Phylogenetic Analysis Of Nucleotide Sequences Research Articles

Exploring the mitogenomes of Batracomorphus (Hemiptera: Cicadellidae: Iassinae): new insights from structural diversity and phylogenomic analyses

Abstract Comparisons of mitogenomes are widely used for species identification and to explore the phylogenetic relationship among insect taxa. Batracomorphus is the third most diverse and widely distributed genus in the Cicadellidae (Hemiptera). However, there have been no analyses of genome structure and phylogenetic relationships within the genus. To compensate for the paucity of genomic information in this genus, we sequenced novel complete mitochondrial genomes of 11 Batracomorphus species and combined these with 23 previously sequenced mitochondrial genomes to perform structural comparisons and phylogenomic studies. Our results reveal generally conserved mitogenome organization, with one case of tRNA gene rearrangement, with trnI-trnQ reversed to trnQ-trnI when compared with the ancestral arrangement. Analysis of the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks) showed ATP8 is the fastest and COI is the slowest evolving gene. ND2 and ND6 have highly variable nucleotide diversity, whereas COI and ND1 exhibit the lowest diversity. Phylogenetic analysis of nucleotide sequences grouped Batracomorphus species into a clade within the subfamily Iassinae. Within Batracomorphus, 3 clades were reconstructed consistent with the observed gene rearrangement, indicating that such rearrangements can serve as reliable molecular markers supporting phylogenetic hypotheses. These clades also correspond to clusters of species recovered by morphometric analysis of aedeagal shape, suggesting that characters of the male genitalia traditionally used for species delimitation are phylogenetically informative. Molecular divergence time estimates indicate that most speciation events within Batracomorphus occurred between the Paleogene and Neogene. This study provides insight into the population genetics, molecular biology, phylogeny, and morphological evolution of the leafhopper subfamily Iassinae and its largest genus, Batracomorphus.

XBB.1, BQ1.1 and atypical BA.4.6/XBB.1 recombinants predominate current SARS-CoV-2 Wavelets with flu-like symptoms in Cameroon: A snapshot from genomic surveillance.

As of December 2022, Cameroon had observed a slight resurgence of COVID-19, raising concerns on genomic surveillance of related-SARS-CoV-2 variants under circulation. Following a laboratory-based survey, positive SARS-CoV-2 samples detected from December-2022 through March-2023 were processed for targeted sequencing at the Chantal BIYA International Reference Centre (CIRCB) in Yaoundé-Cameroon. From all positive cases detected, 13 were successfully sequenced (mean age 34 years, 70% female); the majority of the cases were unvaccinated (70%, 9/13) and symptomatic (92%, 12/13); all with flu-like symptoms (100%, 12/12). Following RT-PCR, the median cycle threshold was 22.23 [18-24] for the N gene; and 24.09 [20-26] for the ORF gene, underscoring high viral loads. Phylogenetic analysis of nucleotide sequences identified four major sub-variants in circulation, of which BA.5 (3/13), the recombinants BQ.1.1 (4/13), XBB.1 (4/13) and novel atypical variant of BA.4.6/XBB.1 (2/13). This snapshot surveillance indicates the introduction/emergence and circulation of new Omicron sub-variants, all accompanied by minor/mild symptoms. However, these new sub-variants and recombinants call for continuous genomic surveillance to prevent further resurgence of Covid-19 epidemiological wave.

Phylogenetic Analysis to Detect COVID Superspreaders

Aims: Detection of superspreading events by phylogenetic analysis of nucleotide sequences from a population of individuals collected from a narrow time interval.
 Study Design: Retrieve nucleic acid sequences, construct multiple sequence alignments, and build phylogenetic networks to determine sources of infection.
 Place and Duration of Study: This study was performed at the Delaware Biotechnology Institute of the University of Delaware over the period: June-August, 2022. The data used were from the GIS AID database.
 Methodology: Sequences for analysis were sampled from the GISAID initiative’s open-access SARS-CoV-2 genome database. We selected high-quality nucleotide sequences submitted by Delaware labs between March 18 and April 14, 2021, an important period of 4 weeks which saw the Alpha variant spread rapidly in the Delaware population.
 Results: Four sources accounted for 215 of the 401 sequences. In other words, 54% of all cases were rooted in just five sources.
 Conclusion: Thus, superspreading seems to have a major impact on the proportion of individuals in a population affected with COVID.

