Complete Gene Sequences Research Articles

Genetic characterization of pigeon- origin avian avulavirus-1 reveals unique substitutions in F and HN proteins.

Since decades, Newcastle disease (ND) has become endemic in the poultry population of the Indian subcontinent. ND is a highly contagious disease of poultry and other avian species. However, the genetic nature of ND viruses circulating in the rock pigeons is unraveled. The present investigation is a part of Newcastle disease virus (NDV) surveillance in wild birds. Two velogenic NDV strains could be isolated from apparently healthy rock pigeons, thus establishing the status of carrier/reservoir host. The fusion protein cleavage site in the fusion protein has multiple basic amino acid (RRRKRF) motifs similar to velogenic isolates. Phylogenetic analysis based on complete fusion gene sequences confirmed that the isolates belong to NDV sub genotype XIII 2.2. Further analysis revealed several amino acid substitutions in the hypervariable region, heptad repeat regions and neutralizing epitopes of the fusion protein and heptad repeat regions and antigenic sites of the hemagglutinin-neuraminidase (HN) protein that are critical for fusion. A unique D170A substitution in the neutralizing epitope is identified that is critical for structure and function of the fusion protein. Mutations within the virulence determinants including fusion (F) and HN, elucidate continuous evolution of the viruses among the rock pigeons. Accidental spillover of these mutated viruses into commercial poultry operations may result in disease outbreaks with economic breakdown.

CDNA characterization of the ribosomal protein L10a gene and its functional analysis in ovarian development of Macrobrachium nipponense

Ribosomal proteins (RPs) not only play an important role in protein synthesis but also have extraribosomal functions. In this study, the entire cDNA sequence of the RPL10a gene of Macrobrachium nipponense (MnRPL10a) was cloned by RACE-PCR. The obtained complete cDNA sequence of the MnRPL10a gene was 885 bp encoding 217 amino acids (AAs). The expression pattern of the MnRPL10a gene was analysed by quantitative real-time fluorescence PCR (qPCR), and its mRNA location was determined by fluorescence in situ hybridization (FISH). The results showed that during development, the highest expression of MnRPL10a in the fertilized ovum. Among tissues, it was mostly expressed in the ovary, and its highest expression was found in stage V ovaries. MnRPL10a mRNA was mainly distributed in the cytoplasm of oogonia and oocytes. The role of the MnRPL10a gene in ovarian development was verified by RNA interference (RNAi) and ovarian explant incubation with 5-hydroxytryptamine (5-HT) and dopamine (DA) experiments. The results indicated that the expression of the genes that positively regulate ovarian development, including vitellogenin (Vg), vitellogenin receptor (Vgr), cell cycle protein B (CyclinB) and cell division cyclin 2 (cdc2), decreased, while the expression of the genes that negatively regulate ovarian development, including Wee1 kinase (Wee1) and OTU domain-containing ubiquitin aldehyde-binding protein B (OTUB), increased with the decrease in MnRPL10a expression after RNAi and DA incubation. However, 5-HT incubation showed the opposite results. In summary, the MnRPL10a gene may regulate the development of the ovary in M. nipponense by affecting vitellin synthesis, oocyte meiosis and the oestrogen signalling pathway.

Prevalence and structural protein encoding gene sequence (VP) of porcine parvovirus 2 (PPV2) in slaughtered pigs in Central provinces of Vietnam

