Genome Length Research Articles

Mitochondrial genome of the Indian spot-billed duck and its phylogenetic and conservation implications.

The Indian spot-billed duck, Anas poecilorhyncha is a large dabbling and non-migratory breeding bird. The identification and phylogenetic relationship of A. poecilorhyncha remain uncertain due to the presence of overlapping meristic characters and hybridization with closely related species. Molecular data aids when there are challenges in morphological identification. However, genetic characterization of A. poecilorhyncha has been paid less attention. Apart from their functional and physiological role, mitochondrial genome can also be used for various purposes, including species identification, phylogenetic analysis, understanding the domestication history of species etc. Therefore, the present study aimed to sequence the mitochondrial genome of A. poecilorhyncha and its closely related domestic species A. platyrhynchos (mallard duck) to understand their mitochondrial genome structure and phylogenetic relationships. The length of mitochondrial genome of A. poecilorhyncha and A. platyrhynchos was 16,608 and 16,604bp respectively. Mitochondrial genome contained 37 genes and a non-coding control region. Overall, the characteristics of mitochondrial genome of both species were found to be conserved. The phylogenetic tree exhibited seven major clades (A to G) with a high bootstrap support. Notably, the Indian A. poecilorhyncha population formed a distinct clade (C) whereas the A. poecilorhyncha that were probably sampled from China grouped along with A. zonorhyncha (clade B). Besides, one of the A. poecilorhyncha probably sampled from China was placed in the clade A, which predominantly consisted of A. platyrhynchos. It suggests that Indian A. poecilorhyncha population is genetically different from Chinese A. poecilorhyncha population. Further, it sheds light on the importance of conducting a comprehensive phylogenetic study on these species. The newly sequenced mitochondrial genome of A. poecilorhyncha and A. platyrhynchos would be useful not only to have a better understanding of the phylogeny and evolution of Anas species but also to help in the conservation of A. poecilorhyncha which is under constant threat from rapid urbanization, interspecific hybridization and other human activities.

The genome sequence of the corn cockle, Agrostemma githago L., 1753 (Caryophyllaceae)

We present a genome assembly from an individual Agrostemma githago (the corn cockle; Tracheophyta; Magnoliopsida; Caryophyllales; Caryophyllaceae). The genome sequence has a total length of 1,735.0 megabases. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules suggesting the individual is a tetraploid (2n = 4x = 48). The organelle genomes have been assembled, and the length of the mitochondrial genome is 262.91 and the plastid genome 151.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 38,816 protein-coding genes.

Signature of viral fossils: a comparative genomics approach to understand the diversity of endogenous retroviruses in bats

Endogenous retroviruses (ERVs) are traces of past viral infections commonly found in vertebrate genomes. Many ERVs are tightly regulated by the host genomes and co-opted for various functions within the hosts. Bats are the only true volant mammals, with the smallest mammalian genomes and a high fraction of ERVs within the genomes. They are important hosts for various zoonotic viral pathogens and can effectively modulate their immune response to tolerate viral infections. Integrations of retroviruses have been implicated as one of the mechanisms by which bats have co-evolved strategies to combat viral infections. In this study, we investigated the diversity of ERVs in over 40 publicly available bat genomes to understand the distribution and the evolution of ERVs within bats. We observed all classes of ERVs within bat genomes including even the complex lenti retroviruses. Alpha and spuma retroviruses which are, generally considered rare in mammals, were common within bats. We observed a positive correlation between bat genome size and length of ERV elements. Interestingly, nearly 30% of the ERVs within bats are intact suggesting a recent origin or co-option by the host genome. Future studies focusing on comparative genomic and experimental data will be critical to understand the role of these ERVs in host genome evolution.

The complete mitochondrial genome of the endangered Atlantic Pygmy Devil Ray, Mobula hypostoma (Bancroft, 1831), from Brazil.

Mobulidae is a monophyletic family within the Myliobatiformes that comprises pelagic species represented by manta and devil rays. Among the genus Mobula, the Atlantic Pygmy Devil Ray - Mobula hypostoma - is reported in coastal regions exclusively in tropical and subtropical Atlantic Ocean from 1 to 100m deep. In Brazil, M. hypostoma is one of the least studied Mobula species. It is regularly misidentified, especially as Mobula thurstoni, and is commonly listed as bycatch, in fishery inventories, or related to opportunistic sightings in the national territory. Here, we describe the complete nucleotide sequence of the mitochondrial genome (mitogenome) from Mobula hypostoma, which is 18,141bp in length and comprises 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes. The M. hypostoma mitochondrial genes organisation and mitochondrial genome length are similar to other Mobula species, and the phylogenetic reconstruction indicates M. hypostoma as closely related to Mobula munkiana. The Brazilian mitogenome of M. hypostoma is expected to be a valuable resource for molecular-based species identification, and evolutionary and phylogeography studies.

