best of our knowledge, this is the first report of ToLCNDV with associated satellites infecting L. cylindrica in Pakistan. The importance of begomovirus extended host range with different combinations of associated satellites has been discussed. [ABSTRACT FROM AUTHOR]

Bryophyllum daigremontianum is a very important traditional medicine and ornamental plant. Although Bryophyllum and Kalanchoe have been supported to form a clade, however, lack of chloroplast genomic severely hinders our understanding the phylogenetic relationships between them. In this study, the complete chloroplast genome of B. daigremontianum is first presented. It is 150,058 bp in length consisted a large single-copy (LSC, 82,164 bp) and a small single-copy (SSC, 17,042bp) separated by a pair of inverted repeats (IR, 25,426 bp) including 86 protein-coding genes, 37 tRNA, and 8 rRNA. Phylogenetic analysis supported that B. daigremontianum was closer to K. tomentosa than other species, which showed that chloroplast genome sequences offer a useful resource for future phylogenetic studies of Kalanchoe and Bryophyllum species.

Barnacles and their allies (Thecostraca) are a biologically diverse, monophyletic crustacean group, which includes both intensely studied taxa, such as the acorn and stalked barnacles, as well as cryptic taxa, for example, Facetotecta. Recent efforts have clarified phylogenetic relationships in many different parts of the barnacle tree, but the outcomes of these phylogenetic studies have not yet been combined into a single hypothesis for all barnacles. In the present study, we applied a new “synthesis” tree approach to estimate the first working Barnacle Tree of Life. Using this approach, we integrated phylogenetic hypotheses from 27 studies, which did not necessarily include the same taxa or used the same characters, with hierarchical taxonomic information for all recognized species. This first synthesis tree contains 2,070 barnacle species and subspecies, including 239 barnacle species with phylogenetic information and 198 undescribed or unidentified species. The tree had 442 bifurcating nodes, indicating that 79.3% of all nodes are still unresolved. We found that the acorn and stalked barnacles, the Thoracica, and the parasitic Rhizocephala have the largest amount of published phylogenetic information. About half of the thecostracan families for which phylogenetic information was available were polyphyletic. We queried publicly available geographic occurrence databases for the group, gaining a sense of geographic gaps and hotspots in our phylogenetic knowledge. Phylogenetic information is especially lacking for deep sea and Arctic taxa, but even coastal species are not fully incorporated into phylogenetic studies.

Barnacles and their allies (Thecostraca) are a biologically diverse, monophyletic crustacean group, which includes both intensely studied taxa, such as the acorn and stalked barnacles, as well as cryptic taxa, for example, Facetotecta. Recent efforts have clarified phylogenetic relationships in many different parts of the barnacle tree, but the outcomes of these phylogenetic studies have not yet been combined into a single hypothesis for all barnacles. In the present study, we applied a new "synthesis" tree approach to estimate the first working Barnacle Tree of Life. Using this approach, we integrated phylogenetic hypotheses from 27 studies, which did not necessarily include the same taxa or used the same characters, with hierarchical taxonomic information for all recognized species. This first synthesis tree contains 2,070 barnacle species and subspecies, including 239 barnacle species with phylogenetic information and 198 undescribed or unidentified species. The tree had 442 bifurcating nodes, indicating that 79.3% of all nodes are still unresolved. We found that the acorn and stalked barnacles, the Thoracica, and the parasitic Rhizocephala have the largest amount of published phylogenetic information. About half of the thecostracan families for which phylogenetic information was available were polyphyletic. We queried publicly available geographic occurrence databases for the group, gaining a sense of geographic gaps and hotspots in our phylogenetic knowledge. Phylogenetic information is especially lacking for deep sea and Arctic taxa, but even coastal species are not fully incorporated into phylogenetic studies. [ABSTRACT FROM AUTHOR]