Porcine parvovirus (PPV) is a DNA virus and causative agent of several reproductive problems in sows. This study was conducted to determine the prevalence and analyze the DNA sequence of structural protein encoding gene (VP) of PPV2 genotype in pigs. A total of 146 samples (lung and blood samples) were collected from slaughtered pigs of seven provinces in Central Vietnam during 2018-2019. The overall prevalence of PPV2 was 56.2% (82/146). PPV2 positive rate in each province ranged from 37.5% for Quang Nam to 100% for Quang Binh, with the exception of Da Nang, where no PPV2 positive samples were detected. Nearly complete PPV2-VP gene sequences of three strains were identified with the length of 2,493 nucleotides and deposited in GenBank with accession numbers of OL913365-OL913367. Four nucleotide substitutions were detected in Vietnamese PPV2 isolates and were not observed in PPV2 reference strains. Multiple alignment and comparison of nucleotide and deduced amino acid sequences showed the high similarity within Vietnamese PPV2 strains (95.6-96.5% and 94.7-96.9%, respectively). The PPV2 strains from this study clustered together with the "primitive" PPV2 strains from Myanmar, and strains from China in a main clade in the phylogenetic tree (Cluster A). This is the first report on the prevalence of PPV2 genotype and its VP gene sequence in pigs in Vietnam. This also provides the valuable information on the molecular evolution of locally circulating PPV2 and contributes to the control of PPV-induced SMEDI syndrome in sows, especially in the central provinces of Vietnam.

Genomic Characterization of Escherichia coli Co-Producing KPC-2 and NDM-5 Carbapenemases Isolated from Intensive Care Unit in a Chinese Hospital.

Background: Around the world, carbapenemase-producing Escherichia coli is becoming more prevalent. The purpose of this research was to analyze the whole plasmid sequences from YL03 isolates of the E. coli strain that produce both KPC-2 and NDM-5 carbapenemases. Materials and Methods: Whole-genome sequencing (WGS) and analysis of E. coli strain YL03, which was isolated from a wound sample, was performed by Illumina Novaseq 6000 and Pacific Biosciences Sequel (PacBio, Menlo Park, CA) sequencers. Following that, the WGS results were used to predict and analyze the YL03 genome composition and function. A complete gene sequence for YL03 with the accession number CP093551 has been uploaded to GenBank. Results: The results showed that YL03 co-carried five resistance genes, which included blaKPC-2, blaNDM-5, blaTEM-1B, blaCTX-M-14, and mdf(A). Furthermore, three resistance plasmids were found in YL03: pYL03-KPC, pYL03-NDM, and pYL03-CTX. Among them, the 53 kb-long pYL03-KPC plasmid belonging to the IncP, carried the replicase gene (repA) and the carbapenemase gene (blaKPC-2). The blaKPC-2 gene was flanked by a composite transposon-like element (Tn3-[Tn3] tnpR-ISKpn27 blaKPC--ISKpn6). Conclusions: The YL03 strain co-carried blaKPC-2 and blaNDM-5 and had a unique multidrug resistance plasmid containing blaKPC-2.

Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus.

An important feature of ruminal ciliates is their phenotypic plasticity, which makes their identification difficult. The common manifestation of the phenotypic plasticity in rumen ciliates is a change in their cell size and caudal spination. We analyzed various morphotypes of Epidinium with five caudal processes (spines) taken from the rumen of European bison (Bison bonasus). In the study, the cluster analysis and K-means analysis of morphometric data could not distinguish very similar morphotypes of Epidinium with five caudal processes. However, the morphotype of E. parvicaudatum prevailed (70%). The DNA of four individual E. parvicaudatum was isolated successfully from formaldehyde-preserved samples. The partial 18S rDNA gene sequences (about 350-400 bp) were identical to Epidinium sequences in GenBank (E. caudatum, a one-spine morphotype, and E. cattanei, a five-spine morphotype). It can be assumed that these short sequences cannot distinguish the differences between the Epidinium morphospecies. Complete gene sequences from various hosts and various molecular markers are necessary to reveal the validity of the Epidinium five-spine species. In conclusion, classical morphology should be supplemented with molecular data when more morphotypes of the rumen ciliate species are present in samples.

Seroepidemiological investigation of Getah virus in the China-Myanmar border area from 2022-2023.