Wildlife Infection of Peste des Petits Ruminants Detected in China, 2024.

In 2013, the second outbreak of peste des petits ruminants occurred in China, leading to a spillover in more than 20 provinces and municipalities over the next few months. Thereafter, the epidemic situation was stable owing to strict prevention and control measures. In February 2024, several bharals and argali with suspected symptoms of PPR were discovered in Rutog country, Tibet Autonomous Region. Samples collected from these animals were delivered to our laboratory for diagnosis; the results of fluorescence quantitative reverse-transcription (RT) PCR indicated that all samples were positive for PPR viral RNA. The N and F gene fragments were amplified successfully via RT-PCR, and these results confirmed that these animals were infected with PPRV. A PPRV strain (subsequently named ChinaTibet2024) was sequenced, and its genome length was 15,954 nucleotides. A phylogenetic tree analysis using N and F genes and viral genomes showed that the ChinaTibet2024 genome was classified into lineage IV of the PRRV genotypes. The genome of the ChinaTibet2024 strain was found to be closely related to PPRVs isolated in China between 2013 and 2014. A base insertion and a base deletion were detected in the M gene 5' untranslated region. Results indicated that the prevalent PPRV strains in China did not show significant changes and that special attention should be paid to the surveillance of wild animals as an important part of PPR prevention and control.

First detection and biological characterization of an avian metaavulavirus 8 isolated from a migratory swan goose in Qinghai Lake, Northwest China.

Avian metaavulavirus 8 (AMAV-8), formerly known as avian paramyxovirus 8 (APMV-8), has been detected sporadically in wild birds worldwide since it was first identified in a Canadian goose in 1976. However, the presence of AMAV-8 in birds has never been reported in China. To understand the epidemiological situation of AMAV-8 and its ability to infect chickens, we conducted a surveillance study and in vivo analysis of the AMAV-8 isolate identified in total of 14,909 clinical samples collected from wild and domestic birds from 2014 to 2022 in China. However, in 2017, only one AMAV-8 virus (Y7) was successful isolated from the fresh droppings of a migratory swan goose in Qinghai Lake in Northwest China. Thereafter, we report the complete genome sequence of the Y7 strain with a genome length of 15,342 nucleotides and the Y7 isolate was genetically closely-related to wild bird-origin AMAV-8 viruses previously circulated in the United States, Japan, and Kazakhstan. Furthermore, AMAV-8 infections of one-day-old specific pathogen-free (SPF) chicks did not induce any clinical signs over the entire observation period but was associated with viral shedding for up to 8 days. Interestingly, although all birds infected with the Y7 strain seroconverted within the first week of infection, virus replication was only detected in the trachea but not in other tissues such as the brain, lung, or heart. Here, we report the complete genome, genetic and biological characterization, replication and pathogenicity analysis in vivo and first detection of AMAV-8 in China.

The complete chloroplast genome of Camellia huulungensis Rosmann et Ninh, a golden Camellia species endemic to Vietnam

Camellia huulungensis Rosmann & Ninh 1997, belonging to the sect. Chrysantha, holds important ornamental value and medicinal value. In this study, the complete chloroplast genome sequence of C. huulungensis was assembled using high-throughput sequencing technology. The entire length of chloroplast genome is 156,546 bp and contains a small single-copy region (18,257 bp), a large single-copy region (86,219 bp), and a pair of inverted repeat regions (26,035 bp). A total of 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 37.33%. The phylogenetic analysis showed that C. huulungensis is sister to C. aurea. The results can provide genetic data for further phylogenetic studies of Camellia.

The complete chloroplast genome and phylogenetic analysis of Garcinia esculenta Y. H. Li. 1981 (Clusiaceae)

Garcinia esculenta Y. H. Li. 1981 (Clusiaceae) is an endemic tree species in China, primarily found in western and northwestern Yunnan Province. In this research, the complete chloroplast genome of G. esculenta was sequenced using the Illumina NovaSeq6000 platform. The result showed that the length of the complete chloroplast genome was 155,853 bp, which was composed of a large single-copy region (LSC) of 84,534 bp, a small single-copy region (SSC) of 17,175 bp, and a pair of inverted repeat (IR) regions of 27,072 bp. The overall GC content was 36.1%. The complete chloroplast genome encompassed 128 genes, comprising 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of the complete chloroplast genome sequences of 22 species revealed that G. esculenta is most closely related to G. oblongifolia.