Prevalence and genotypes distribution of virus hepatitis B and hepatitis delta virus in chronic liver diseases in Kazakhstan

BackgroundThe geographical distribution of hepatitis B virus (HBV) and hepatitis D virus (HDV) genotypes is uneven and has its own clinical and organizational implications for health systems. Despite the introduction of vaccination and successful antiviral therapy the prevalence of chronic hepatitis B (with or without delta agent) increased over the past 5 years. This study aimed for the first time to investigate the molecular epidemiology of HBV and HDV in Kazakhstan.MethodsTotal 834 chronic hepatitis B (with or without delta agent) patients were included to the study from November 2017 to June 2019. The material was collected from the regional hepatological сenters from 13 cities of Kazakhstan. Genotyping of HBV/HDV isolates was carried out using phylogenetic analysis of null-binary sequences of Kazakhstani isolates, in comparison with the reference sequences. Nucleotide sequence alignment was performed using the ClustalW algorithm, the “neighbor-joining” method was used for the construction of phylogenetic trees and subsequent analysis.ResultsOverall 341 samples were PCR-positive and genotyped for HBV. Comparison and phylogenetic analysis of nucleotide sequences of HBV isolates showed that they were represented by genotypes HBV-D (95.9%), HBV-A (3.5%) and HBV-C (0.6%). At the same time, the identity of the nucleotide sequences of Kazakhstani isolates were: HBV-D (95–100%); HBV-A (97.2–100%) and HBV-C (99%). 256 samples were PCR positive and genotyped for HDV, all of them belonged to genotype 1.ConclusionThis study describes for the first time the molecular epidemiology of HBV and HDV in Kazakhstan. The data obtained expand the knowledge of the global epidemiology of viruses; have potential implications for public health policy and for further clinical research on chronic hepatitis in Kazakhstan.Trial registrationClinicalTrials.gov NCT05095181 (registered on 27/10/2021).

Genetic identification and phylogenetic relationships of fish species at Panjnad , Abbasia and Abu Dahbi canals (Punjab, Pakistan) based on mitochondrial COI sequences

Fish is an extremely nutritious food that is abundant in important minerals, vitamin D, protein, and omega-3 fatty acids. Now a day, mislabeling of fish products is a major problem in the fish industry that affects the market prices and causes fluctuations. Phylogenetic analysis of nucleotide sequences is a technique that might be used to verify the identity of misidentified fish species. In this study five species (Cirrhinus mrigala, Hypophthalmichthys molitrix, two Actinopterygii sp., and Mastacembelus armatus) were used for phylogenetic analysis using the COI gene was amplified using the PCR, average product size is 658 base pairs. A comparison of obtained sequences was implemented through National Center for Biotechnology Information database (NCBI) and the Basic Local Alignment Search Tool (BLAST). Most resemble sequences were downloaded for comparison with our sequencing results. By using MAGA X the rates of different transitional substitutions are 11.33 and transversional substitutions are 6.83. The estimated Transition/Transversion bias (R) is 0.83. The K2P model was used for the estimation of this substitution pattern. Because most freshwater fish species were in the same order or family, phylogenetic tree analysis indicated that they grouped together. Using the InterPro database, the activity and regulatory pathways of the Cytochrome C Oxidase 1 gene are identified to show their activity on the protein level, especially for some important physiological functions. Each species of fish could be identified based on their speciation and node position and distance from their parent nodes. Based on the closest phylogenetic relations, DNA sequence-based study was developed for the accurate identification of fish species.

On the new classification of dermatophytes

According to the recent changes in the classification of the family Arthrodermataceae, it may already include 9 genera and 79 species. Dermatophytes associated with human and animal infections belong to the genera Trichophyton, Microsporum and Epidermophyton, whereas Arthroderma, Ctenomyces, Guarromyces, Lophophyton, Nannizzia and Paraphyton are mainly represented by geophilic species. Since morphological and physiological traits in fungi cannot provide reliable basis for classification, the modern system of dermatophytes was built on the basis of phylogenetic analysis of nucleotide sequences. The new dermatophyte classification employs the principle of one fungus, one name, according to which genetically similar perfect and imperfect forms belong to the same species.
 At the current state of genosystematics, the taxonomic identification of dermatophytes in most cases requires the use of molecular methods, in particular, DNA sequencing of the ITS region.
 In this review, we briefly outline the history of dermatophyte classification, summarize generic and species composition of the family and provide data on their ecology, accession numbers for reference sequences of ITS region, and references to major taxonomic publications.