Getah Virus (GETV) is an RNA virus that is transmitted by mosquitoes and can cause disease or death in a variety of vertebrates. Its prevalence is increasingly severe in Asia. This study conducted a GETV epidemiological investigation on 1,300 bovine sera collected in the Honghe Prefecture of Yunnan Province on the China-Myanmar border from 2022 to 2023. The positive rate of GETV antibodies in bovine serum in Honghe Prefecture was determined to be 20.25% through indirect Enzyme-linked immunosorbent test (ELISA) methods. Using Real-time PCR methods to detect GETV RNA in bovine serum, the positive rate was 0.23% (3/1300), and viral nucleic acids were only detected in three bovine sera in Jianshui area in 2022. The YN2305 strain was successfully isolated from mouse neuroblastoma (N2a) cells and the complete gene sequence was obtained. All the above results indicate the existence of GETV infection in cattle in Honghe Prefecture, Yunnan Province. Homology and genetic evolution analysis found that the isolated strain has a high homology with the JL1808 strain isolated from cattle in 2018, with a nucleotide identity of 100%, and a nucleotide identity of 99.8% with the SD17-09 strain isolated from foxes in 2017. Compared with the nucleotides of 44 virus strains published in Genbank, YN2305 has multiple nucleotide site mutations in the structural gene E2 and non-structural gene NS. The nucleotide and amino acid identity of the E2 gene are 94.2-100% and 96.4-100%, respectively. Genetic evolution analysis found that this virus strain is most closely related to the bovine origin JL1808, and it is in gene group III with HuN1, Kochi-01, SD17-09, MI-110-C1, and MI-110-C2 strains that causes significant clinical symptoms in Chinese pig, fox and horse populations, belonging to the same evolutionary branch. This study determined the infection rate, genotype, and main prevalence areas of GETV in bovine sera in the China-Myanmar border area. Therefore, the epidemiological investigation of GETV infection in multiple animal hosts should be further expanded, and research on its pathogenicity and vectors should be carried out.

Sequencing of the Lumbricus terrestris genome reveals degeneracy in its erythrocruorin genes

The erythrocruorin of Lumbricus terrestris (LtEc) is a relatively large macromolecular assembly that consists of at least four different hemoglobin subunits (A, B, C, and D) and four linker subunits (L1, L2, L3, and L4). The complexity and stability of this large structure make LtEc an attractive hemoglobin-based oxygen carrier that could potentially be used as a substitute for donated red blood cells. However, the sequences of the LtEc subunit sequences must be determined before a scalable recombinant expression platform can be developed. The goal of this study was to sequence the L. terrestris genome to identify the complete sequences of the LtEc subunit genes. Our results revealed multiple homologous genes for each subunit (e.g., two homologous A globin genes; A1 and A2), with the exception of the L4 linker. Some of the homologous genes encoded identical peptide sequences (C1 and C2, L1a and L1b), while cDNA and mass spectrometry experiments revealed that some of the homologs are not expressed (e.g., A2). In contrast, multiple sequences for the B, D, L2, and L4 subunits were detected in LtEc samples. These observations reveal novel degeneracy in LtEc and other annelids, along with some new revisions to its previously published peptide sequences.

In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data

BackgroundMacrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination “M. amazonicum complex” is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará.ResultsSequences were obtained from the prawn’s transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91–100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial).ConclusionsIt was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.

Unusual Oligomeric Laccase-like Oxidases from Ascomycete Curvularia geniculata VKM F-3561 Polymerizing Phenylpropanoids and Phenolic Compounds under Neutral Environmental Conditions.