The complete chloroplast genome of Buxus sinica var. parvifolia (Buxaceae) and its phylogenetic analysis

Buxus sinica var. parvifolia is a shrub or small arbor of the Buxaceae family, rich in various medicinal alkaloids and of great horticultural value. In this study, we sequenced, assembled, and annotated the complete chloroplast genome of B. sinica var. parvifolia for the first time. The length of the chloroplast genome is 158,995 bp with 38.1% overall GC content. It includes a large single-copy (LSC) region of 88,140 bp, a small single-copy (SSC) region of 17,761 bp, and two inverted repeat regions of 26,547 bp. Additionally, 132 functional genes in the genome are identified, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis showed that B. sinica var. parvifolia is closely related to Buxus microphylla. The complete chloroplast genome sequence of B. sinica var. parvifolia and its phylogenetic analysis provides useful genomic information for the further study of B. sinica var. parvifolia and other Buxus species.

Construction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species

Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic Nocardia species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for N. cyriacigeorgica, N. farcinica, N. brasiliensis, N. wallacei, and N. abscessus. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) N. brasiliensis diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of Nocardia species.

Complete genome sequence of Mycobacteriophage Eaglepride.

Eaglepride is a mycobacteriophage isolated using Mycobacterium smegmatis mc2155. The genome length is 50,926 bp with 89 open reading frames and 1 tRNA gene. Based on gene content similarity to actinobacteriophages, Eaglepride is assigned to phage subcluster A10 and shares the highest nucleotide identity with mycobacteriophage OKCentral2016.

Characterization of the complete mitochondrial genome of Loxocephala sichuanensis (Hemiptera: Eurybrachidae) with the phylogenetic analyses of Fulgoromorpha

Little is known about the mitochondrial genome of the family Eurybrachidae, with only two species sequenced. This study added one more mitogenome of Loxocephala sichuanensis in this family. The mitochondrial genome length of this species was 15,605 bp, consisting of 37 genes: 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region. An unusually high A + T content, reaching 94.3% at the third codon position of 13 PCGs in Loxocephala, was found in Eurybrachidae, which was the highest among all planthoppers, especially on N-strand. Three tandem repeat regions were detected in the control region. Phylogenetic analyses based on complete mitochondrial genome sequences from 145 species (encompassing 18 planthopper families and 135 species in Fulgoromorpha as ingroup, and 6 other non-planthopper families in Auchenorrhyncha as outgroup) were conducted. Six datasets (PCG123R24, PCG123R2, PCG123, PCG12R24, PCG12R2, PCG12) were established to investigate the influence of 22 tRNAs and the third codon of the 13 PCGs of mitogenome for phylogeny analyses. Both Maximum likelihood and Bayesian trees supported the monophyly of the superfamilies Delphacoidea and Fulgoroidea. Delphacoidea, consisting of Cixiidae and Delphacidae as sister group, was in the basal position of Fulgoromorpha. In Fulgoroidea, the families Meenoplidae and Kinnaridae, Dictyopharidae and Fulgoridae, Acanaloniidae and Tropiduchidae were sister groups which were strongly supported. Caliscelidae was close to the sister group Lophopidae with Eurybrachidae. The four families Flatidae, Nogodinidae, Ricaniidae and Issidae were closely related. The position of Tettigometridae was uncertain. Derbidae and Achilidae form a sister group when 22 tRNAs were included in the phylogeny. The joining of the tRNA sequences of mitochondrial genome enhanced the stability of family-level nodes and adjusted some phylogenetic positions, highlighting the significant role of joining tRNAs in phylogenetic analyses. Including or excluding the third codon position of 13 PCGs generally did not affect the overall phylogenetic structures of Fulgoromorpha.

Complete chloroplast genome of a montane plant Spathoglottis aurea Lindl.: Comparative analyses and phylogenetic relationships among members of tribe collabieae.

The yellow-flowered Spathoglottis aurea (tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship between S. aurea and the geographically isolated S. microchilina from Borneo that has encouraged further study of the S. aurea populations, but the genomic resource for S. aurea has not yet been reported. The present study reports the first work to characterize a chloroplast (cp) genome among the Spathoglottis genus. The complete cp genome of S. aurea was assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome of S. aurea is 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite cp genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of the S. aurea cp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed that S. aurea has a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such as Phaius and Cephalantheropsis.