Piroplasmosis is a zoonotic disease mainly caused by the Babesia and Theileria parasites. Piroplasmosis is often a subclinical infection in dogs and cats that is difficult to detect and is often suspected when clinical signs such as anemia are present. It has been reported to be prevalent in China. However, molecular evidence of the disease has not been reported in pet dogs and cats in Guiyang. In this study, we collected 307 anticoagulated blood samples from an animal hospital in the Wudang District of Guiyang during the period March 2021 to November 2021 and extracted DNA from the samples. The 18S rDNA gene was amplified using PCR, and the positive amplification product was sequenced. The sequences were then analyzed for homology and phylogeny. Of the 307 samples collected, 164 were feline and 143 were canine, with a total of 23 amplifying a target band of approximately 400 bp. The percentage of positives of piroplasms infection in pet cats was 4.27% (7/164), with the pathogens being T. uilenbergi (3) and T. luwenshuni (4). One Colpodella sp. and two undetermined species were also detected in the cat samples. The percentage of positives of piroplasms infection in pet dogs was 7.69% (11/143), with the pathogen being T. uilenbergi (11). One Colpodella sp. was also detected in the dog samples. The results confirmed that T. uilenbergi and T. luwenshuni are prevalent in pet cats and dogs in this area. In addition, the study found a rare zoonotic pathogen, Colpodella sp., in cats and dogs. Therefore, this study is expected to serve as a valuable reference for decision-making regarding animal health management and public health work., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wu, Meng, Yu, Zhou, Yang, Chen, Yang, Sun, Cao, Jiang, Wu and Zhan.)

Monomeric isocitrate dehydrogenases (IDHs) have a single polypeptide sizing around 85 kDa. The IDH2 from the opportunistic bacterium Acinetobacter baumannii (AbIDH2) with a mass of 83 kDa was formerly recognized as a typical monomeric IDH. However, both size exclusion chromatography and analytical ultracentrifugation analysis indicated that AbIDH2 exists as a homodimer in solution. The crystallographic study of the substrate/coenzyme-free AbIDH2 gave a dimeric structure and each subunit contained a domain I and a domain II. The dimeric assembly is mainly stabilized by hydrophobic interactions (16 hydrogen bonds and 11 salt bridges) from the dimer's interface platform, which centered around the three parallel helices (α4, α12, and α17) and one loop from the domain II. Kinetic analysis showed that the dimeric AbIDH2 showed much lower catalytic efficiency (0.39 μM-1·s-1) as compared to the typical monomeric IDHs (~15 μM-1·s-1). Key residues crucial for dimer formation were simultaneously changed to generate the mutant mAbIDH2. The disruption of the hydrophobic forces disassociated the dimeric AbIDH2, making mAbIDH2 a monomeric enzyme. mAbIDH2 sustained specific activity (21.9 ° 2U/mg) comparable to AbIDH2 (25.4 ° 0.7 U/mg). However, mAbIDH2 proved to be a thermolabile enzyme, indicating that the thermostable dimeric AbIDH2 may have a physiological significance for the growth and pathogenesis of A. baumannii. Phylogenetic analysis demonstrated the existence of numerous AbIDH2 homologous proteins, thus expanding the monomeric IDH protein family. [ABSTRACT FROM AUTHOR]

Achaea janata granulovirus (AcjaGV), an insect virus belonging to Baculoviridae, infects semilooper, a widely distributed defoliating pest on castor beans ( Ricinus communis L.) and several other plant hosts in India. The propagation and purification of the Hyderabad isolate AcjaGV were performed, granulin gene from this isolate was amplified, cloned and sequenced, and its homology with other known granulin genes was assessed. The 753-bp granulin ORF of AcjaGV encoded for a granulin protein of 250 amino acids with a molecular mass of 29.5 ± 0.7 kDa. This amino acid sequence exhibited significant homology with Spodoptera litura granulovirus (SpliGV) and other GVs infecting insects in the same Noctuidae family of Lepidoptera. Peptide analysis of granulin protein indicated close homology with that of SpliGV. Virtual RFLP patterns from in silico digestions of granulin gene of 18 granuloviruses mapped by 12 restriction enzymes were used for simulated digestions. Implications of the phylogenetic relationships of granulin nucleotide and deduced amino acid sequence are discussed. We have established the sequence identity of granulin gene of AcjaGV and characterized its protein product and the phylogenetic relationship with other known GVs. Our results indicate the presence of unique restriction sites for three restriction enzymes, and this can be used as a tool for identification of AcjaGV from various sources. This is the first report from the Indian subcontinent to describe the complete granulin gene of a GV isolated from A. janata. [ABSTRACT FROM AUTHOR]