The unique oligomeric alkaliphilic laccase-like oxidases of the ascomycete C. geniculata VKM F-3561 (with molecular masses about 1035 and 870 kDa) were purified and characterized for the first time. The ability of the enzymes to oxidize phenylpropanoids and phenolic compounds under neutral environmental conditions with the formation of previously unknown di-, tri-, and tetrameric products of transformation was shown. The possibility to obtain industrially valuable compounds (dihydroxybenzyl alcohol and hydroxytyrosol) from caffeic acid using laccase-like oxidases of C. geniculata VKM F-3561 has been shown. Complete nucleotide sequence of the laccase gene, which is expressed at the peak of alkaliphilic laccase activity of the fungus, and its promoter region were determined. Based on the phylogenetic analysis of the nucleotide sequence, the nearest relationship of the isolated laccase gene with similar genes of fungi of the genera Alternaria, Bipolaris, and Cochliobolus was shown. Homologous model of the laccase structure was predicted and a proton channel was found, which was presumably responsible for the accumulation and transport of protons to T2/T3-copper center in the alkaliphilic laccase molecule and providing the functional activity of the enzyme in the neutral alkaline environment conditions.

A revised taxonomy and phylogeny of opalinids (Stramenopiles: Opalinata) inferred from the analysis of complete nuclear ribosomal DNA genes

Abstract The Opalinida comprise ciliated protists that live as intestinal endoparasites in poikilothermic vertebrates. They are classified as one group of colourless Stramenopiles, the Opalinata, along with Proteromonadida (Proteromonas and Karotomorpha). The validity of certain opalinid genera is questionable, and their genetic relationships remain unclear. In this study, we conducted complete ribosomal DNA gene sequencing of nine opalinid species (belonging to Opalina, Protoopalina, Zelleriella, and Cepedea) from China. We compared the primary sequences, secondary structures, and characteristics of short tandem repeats within the expansion segments of the sequences. Additionally, a TimeTree analysis was performed to estimate divergence times. Our findings suggest that opalinids diverged from proteromonads ~250–220 Mya, with Protoopalina being the ancient genus. There is no genetic evidence supporting the differentiation of Cepedea and Bezzenbergeria as distinct genera, and they have been synonymized: Opalina (= Cepedea) and Protoopalina (= Bezzenbergeria); new combinations of species names are listed. Opalinid rDNA sequences exhibit greater length compared with other groups owing to A-T insertions within the expansion segments. These insertions consist of short tandem repeats and appear to be associated with speciation events that led to genus differentiation.

Complete viral protein coding genes NS1 and VP1 sequences and phylogenetic analysis of a novel recombinant Mink Enteritis Virus isolated in China

The primary objective of this study was to detect the presence of MEV in mink samples and investigate the genetic characteristics of the virus. In 2017, a newly identified strain of MEV, named MEV-HLJ, was isolated. The virus’s complete NS1 and VP1 gene sequences were amplified using PCR and subjected to phylogenetic analysis. The results indicated that despite moderate virulence, MEV- HLJ belonged to the attenuated group. Recombination analysis using the GARD programme identified a putative recombination breakpoint at nucleotide position 2,075 between the NS1 and VP1 genes. Separate phylogenetic trees were constructed to confirm the recombinant event. This study provides insights into the genetic diversity and evolution of MEV isolates.

Sidedness-Dependent Prognostic Impact of Gene Alterations in Metastatic Colorectal Cancer in the Nationwide Cancer Genome Screening Project in Japan (SCRUM-Japan GI-SCREEN).

The treatment strategies and prognoses of patients with metastatic colorectal cancer (CRC) differ according to the sidedness of the primary tumor. TP53 gain-of-function (GOF) and non-GOF variants have been reported to be differentially associated with prognosis by sidedness. We aimed to evaluate the sidedness-dependent prognostic impact of gene alterations in metastatic CRC. Patients enrolled between April 2017 and March 2019 were included in this study. Those excluded were individuals whose tumor tissues were obtained after chemotherapy and those who were enrolled in the study more than six months after starting first-line chemotherapy. Finally, we assessed 531 patients who underwent complete gene sequencing. The study revealed a significant difference in overall survival between individuals with left-sided CRC (n = 355) and right-sided colon cancer (CC) (n = 176) when considering the TP53 non-GOF variant, KRAS wild-type, NOTCH1 wild-type, NOTCH1 covariant, NOTCH3 sole variant, and MYC amplification. Multivariate analysis on each side revealed that the TP53 GOF and KRAS variants were independent poor prognostic factors for left-sided CRC (p = 0.03 and p < 0.01, respectively), and the TP53 non-GOF variant, BRAF V600E, and MYC amplification for right-sided CC (p < 0.05, p < 0.01, and p = 0.02, respectively). The NOTCH3 sole variant was an independent and favorable prognostic factor for left-sided CRC (p < 0.01). The prognostic significance of gene alterations differed between left-sided CRC and right-sided CC.