Salient Findings on Host Range, Resistance Screening, and Molecular Studies on Sterility Mosaic Disease of Pigeonpea Induced by Pigeonpea sterility mosaic viruses (PPSMV-I and PPSMV-II).

Two distinct emaraviruses, Pigeonpea sterility mosaic virus-I (PPSMV-I) and Pigeonpea sterility mosaic virus-II (PPSMV-II) were found to be associated with sterility mosaic disease (SMD) of pigeonpea [Cajanus cajan (L.) Millsp.]. The host range of both these viruses and their vector are narrow, confined to Nicotiana benthamiana identified through mechanical transmission, and to Phaseolus vulgaris cvs. Top Crop, Kintoki, and Bountiful (F: Fabaceae) through mite transmission. A weed host Chrozophora rottleri (F: Euphorbiaceae) was also infected and tested positive for both the viruses in RT-PCR. Among the wild Cajanus species tested, Cajanus platycarpus accessions 15661, 15668, and 15671, and Cajanus scarabaeoides accessions 15683, 15686, and 15922 were infected by both the viruses and mite vector suggesting possible sources of SMD inoculum. Though accession 15666 of C. platycarpus, 15696 of C. scarabaeoides, and 15639 of Cajanus lanceolatus were infected by both the viruses, no mite infestation was observed on them. Phylogenetic analysis of nucleotide sequences of RNA-1 and RNA-2 of PPSMV-I and PPSMV-II isolates in southern India revealed significant divergence especially PPSMV-II, which is closely related to the Fig mosaic virus (FMV) than PPSMV-I. In multilocation testing of pigeonpea genotypes for their broad-based resistance to SMD for two consecutive years, genotypes ICPL-16086 and ICPL-16087 showed resistance reaction (<10% incidence) in all three locations studied. Overall, the present study gives a clear idea about the host range of PPSMV-I and PPSMV-II, their molecular relationship, and sources of resistance. This information is critical for the development of reliable diagnostic tools and improved disease management strategies.

The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements.

The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein‐coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein‐coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co‐occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro‐ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.

Analysis of marker substitutions in A/chicken/Astrakhan/2171-1/2020 H5N8 isolate of avian influenza virus recovered in the Astrakhan Oblast

At the end of 2020, a large-scale bird death was registered at one of the poultry farms in the Astrakhan region, the cause of which was avian influenza. Data on detection of the marker substitutions in viral proteins of avian influenza virus A/chicken/Astrakhan/2171-1/2020 isolate are presented in the paper. Type A Н5N8 avian influenza virus was identified with complex PCR-based methods in the submitted samples. Hemagglutinin gene fragment sequencing identified REKRRKR/ GLF, highly pathogenic avian influenza virus isolate-characteristic amino acid sequence of the hemagglutinin cleavage site. Phylogenetic analysis of nucleotide sequences of hemagglutinin gene segment (848–1105 bp ORF) allowed A/chicken/Astrakhan/2171-1/2020 H5N8 isolate to be classified to highly pathogenic avian influenza virus genetic clade 2.3.4.4. Comparative analysis of genome segments using available databases showed that A/chicken/Astrakhan/2171-1/2020 H5N8 virus related to А/Н5 avian influenza virus isolates detected in the Russian Federation in 2016–2020. Analysis of the studied virus isolate hemagglutinin amino acid identified AIV-characteristic G225QRG228amino acids in the receptor-binding domain of the protein enabling high-affinity binding to avian epithelial cell SAα-2,3- gal receptors. Single mutations, 70G in NEP protein and 13Р in PB1 protein, out of the list of the reported influenza virus mutations affecting successful influenza virus replication in mammals were identified. No mutations affecting virus sensitivity to anti-viral medicines, rimantadin, amantadine, oseltamivir and zanamivir, were detected. The following mutations recognized as pathogenicity determinants in mice were found: 42S in the NS1 protein and 30D protein 215A in M1 protein.