Conservation of locally adapted indigenous livestock has become an important objective in sustainable animal breeding. The current study is first detailed analysis of the genetic diversity harboured by Kaunayen chicken of Manipur. The genotype data generated on 24 microsatellite markers was analysed to establish distinctness of Kaunayen from other registered poultry breeds of India. Large number of observed alleles (212) and heterozygosity (0.66) indicated high genetic diversity. Mean number of alleles observed in Kaunayen chicken were 8.83±0.31 and ranged between 4 (MCW250 and LEI174) and 15 (LEI120). Mean effective number of alleles was significantly less (4.11±0.38) than the observed number of alleles. The maximum observed heterozygosity (1.0) was observed in MCW262 locus and the minimum (0.368) in LEI166. The expected heterozygosity (0.706) was more than the observed heterozygosity (0.664±0.036) which points to heterozygote deficiency and was also reflected in positive FIS estimate (0.06) for the population. Non-significant heterozygote excess on the basis of Infinite allele model and Two-phase model in conjunction with mode-shift analysis test, indicated an absence of bottleneck. Phylogenetic reconstruction on the basis of genetic distance places Kaunayen chicken as a distinct population with respect to other poultry breeds of India. All analysis showed that a significant amount of genetic variation is maintained in Kaunayen chicken population and has appropriately been registered as the 17th chicken breed of India. [ABSTRACT FROM AUTHOR]

We investigated the first laboratory-confirmed human case of cowpox virus infection in Russia since 1991. Phylogenetic studies of haemagglutinin, TNF-α receptor-like protein and thymidine kinase regions showed significant differences with known orthopoxviruses, including unique amino-acid substitutions and deletions. The described cowpox virus strain, taking into account differences, is genetically closely related to strains isolated years ago in the same geographical region (European part of Russia and Finland), which suggests circulation of viral strains with common origin in wild rodents without spread over long distances and appearance in other parts of the world. [ABSTRACT FROM PUBLISHER]

Given that Newcastle disease (ND) is one of the major threats for the poultry industry, testing of Newcastle disease virus (NDV) has been carried out since 2010 in cases of mortality in wild birds (passive surveillance) in Catalonia. The objective is to provide an early warning system to prevent the infection of poultry. Since 2010, 35 episodes of mortality in wild birds were attributed to NDV infection. Throughout this period there was a progressive expansion of NDV to new areas, with an increase in the episodes of mortality, although it is not clear whether they were the result of the spread of the virus, or of the improvement of the surveillance. Phylogenetic analyses indicate that two distinct sublineages of NDV, 4a and 4b, were circulating in Catalonia. Both sublineages seem to be endemic in the wild bird population, affecting mainly Eurasian-collared doves, with a clear pattern in relation to its spatial distribution (coincident with the distribution of this species), and its temporal distribution (with the majority of cases between September and February). So far, endemicity in wild birds has not resulted in ND outbreaks in poultry. However, there are still many uncertainties about, for example, whether NDV may expand to new areas of Catalonia (with higher poultry density), or about the threat that the apparently more novel sublineage 4a may represent. Hence, efforts should be made so that measures to prevent infection of poultry farms (particularly in high-risk areas and periods) are encouraged, and surveillance is maintained. [ABSTRACT FROM PUBLISHER]