Precision detection of recent HIV infections using high-throughput genomic incidence assay.

HIV incidence is a key measure for tracking disease spread and identifying populations and geographic regions where new infections are most concentrated. The HIV sequence population provides a robust signal for the stage of infection. Large-scale and high-precision HIV sequencing is crucial for effective genomic incidence surveillance. We produced 1,034 full-length envelope gene sequences from a seroconversion cohort by conducting HIV microdrop sequencing and measuring the genomic incidence assay's genome similarity index (GSI) dynamics. The measured dynamics of 9 of 12 individuals aligned with the GSI distribution estimated independently using 417 publicly available incident samples. We enhanced the capacity to identify individuals with recent infections, achieving predicted detection accuracies of 92% (89%-94%) for cases within 6 months and 81% (74%-87%) for cases within 9 months. These accuracy levels agreed with the observed detection accuracy intervals of an independent validation data set. Additionally, we produced 131 full-length envelope gene sequences from eight individuals with chronic HIV infection. This analysis confirmed a false recency rate (FRR) of 0%, which was consistent with 162 publicly available chronic samples. The mean duration of recent infection (MDRI) was 238 (209-267) days, indicating an 83% improvement in performance compared to current recent infection testing algorithms. The shifted Poisson mixture model was then used to estimate the time since infection, and the model estimates showed an 88% consistency with the days post infection derived from HIV RNA test dates and/or seroconversion dates. HIV microdrop sequencing provides unique prospects for large-scale incidence surveillance using high-throughput sequencing. IMPORTANCE Accurate identification of recently infected individuals is vital for prioritizing specific populations for interventions, reducing onward transmission risks, and optimizing public health services. However, current HIV-specific antibody-based methods have not been satisfactory in accurately identifying incident cases, hindering the use of HIV recency testing for prevention efforts and partner protection. Genomic incidence assays offer a promising alternative for identifying recent infections. In our study, we used microdroplet technologies to produce a large number of complete HIV envelope gene sequences, enabling the accurate detection of early infection signs. We assessed the dynamics of the incidence assay's metrics and compared them with statistical models. Our approach demonstrated high accuracy in identifying individuals with recent infections, achieving predicted detection rates exceeding 90% within 6 months and over 80% within 9 months of infection. This high-resolution method holds significant potential for enhancing the effectiveness of HIV incidence screening for case-based surveillance in public health initiatives.

Improvement the expression and purification of Loa22: a lipoprotein with OmpA domain from pathogenic Leptospira serovars.

One of the highly conserved outer membrane proteins expressed only by pathogenic Leptospires is Loa22. The study aims is to achieve the optimum conditions for high expression of recombinant Loa22 (rLoa22) protein. Complete coding sequence of loa22 gene sub-cloned into a pET32a (+) expression vector. BL21 competent E. coli (pLysS) used as expression host for transformation. The recombinant clones selected on ampicillin plates and subjected to PCR by using pET T7 primers. Then expression conditions optimized by adjusting parameters such as culture media, induction time, temperature, and IPTG concentration. SDS-PAGE analysis showed that high production of rLoa22 protein obtained when post induction incubation, IPTG concentration, and duration of induction were 37°C, 0.1 M and 5 h in 2×TY medium respectively. The purification of rLoa22 protein under native conditions using Ni-NTA pull-down was optimum in one hour binding at 37°C, five times washing process and elution buffer with a pH 7.4 and a 0.3 M imidazole concentration. The findings of the study led to high production of pure Loa22 protein, which can form the basis for future investigation on the design of rapid diagnostic tests and more effective vaccine candidates for leptospirosis.