Evaluation of the HIV-1 drug resistance to elsulfavirine and the effectiveness of it among Russian treatment-naïve patients

The aim of the study: to analyze the prevalence of resistance mutations to elsulfavirine and to evaluate the effectiveness of it among HIV-infected treatment-naïve patients in real clinical practice.Materials and methods. The study included 578 patients with HIV infection, which divided into 3 groups. The first group is 354 HIV-infected treatment-naïve patients for whom HIV-1 nucleotide sequences were obtained as part of routine drug resistance testing. The second study group included 111 HIV-infected treatment-naïve patients, tested for drug resistance before the antiretroviral therapy containing elsulfavirine. The third study group included 113 HIV-infected treatment-naïve patients, each of whom was assigned a treatment regimen containing elsulfavirine without prior drug resistance testing. The observation period for patients of the second and third groups who received treatment was 24 weeks. To assess the effectiveness of antiretroviral therapy in patients, viral load, CD4+ T-cell counts, and adherence to therapy were assessed. HIV-1 subtypes and drug resistance mutations were determined using the Stanford HIV Resistance Database (v. 8.9-1). To clarify the results of subtyping, phylogenetic analysis of nucleotide sequences was carried out using the MEGA program (v. 6.0).Results. The prevalence of mutations associated with decreased susceptibility to elsulfavirine among HIV-infected treatment-naïve patients was 1.7% and 4.5% for the first and second groups of patients, respectively. All of the patients have only single resistance mutations which, according to the results of preclinical studies, cannot cause drug resistance. The use of elsulfavirine in real clinical practice among treatment-naïve patients has demonstrated good virological and immunological efficacy of the drug. As a result of 24 weeks of therapy in patients of the second group, no treatment ineffectiveness, and the development of drug resistance were observed. Among the patients of the third group, 6 patients (5.3%) have the virological failure of therapy associated with the resistance to the used drugs. All patients with virological failure had a resistance mutation profile associated with a high level of drug resistance to one of the drugs in the treatment regimen, lamivudine. Additionally, 1 patient had a combination of mutations that reduce susceptibility to elsulfavirine, and 4 patients had mutations that can reduce susceptibility to elsulfavirine in combination with other mutations.Conclusion. The low prevalence of mutations associated with a decrease in susceptibility to elsulfavirine and the absence of combinations of mutations make it possible to predict the successful use of this drug for Russian treatment-naïve patients. Reported cases of virological failure of antiretroviral therapy are difficult to interpret in the context of elsulfavirine due to the lack of an exact list of mutations and their combinations, and associations with the degree of resistance to it. This study describes for the first time the mutation profiles in patients with virological failure of therapy containing elsulfavirine and demonstrates the necessity of the further study of drug resistance profile to drug in vitro and in vivo.

Occurrence, Distribution and Molecular Characterization of Phytoplasma Infecting Chickpea (Cicer arietinum L.) from Tamil Nadu

Phytoplasma is an obligate prokaryote infecting a wide array of crops such as urdbean, sesame, brinjal and many other vegetable crops in India. Several workers have noticed the recent outbreak of phytoplasma disease in several pulse crops. A study was conducted to identify the phytoplasma infection in chickpea from Tamil Nadu. The average disease incidence due to phytoplasma was recorded with a range of 5-20% under field condition. The infected plants produced symptoms including stunting of plants, bushy appearance, reduced leaf size, chlorosis and reddening of infected leaves. The association of phytoplasma with these symptoms was confirmed by nested PCR assay using the universal primers P1/P7 and R16F2n/R16R2. The infected samples were amplified with an amplicon size of 1.2 kb and sequence analysis showed more than 99% similarity with phytoplasma belongs to Candidatus Phytoplasma aurantifolia. Phylogenetic analysis of nucleotide sequences confirmed the chickpea phyllody phytoplasma forms a single subgroup with other Indian isolates of various crops.