Leucomeris decora is a traditional medicinal plant that is listed as an endangered species in China. Recently, L. decora has become locally rare. Here the complete chloroplast genome of L. decora was assembled and reported for the first time. Its plastome was 151,491 bp in length, including a large single-copy region (LSC; 83,155 bp), a small single-copy region (SSC; 18,216 bp), and a pair of inverted repeated regions (IRa and IRb; 25,060 bp). The overall GC content was 37.8%, and the genome contains 134 genes, including 92 protein-coding genes, 8 rRNA genes, and 34 tRNA genes. Phylogenetic analysis of thirteen representative species from the family of Asteraceae showed that L. decora is clustered into one clade with Gerbera jamesonii with high bootstrap values, indicating a close relationship between these two species. [ABSTRACT FROM AUTHOR]

RoTat 1.2 variant surface glycoprotein (VSG) is considered to be one of the most important VSGs expressed in many of the isolates of Trypanosoma evansi. This accounts for its utility as a potent molecule for both molecular and serological based detection of Surra. Of late, there are reports of its absence and variation from a fewer isolates of T. evansi. The study of these variations by means of molecular phylogenetic studies is of immense significance in determining the evolutionary phylogeny of these T. evansi isolates. With this information in the background, the present study was designed to clone and characterize RoTat 1.2 VSG from horse isolate of T. evansi from semi arid regions of India. Thereafter, the gene was compared with various other isolates across the world. Interestingly, the isolate was found to be closer to camel isolates from Egypt than the other known isolates from India and Kenya. The finding is important from evolutionary point of view. [ABSTRACT FROM AUTHOR]

Throughout evolution, parasites have adapted in order to successfully intervene in the host defense, producing specific peptides and proteins. Interestingly, these peptides and proteins have been exploited as potential drug candidates against several diseases. Furthermore, biotechnology studies and cDNA libraries have remarkably contributed to identify potentially bioactive molecules. In this regard, herein, a cDNA library of salivary complexes from Haementeria vizottoi leeches was constructed, the transcriptome was characterized and a phylogenetic analysis was performed considering antistasin-like and antiplatelet-like proteins. Hundred twenty three transcripts were identified coding for putative proteins involved in animal feeding (representing about 10% of the expression level). These sequences showed similarities with myohemerythrins, carbonic anhydrases, anticoagulants, antimicrobials, proteases and protease inhibitors. The phylogenetic analysis, regarding antistasin-like and antiplatetlet-like proteins, revealed two main clades in the Rhynchobdellida leeches. As expected, the sequences from H. vizottoi have presented high similarities with those types of proteins. Thus, our findings could be helpful not only to identify new coagulation inhibitors, but also to better understand the biological composition of the salivary complexes. [ABSTRACT FROM AUTHOR]

Since most microorganisms in natural environments cannot be cultured in laboratory media, due to low growth rates or their dependency on specific conditions, culture-based systems are unable to estimate the full microbial diversity of an environment. However, molecular techniques can provide this ability by analysing the diversity of macromolecules, such as proteins, RNA or DNA, present in the environment. Metagenomic methods employ sequencing procedures for the determination of the microbial diversity of a community (sequence-driven metagenomic analysis) or for examining a particular functional ability of microorganisms in the environment (function-driven metagenomic gene identification), using genomic DNA obtained directly from environmental samples. Application of metagenomic methods provides a huge amount of data that can be analysed only by using powerful computational bioinformatics tools. Currently, these bioinformatic tools are adequate to allow the ecological structure of a community and the possible functions of its members to be determined. The resulting data can be useful for phylogenetic and biotechnological studies. This paper reviews the emergence of new technologies based on sequencing environmental DNA and on bioinformatics. We assess its potential for application in environmental studies, particularly for developing new biomolecules that can be applied to degrading recalcitrant pollutants in terrestrial and aquatic systems. [ABSTRACT FROM AUTHOR]