Epidemiological characteristics of mpox epidemic in Guangzhou

Objective: To understand the epidemiological characteristics of mpox epidemic in Guangzhou and provide scientific evidence for the prevention and control of the disease. Methods: Based on the mpox surveillance system in Guangzhou, suspected mpox cases with fever and rash were reported by local hospitals at all levels to centers for disease control and prevention in Guangzhou for sampling, investigation and diagnosis. Descriptive epidemiological analysis was conducted on the clinical characteristics and treatment of the mpox cases and positive detection rate reported in Guangzhou as of 24:00 on June 23. Whole genome sequencing of the virus isolates was performed using Illumina Miniseq high-throughput sequencing platform. Results: The first mpox case in Guangzhou was reported on June 10 in 2023. As of 24:00 on June 23, a total of 25 confirmed mpox cases were reported. All the mpox cases were men with a M(Q1,Q3) of 32 (26, 36) years, the majority of the cases were MSM (96.0%). The main clinical features were rash (100.0%, 25/25), lymphadenectasis (100.0%, 25/25) and fever (52.0%, 13/25). Rash usually occurred near the genitals (88.0%, 22/25). The close contacts, mainly family members (40.4%, 23/57), showed no similar symptoms, such as fever or rash. The positive rate of mpox virus in household environment samples was 30.5%. The analyses on 3 complete gene sequences of mpox virus indicated that the strains belonged to West African type Ⅱb clade, B.1.3 lineage. Conclusions: Hidden transmission of mpox virus had occurred in MSM in Guangzhou. However, the size of affected population is relatively limited, and the possibility of wide spread of the virus is low.

Complete genome sequence of a divergent strain of cardamom mosaic virus.

Cardamom mosaic virus (CdMV; genus Macluravirus), which causes mosaic (katte) disease in cardamom, is a highly variable member of the family Potyviridae. So far, the complete genome sequence of one isolate from Karnataka (KS) has been reported. In the present study, we determined the complete genome sequence of a CdMV isolate from Kerala (KI) and the complete CP gene sequences of nine isolates of CdMV from Kerala, Karnataka, and Tamil Nadu, India. The complete genome of CdMV (KI) consists of 8255 nucleotides (nt) with two open reading frames (ORFs). The large ORF, potentially coding for a polyprotein of 2638 amino acids (aa), is further processed into nine mature proteins at eight cleavage sites. The second ORF, PIPO (pretty interesting Potyviridae ORF) starting with a C(A)6 motif, encodes a small protein of 56 aa. The viral genome contains an additional 13 nt in the 5' untranslated region (UTR) and 6 nt in the CP gene, as well as a deletion of 13 nt at the 3' UTR in comparison to the KS isolate of CdMV. The complete viral genome and polyprotein share 76% and 85% sequence identity with the KS isolate of CdMV, indicating that the present isolate is highly divergent from the KS isolate. Sequencing and analysis of the CP sequences of 16 CdMV isolates from different regions revealed high heterogeneity among them, suggesting that they should be considered members of more than one species.

Validation of 16S rRNA and Complete rpoB Gene Sequence Analysis for the Identification of Elizabethkingia Species.