Molecular detection of G1 marker for orange rust resistance and analysis of candidate resistance &amp;lt;italic&amp;gt;WAK&amp;lt;/italic&amp;gt; gene in sugarcane

<p indent=0mm>Sugarcane orange rust is an important fungal disease caused by <italic>Puccinia kuehnii</italic> Butler, which could lead to a reduction in sugarcane production and sugar content and cause serious losses to the sugarcane industry in worldwide. In this study, the molecular marker G1 was used to detect orange rust resistance genes in cultivars, ancestral species and the related <italic>genus</italic> of <italic>Saccharum </italic>in the world. The representative amplified bands were cloned, sequenced, functionally annotated, and clustered, and the origin and evolution of resistance genes was then analyzed. The results showed that 83 and 34 were detected with G1 marker, accounting for 66.9% and 67.4% in 124 Chinese and 46 foreign sugarcane cultivars, respectively. Among 34 sugarcane ancestral species and the related genus of <italic>Saccharum</italic>, 17 were detected by G1 marker, accounting for 50%, of which the highest percentage (100%) was in <italic>Saccharum spontaneum</italic>. Functional annotation revealed that G1 target gene encoded a wall-associated receptor-like kinase (WAK), and three proteins with high similarity were identified from the haploid proteome database of sugarcane cultivars. These proteins all contain the extracellular domain, transmembrane domain and intracellular domain with kinase activity of typical cell wall receptor structures. Phylogenetic analysis of nucleotide sequences clearly showed the origin and evolution of the candidate resistance <italic>WAK</italic> genes. Specifically, the <italic>WAK</italic> genes amplified by G1 marker could be divided into three groups. The first group is from <italic>S</italic>.<italic> spontaneum</italic> and <italic>Saccharum robustum</italic>. The second group is from <italic>S</italic>.<italic> robustum</italic>,<italic> Saccharum officinarum</italic> and <italic>Narenga porphyrooma</italic>. The third group is from <italic>S</italic>.<italic> spontaneum</italic>,<italic> S</italic>.<italic> robustum</italic>,<italic> Saccharum sinense</italic> and cultivars. These results provided an important support for breeding of sugarcane cultivars resistant to orange rust, and lay a foundation for further analysis of molecular mechanism of resistance genes.

Cladocopium infistulum sp. nov. (Dinophyceae), a thermally tolerant dinoflagellate symbiotic with giant clams from the western Pacific Ocean

ABSTRACT Members of the genus Cladocopium are the most ecologically dominant and geographically widespread group of mutualistic dinoflagellates. The addition of species descriptions to this newly erected genus should stimulate scientific investigations and communication about the biology of these important symbionts. Here we combine morphology and genetic evidence with ecology to formally describe Cladocopium infistulum sp. nov. An emended description for C. goreaui is also provided. Both are among the few species of Cladocopium capable of growing in culture medium. The cells of C. infistulum are significantly smaller in size and differ in amphiesmal plate tabulation (morphology of the motile cell) from C. goreaui. Both appear to lack knob ornamentation typical of the elongate amphiesmal vesicle (EAV) in other Symbiodiniaceae. Phylogenetic analyses of nucleotide sequences from nuclear ribosomal, chloroplast, and mitochondrial genes differentiate C. infistulum from other Cladocopium spp. This new species is ecologically specialised, and known to occur only at high densities in digestive diverticula–a complex system of capillary-like hollow tubes that ramify the siphonal mantles of giant clams (Tridacnidae). Clams living in predominantly warm and shallow inshore reefal environments harbour this symbiont; and its biogeographic range appears restricted to the equatorial western Pacific Ocean. This new species description emphasises the need to formally recognise the high species diversity and corresponding physiological and ecological breadth that encompass Cladocopium.

Histopathology and molecular identification of Henneguya pseudoplatystoma

The present study proposes to characterize the parasites isolated during the initial phase of production in fish farms located in Mato Grosso do Sul in the central-western region of Brazil, using histopathology analysis and molecular techniques. A total of 340 hybrid surubim fish (Pseudoplatystoma reticulatum × P. corruscans) from four farms were examined during the co-feeding phase. Histopathology analysis showed that 10.9% (n = 37) of the fish were infected with parasites. Branchitis, lifting epithelium, hypertrophy of epithelial cells, lamellar fusion, aneurisms and infection in the bone tissue of the gill filament was observed. The parasite species was determined by amplification of the 18S rRNA gene followed by sequencing. The phylogenetic analysis of nucleotide sequences indicates a close relationship (99.6%) with Henneguya pseudoplatystoma reported to be infecting the hybrid Pseudoplatystoma. This study demonstrates the occurrence of H. pseudoplatystoma in hybrid surubim (P. reticulatum × P. corruscans) during the co-feeding phase in fish farms in Mato Grosso do Sul. Also, molecular techniques provide a faster and sensitive method to identify fish parasites, and may assist in the development of new management techniques aimed at improving the sanitary conditions contributing to the reduction of mortality rates in these animals.