• AdV pollution in fishing ports was associated with nearby polluted river water. • HAdV 41 and PAdV 5 were the dominant serotypes in the waters of the fishing ports. • The seasonal distributions of HAdV and PAdV differed significantly. • The AdV detection rate significantly differed according to regional distribution. • The presence of AdV was associated with total plate count, pH, and salinity. Adenoviruses (AdVs) are a major cause of clinical infections and have been proposed as indicators of water quality. However, quantitative data on the environmental prevalence of AdVs is lacking. We investigated the prevalence, distribution, seasonal occurrence, quantity, and genotype of AdVs in 13 fishing harbours in Taiwan. AdVs in the water samples were isolated by membrane filtration and the AdV DNA was extracted. Next, AdVs were detected using nested polymerase chain reaction. Genotyping and phylogenetic analysis were performed to identify various AdV genotypes present in the water samples. The F species human AdV (HAdV) serotype 41 (63.6%) and C species porcine AdV (PAdV) serotype 5 (33.3%) were more prevalent than the other serotypes. The prevalence of AdVs was highest in the fall, followed by in the spring and summer. Among the fishing harbours, the highest detection rate of AdVs was observed in Yenpudongang in all seasons. However, Puoziliao was the only site at which AdVs were not detected during the study period. AdV detection at sampling sites may be correlated with sewage and livestock wastewater discharge via outflow of nearby rivers to fishing ports. Statistical analysis (Mann–Whitney U test) based on data from water quality indicators revealed that the presence of AdVs was significantly associated with the heterotrophic plate count, pH, and salinity. Human and swine population data from nearby local townships and river/drainage basins were collected from the Taiwan Central Government's website. The data were analyzed using Spearman's rank correlation coefficient to determine the relationship between the prevalence of AdVs, HAdVs, and PAdVs in fishing harbours, and microbial water quality indicators. Statistical evidence indicated that the detection levels of HAdVs and PAdVs in fishing harbours were mainly associated with human and swine populations in the corresponding river/drainage basin, respectively. Additionally, the swine population in the river/drainage basin was positively correlated with microbial water quality indicators. [Display omitted] [ABSTRACT FROM AUTHOR]

Prokaryotic MazF family toxins cooccur with cognate antitoxins having divergent DNA-binding folds and can be of chromosomal or plasmid origin. Sequence similarity search was carried out to identify the Toxin–Antitoxin (TA) operons of MazF family followed by sequence analysis and phylogenetic studies. The genomic DNA upstream of the TA operons was searched for the presence of regulatory motifs. The MazF family toxins showed a conserved hydrophobic pocket in a multibinding site and are present in pathogenic bacteria. The toxins of the MazF family are associated with four main types of cognate antitoxin partners and cluster as a subfamily on the branches of the phylogenetic tree. This indicates that transmission of the entire operon is the dominant mode of inheritance. The plasmid borne TA modules were interspersed between the chromosomal TA modules of the same subfamily, compatible with a frequent interchange of TA genes between the chromosome and the plasmid akin to that observed for antibiotic resistance gens. The split network of the MazF family toxins showed the AbrB-linked toxins as a hub of horizontal gene transfer. Distinct motifs are present in the upstream region of each subfamily. The presence of MazF family TA modules in pathogenic bacteria and identification of a conserved binding pocket are significant for the development of novel antibacterials to disrupt the TA interaction. However, the role of TAs in stress resistance needs to be established. Phylogenetic studies provide insight into the evolution of MazF family TAs and effect on the bacterial genome. [ABSTRACT FROM AUTHOR]