Bacteria in the genus Elizabethkingia have emerged as a cause of life-threatening infections in humans. However, accurate species identification of these pathogens relies on molecular techniques. We aimed to evaluate the accuracy of 16S rRNA and complete RNA polymerase β-subunit (rpoB) gene sequences in identifying Elizabethkingia species. A total of 173 Elizabethkingia strains with whole-genome sequences in GenBank were included. The 16S rRNA gene and rpoB gene sequences from the same Elizabethkingia strains were examined. Of the 41 E. meningoseptica strains, all exhibited >99.5% 16S rRNA similarity to its type strain. Only 83% of the 99 E. anophelis strains shared >99.5% 16S rRNA gene similarity with its type strain. All strains of E. meningoseptica and E. anophelis formed a cluster distinct from the other Elizabethkingia species in the 16S rRNA and rpoB gene phylogenetic trees. The polymorphisms of 16S rRNA gene sequences are not sufficient for constructing a phylogenetic tree to discriminate species in the E. miricola cluster (E. miricola, E. bruuniana, E. occulta, and E. ursingii). The complete rpoB gene phylogenetic tree clearly delineates all strains of Elizabethkingia species. The complete rpoB gene sequencing could be a useful complementary phylogenetic marker for the accurate identification of Elizabethkingia species.

Genomes of two type strains of the Rhizobium tropici group: R. calliandrae CCGE524T and R. mayense CCGE526T.

The genome sequences of two nitrogen-fixing type strains of the Rhizobium tropici group were obtained: Rhizobium calliandrae CCGE524T and R. mayense CCGE526T. Genomic analyses confirmed their taxonomic position and identified three complete sequences of the repABC genes, indicative of three plasmids, one of them carrying symbiotic genes.

Molecular detection of Leptospira and Bartonella in Mastomys natalensis and its ectoparasites in Morogoro, Tanzania

Abstract Rodents play an important role in the transmission of zoonotic diseases. This study investigated the prevalence of Leptospira spp. and Bartonella spp. in Mastomys natalensis and its ectoparasites (fleas and mites) in selected villages of Morogoro, Tanzania. Mastomys natalensis were captured live in fallow habitats using Sherman® traps and anesthetized using Halothane. Blood samples were obtained from the retroorbital sinus Ectoparasites were removed from the fur using a hard brush and preserved in 70 % ethanol. Real time–qPCR was used to detect Leptospira spp. and Bartonella spp. from Mastomys natalensis blood and ectoparasites respectively. The study revealed a relatively larger number of males than females captures. Leptospira spp. was demonstrated in one out of 100 Mastomys natalensis. For Bartonella spp., prevalence of (14 %) was recorded in mites with a higher proportion in mites from adult male Mastomys natalensis than females. Upon Sanger sequencing, four positive samples showed a complete sequence of the ITS gene. Indicating that all samples belonged to Uncultured Bartonella. Low prevalence of Leptospira spp. and a high prevalence of Bartonella spp. was observed in Mastomys natalensis. Further exploration of rodent pathogens is recommended to raise awareness of the role of commensal rodents in disease transmission via their ectoparasites.

TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups

Abstract Transcriptome sequencing technologies have revolutionized the field of phylogenomics by facilitating the identification of homologous genes for species without whole genome sequences. To infer complex evolution relationship among eukaryotes, it is essential to obtain complete sequences of protein‐coding genes to provide informative mutations. However, transcriptomes in eukaryotes often consist of a large number of duplicated genes and alternative isoforms, bringing great challenges for developing effective tools to obtain complete coding gene sequences. Here, we present a net‐flow based assembler TransMCL, which aims to assemble fragmented transcripts into complete sequences while eliminating redundant isoforms during homologue clustering. By employing Markov clustering strategies and homologous gene guidance, TransMCL can accurately assemble genes for multiple organisms in an affordable time frame, making it well‐suited for phylogenomic studies based on transcriptomic data. Our results demonstrate that TransMCL can assemble 89.95%–92.95% of the total expressed genes into near‐complete transcripts on benchmark plant/animal datasets. Furthermore, applying TransMCL to multiple transcriptomes in a single run enhances the completeness of genes, even in the absence of guidance homologues from closely related species. These findings highlight the potential of TransMCL in phylogenomic studies, enabling the comprehensive characterization of gene families at the whole genome scale. By overcoming the challenges of complex gene contents in eukaryotes, TransMCL can significantly enhance our understanding of evolution of gene families across species.