Two new species of Laccaria from South China, with a note on Hodophilus glaberipes

Laccaria fengkaiensis and L. prava, collected from Heishiding Nature Reserve, South China, are proposed here as new taxa based on morphological and molecular evidences. These two new species along with Hodophilus glaberipes Ming Zhang et al. are described with photographs and line drawings and compared against related species. Morphologically, Laccaria fengkaiensis is characterized by a medium-sized to large pinkish white to light orange, strong striate to rugulose-striate or rugulose-sulcate pileus, a strong, solid stipe of the same color, 4-spored basidia, globose to obellipsoid basidiospores with moderate echinulae, and a pileipellis with abundant pileocystidia. Laccaria prava is characterized by a moderate-sized but very thin pinkish white to light orange, strong striate to rugulose-striate or rugulose-sulcate pileus, a distorted same colored stipe, 4-spored basidia, obellipsoid to globose basidiospores with moderate echinulae, and a stipitipellis with abundant caulocystidia. Hodophilus glaberipes is characterized by a small basidioma, with a pileus and its lamellae white at first, orange white to brownish orange with age, a white stipe, subglobose to globose basidiospores, and discoloring pastel red in wounds. Phylogenetic analysis of nucleotide sequences of the internal transcribed spacer (ITS) region provided further evidence that Laccaria fengkaiensis and L. prava are new species which are clearly separated from all other Laccaria species with rDNA sequence data available; Hodophilus glaberipes belongs to the H. micaceus superclade, with H. indicus K.N.A. Raj et al. as a closely related sister species.

Heterocephalacria mucosa sp. nov., a new basidiomycetous yeast species isolated from a mangrove forest in Thailand.

Strains of yeast were isolated under a nitrogen-depleted culture condition from decaying tree bark (strain N-12.1) and from mangrove forest water (strain 1-7W.1) sampled at different locations within a mangrove forest site in Ranong province, Thailand. They were found to be genetically and phenotypically different from any currently recognised yeast species. Phylogenetic analysis of nucleotide sequence of three genes, the internal transcribed spacer region 1 and 2 plus 5.8S ribosomal RNA gene (ITS), D1/D2 domain of the large subunit ribosomal RNA gene (LSU D1/D2) and the small subunit of the ribosomal RNA gene (SSU), revealed that these two strains were related to but distinguished from Heterocephalacriaarrabidensis. Several distinct physiological characteristics of these two strains were detected, namely inability to assimilate glycerol, dl-lactic acid, succinic acid, citric acid, d-gluconic acid, and ability to grow well at 25 °C, which were different from those of H. arrabidensis. Accordingly, the name Heterocephalacria mucosa sp. nov., is proposed to accommodate this novel species. The MycoBank number is MB 828624.

Characterization of cucumber mosaic virus infecting coleus (Plectranthus barbatus) in Karnataka.

Plectranthus barbatus also known by the synonym Coleus forskohlii it is called as forskohlii and Indian coleus. It is a tropical perennial herb belongs to the family Lamiaceae widely cultivated in India used as traditional medicinal crop. Its tuberous roots produce forskolin, an extract useful for pharmaceutical preparations and research in cell biology. The incidence of mosaic with dark and light green patches, mottling, leaf distortion and reduction growth was noticed in commercial cultivation of coleus. For identification of the virus, the infected leaf sample extract was mechanically inoculated to different hosts such as chilli, tobacco, tomato, cucumber, cowpea and Chenopodium amaranticolor. Host range studies revealed that the virus showed severe mosaic symptoms on Nicotiana spp. and Cucumis spp. The virus produced systemic and local lesion symptoms in a different host. The Leaf dip preparation of virus infected leaf extract was observed under an electron microscope showed the presence of isometric particles of 28nm in size. The healthy and infected samples were tested using DAC-ELISA against antibodies of CMV, GBNV and TSV the infected samples showed strong positive reaction with 1.85 optical density to CMV antibodies indicated the presence of CMV. For molecular identification, total RNA was isolated and used for RT-PCR amplification using CMV specific primers. RT-PCR resulted in the positive amplification in virus infected samples but not from a healthy control. The complete genome of CMV RNA-1 consists of 3360 nucleotides (nt) encoding replicase gene of 807 amino acids (aa). The CMV RNA-2 was 2983 nt in length containing 2a (859 aa) encoding RNA dependent RNA polymerase protein and 2b encoding viral silencing suppressor (112 aa), while RNA-3 encoding 3a movement protein (280 aa) and coat protein (219 aa) was 2223 nt in length. Phylogenetic analyses of nucleotide sequences of coleus CMV isolate is closely related to subgroup IB than to subgroup IA or II with other CMV isolates. In recombination analysis, the recombination event occurs between the subgroups of I, II as well as IA and IB in RNA 1, RNA2 and RNA3 of coleus isolate with other CMV isolates. To best of our knowledge, this is the first report of CMV infection in coleus.