A genomic DNA fragment ( pAA7- 2) amplified by a random amplified polymorphic DNA primer from the rice cultivar IR68 was used to assess the genetic variation and genetic relationships among the species of genus Oryza. A Southern hybridization experiment of diverse upland rice accessions using a single restriction enzyme HindIII generated unique DNA fingerprint for each accession. The differential hybridization pattern reflecting the copy number variation of pAA7- 2 in a collection of wild species and cultivated species of rice provided insight about the genetic relationships among them. All AA genome species exhibited clear banding pattern suggesting presence of fewer copies of this sequence. Strongest hybridization signal was obtained in species belonging to BB, CC, GG, BBCC, CCDD genomes, whereas weakest hybridization signal was visible in EE, FF, and HHJJ genome species. Oryza brachyantha was the most divergent species. Clear difference in banding pattern was evident between Oryza schlechteri and Oryza coarctata belonging to HHKK genome. Although pAA7- 2 had no repetitive sequences often associated with hypervariable loci, homology to a putative unclassified expressed retrotransposon distributed over several rice chromosomes was responsible for the complex banding patterns. There were more sites homologous to pAA7- 2 sequence in corn and sorghum genome compared with the rice genome. The study demonstrates the potential of pAA7- 2 as a powerful molecular tool for DNA fingerprinting, genetic diversity, phylogenetic, and evolutionary studies in Oryza sativa and its wild relatives and other grasses. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships within and among three genera of the family Acroporidae, namely Acropora, Montipora and Astreopora were examined based on mitochondrial cytochrome b (690 bp) gene sequences with special emphasis on Indian scleractinian corals. Analyses using mitochondrial DNA sequences highlight the usefulness of a molecular approach for examining the phylogenetics, evolution and diversity of corals. The analysis based on various algorithms, including neighbour joining and maximum parsimony along with network analysis clearly establishes the monophyly of Acropora and Montipora. The average number of pairwise differences within the three genera revealed maximum intragenus variability in Acropora, followed by Montipora and Astreopora. [ABSTRACT FROM AUTHOR]

Comparison of the common floristic elements between the West Indies and the surrounding continents shows a mosaic of affinities that are stronger to Central America and South America as a whole than with either one of them separately or with North America. However, since only 28% of the total West Indian seed plant flora is shared with other geographic regions of the world, the referred exercise is of limited value. Numerous tables are provided to show the distribution of genera throughout the archipelago. The application of phylogenetic studies into the service of biogeography is herein regarded as the next necessary step in elucidating the origins and affinities of the West Indian flora. [ABSTRACT FROM AUTHOR]

AcanthoscelidesSchilsky is a large genus of neotropical bruchid beetles, in which most species show host plant specialization.Acanthoscelides obtectusandAcanthoscelides obvelatusare two sibling species specialized onPhaseolusbeans, and are therefore considered pests. Up to now, the status of these two taxa has remained unclear, the few studies conducted having failed to elucidate whether these are two differentiated species or a single morphologically variable species. In addition,A. obvelatushas not been taken into account in the great majority of studies of bean bruchids. In this morphological and genetic study, we show thatA. obtectusandA. obvelatusare two‘true’ non-hybridizing species, which diverged about 22 Mya. Although the two species demonstrate only few morphological differences, we point out some diagnostic characters that enable their identification in the field. We also address a genetic method of differentiation of the two species, based on species-specific microsatellite loci. The strong morphological resemblance of these two species, despite their ancient divergence, may be the result of evolutionary stasis, which could be the consequence of stabilizing selection. Niche differentiation could enable the two species to coexist indefinitely. [ABSTRACT FROM AUTHOR]

Leucomeris decora is a traditional medicinal plant that is listed as an endangered species in China. Recently, L. decora has become locally rare. Here the complete chloroplast genome of L. decora was assembled and reported for the first time. Its plastome was 151,491 bp in length, including a large single-copy region (LSC; 83,155 bp), a small single-copy region (SSC; 18,216 bp), and a pair of inverted repeated regions (IRa and IRb; 25,060 bp). The overall GC content was 37.8%, and the genome contains 134 genes, including 92 protein-coding genes, 8 rRNA genes, and 34 tRNA genes. Phylogenetic analysis of thirteen representative species from the family of Asteraceae showed that L. decora is clustered into one clade with Gerbera jamesonii with high bootstrap values, indicating a close relationship between these two species., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The efficiency of enzymatic conversion of glucose into glucose-6-phosphate in fish fed carbohydrates is still a matter of debate. This study reports the first ever identification of hexokinase-family members at a molecular level in fish. The deduced amino acid sequences of six cDNA clones allowed their assignement either to hexokinase IV (glucokinase) for rainbow trout (Oncorhynchus mykiss), common carp (Cyprinus carpio) and gilthead seabream (Sparus aurata) or to hexokinase I/II for the common carp (two clones) and the gilthead seabream, based on their similarities to known members of the HK family. The evolutionary relationships among these sequences were investigated by phylogenetic analysis. These hexokinase sequences constitute potential molecular tools for analysis of interspecific differences in dietary carbohydrate utilization in fish. [ABSTRACT FROM AUTHOR]