Screening, characterization and molecular-genetical identification of a new bacterial strain Paenibacillus species

Bacterial variant PS-K-17 was isolated from wheat grain contaminated by polysaccharide-producing microbiota for further characterization. It was found that the isolate grown on agar slants and in submerged culture on media with specific substrates synthesized beta-galactosidase, amylase, protease, pectinase, cellulase, beta-glucanase, lipase (esterase), alginase, extracellular polysaccharides, and pigments, probably carotenoids. Based on cultural-morphological and physiological-biochemical properties and phylogenetic analysis of nucleotide sequences of 16S rRNA gene (access code MF443394 in GenBank) the bacterial culture was identified as Paenibacillus species PS-K-17. The studied isolate forms one phylogenetic branch with type strains Paenibacillus nicotianae (98.3 %), Paenibacillus hordei (98.2 %), Paenibacillus kyungheensis (97.9 %), holding wherein a separate position. Strain Paenibacillus sp. PS-K-17 may find use in biotechnology as a producer of extracellular polysaccharides and enzymes splitting plant polymeric substances as well as a component of microbial consortium-ingredient of a new complex feed additive.

Molecular phylogenetic analysis of subfamilial placement of Haplotropis Saussure, 1888 (Orthoptera: Pamphagidae) based on mitochondrial and nuclear DNA markers.

The genus Haplotropis Sauss. is a relatively small genus in the family Pamphagidae (Orthoptera:Caelifera). Historically, there has been a discussion on the placement of this genus, whether it belongs in the subfamily Pamphaginae or in the subfamily Thrinchinae. Here we present a phylogenetic analysis of nucleotide sequences of two mitochondrial genes (COI, COII) and the ITS2 rRNA nuclear region of multiple species of the family Pamphagidae and related taxa. Our results clearly support the placement of the genus Haplotropis, and other species of the tribe Haplotropidini, in the subfamily Thrinchinae.

Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses.

The Porcine Sapelovirus (PSV) is an enteric virus of pigs that can cause various disorders. However, there are few reports that describe the molecular characteristics of the PSV genome. In this study, almost the entire genomes of 23 PSVs detected in Japanese pigs were analyzed using bioinformatics. Analysis of the cis-active RNA elements showed that the predicted secondary structures of the internal ribosome entry site in the 5' untranslated region (UTR) and a cis-replication element in the 2C coding region were conserved among PSVs. In contrast, those at the 3' UTR were different for different PSVs; however, tertiary structures between domains were conserved across all PSVs. Phylogenetic analysis of nucleotide sequences of the complete VP1 region showed that PSVs exhibited sequence diversity; however, they could not be grouped into genotypes due to the low bootstrap support of clusters. The insertion and/or deletion patterns in the C-terminal VP1 region were not related to the topology of the VP1 tree. The 3CD phylogenetic tree was topologically different from the VP1 tree, and PSVs from the same country were clustered independently. Recombination analysis revealed that recombination events were found upstream of the P2 region and some recombination breakpoints involved insertions and/or deletions in the C-terminal VP1 region. These findings demonstrate that PSVs show genetic diversity and frequent recombination events, particularly in the region upstream of the P2 region; however, PSVs could currently not be classified into genotypes and conserved genetic structural features of the cis-active RNA elements are observed across all PSVs.