The 459-bp HindIII (pBN-4) and the 1732-bp Eco RI (pBNE8) fragments from the Brassica nigra genome were cloned and shown to be members of a dispersed repeat family. Of the three major diploid Brassica species, the repeat pBN-4 was found to be highly specific for the B. nigra genome. The family also hybridized to Sinapis arvensis showing that B. nigra had a closer relationship with the S. arvensis genome than with B. oleracea or B. campestris. The clone pBNE8 showed homology to a number of tRNA species indicating that this family of repeats may have originated from a tRNA sequence. The species-specific 459-bp repeat pBN-4 was localized on the B. nigra chromosomes using monosomic addition lines. In addition to the localization of pBN-4, the chromosomal distribution of two other species-specific repeats, pBN34 and pBNBH35 (reported earlier), was studied. The dispersed repeats pBN-4 and pBNBH35 were found to be present on all of the chromosomes, whereas the tandem repeat pBN34 was localized on two chromosomes. [ABSTRACT FROM AUTHOR]

The construction and characterization of two genome-specific recombinant DNA clones from B. nigra are described. Southern analysis showed that the two clones belong to a dispersed repeat family. They differ from each other in their length, distribution and sequence, though the average GC content is nearly the same (45%). These B genome-specific repeats have been used to analyse the phylogenetic relationships between cultivated and wild species of the family Brassicaceae. [ABSTRACT FROM AUTHOR]

The group 1 and group 2 σ70-type sigma factors of the green sulfur bacterium Chlorobium tepidum and of the green nonsulfur bacterium Chloroflexus aurantiacus were cloned and characterized. Cb. tepidum was found to contain one σ70-type sigma factor; the expression of the gene was analyzed by Northern blot hybridization and primer-extension mapping. Cf. aurantiacus has genes encoding four sigma factors of groups 1 and 2. The expression of these genes was examined in cells grown aerobically and anaerobically. The sigC gene was expressed at approximately equal levels under both conditions, resulting in its designation as the group 1 sigma factor of this organism. The only other detectable transcripts arose from the sigB gene, which was expressed at higher levels during aerobic growth. A phylogenetic tree was obtained using the group 1 sigma factors of Cb. tepidum, Cf. aurantiacus, and diverse eubacteria as the molecular marker. The resulting phylogenetic tree shows that Cb. tepidum and Cf. aurantiacus are related to each other and to the cyanobacteria. The relationship of the group 2 sigma factors of Cf. aurantiacus and the cyanobacteria was more specifically examined phylogenetically. The group 2 sigma factors of Cf. aurantiacus probably arose by gene duplication events after the split of the green nonsulfur bacteria from other photosynthetic eubacteria. [ABSTRACT FROM AUTHOR]

Bryophyllum daigremontianum is a very important traditional medicine and ornamental plant. Although Bryophyllum and Kalanchoe have been supported to form a clade, however, lack of chloroplast genomic severely hinders our understanding the phylogenetic relationships between them. In this study, the complete chloroplast genome of B. daigremontianum is first presented. It is 150,058 bp in length consisted a large single-copy (LSC, 82,164 bp) and a small single-copy (SSC, 17,042bp) separated by a pair of inverted repeats (IR, 25,426 bp) including 86 protein-coding genes, 37 tRNA, and 8 rRNA. Phylogenetic analysis supported that B. daigremontianum was closer to K. tomentosa than other species, which showed that chloroplast genome sequences offer a useful resource for future phylogenetic studies of Kalanchoe and Bryophyllum species., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2021 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)