Genomic characterization and cluster analysis of Carbapenem-resistant Klebsiella pneumoniae

To investigate the genomic features and perform cluster analysis of Carbapenem-resistant Klebsiella pneumoniae (CRKP) to provide an experimental basis for guiding the prevention and treatment of CRKP infections.A retrospective case-cohort study was conducted on 19 non-redundant CRKP strains isolated from the Tenth Affiliated Hospital of Southern Medical University between January and June 2023. Whole genome sequencing (WGS) and multilocus sequence typing (MLST) were performed to compare genomic features and analyze the resistance genes and homology of the strains.The results showed that the 19 CRKP strains were isolated from 8 different clinical departments, mainly from respiratory specimens. The whole genome sequencing revealed that the genomic lengths of CRKP ranged from 4.90 to 5.85 Mbp, with contigs N50 values>20 kb for each genome. The median overall GC content was 57.0% (50.4%-57.1%). Comparative genomic analysis identified three regions with high genomic variability. WGS detected 32 resistance genes across 11 categories. All 19 strains carried carbapenem resistance genes (blaKPC-2 and blaOXA-48), blaTEM-1B extended-spectrum β-lactamase resistance genes, qnrS1 quinolone resistance gene, and fosA fosfomycin resistance gene, with each strain carrying only one carbapenemase gene. The detection rate of blaKPC-2 was 94.7% (18/19). MLST identified three sequence types: ST11, ST437 and ST147, with ST11 being predominant (89.5%, 17/19). Clustering analysis based on acquired resistance genes revealed three clonal transmission patterns among strains 72 and 90, and strains 88, 84, 66 and 79.In conclusion, CRKP strains carry multiple resistance genes, and clustering analysis indicating that nosocomial clonal transmission is closely related to acquired resistance genes. The ST11-blaKPC-2 type strain is the predominant clone. Strengthened surveillance and effective control strategies are necessary to reduce nosocomial transmission of CRKP.

Differences between phytophagous and predatory species in Pentatomidae based on the mitochondrial genome.

Pentatomidae includes many species of significant economic value as plant pests and biological control agents. The feeding habits of Pentatomidae are closely related to their energy metabolism and ecological adaptations. In this study, we sequenced the mitochondrial genomes of 12 Asopinae species using the next-generation sequencing to explore the effect of dietary changes on mitochondrial genome evolution. Notably, all sequences were double-stranded circular DNA molecules containing 37 genes and one control region. We then compared and analyzed the mitochondrial genome characteristics of phytophagous and predatory bugs. Notably, no significant difference was observed in the length of the mitochondrial genomes between the predatory and phytophagous bugs. However, the AT content was higher in the mitochondrial genomes of phytophagous bugs than that of predatory bugs. Moreover, phytophagous bugs prefer codon usage patterns ending in A/T compared with predatory bugs. The evolution rate of predatory bugs was lower than that of phytophagous bugs. The phylogenetic relationships across phytophagous bugs' lineages were largely consistent at depth nodes based on different datasets and tree-reconstructing methods, and strongly supported the monophyly of predatory bugs. Additionally, the estimated divergence times indicated that Pentatomidae explosively radiated in the Early Cretaceous. Subsequently, the subfamily Asopinae and the genus Menida diverged in the Late Cretaceous. Our research results provide data supporting for the evolutionary patterns and classification of Pentatomidae.

The complete mitochondrial genome of the bubble-gum coral Paragorgia papillata (Octocorallia: Coralliidae) from the seamount in the tropical Western Pacific

The complete mitochondrial genome of Paragorgia papillata Li et al. 2021, a deep-sea gorgonian inhabiting at 858 m in Caroline Ridge, was obtained in this study. The length of the mitochondrial genome is 19,018 bp with 14 protein coding genes, one transfer RNA (tRNA-Met) and two ribosomal RNA genes contained in this circular molecule. Phylogenetic analysis indicated that P. papillata and P. coralloides Bayer, 1993 were two closely related species, and a total of 26 mutational sites (four nonsynonymous mutations included) can be detected between their mitochondrial genomes. This exhibits a case that mitochondrial genomes can be applied to differentiate closely related species in gorgonians. The phylogenetic tree constructed with mitochondrial genomes showed that the families in Octocorallia are reciprocally monophyletic, provided that the family names were revised according to the systematic revision of Octocorallia guided by phylogenomics. However, the relationships of the families within each order were different between the previous phylogenomic work and ours. Integrating mitochondrial genomes from a wider array of Octocorallia families is essential for a more accurate comparison of phylogenies derived from nuclear and mitochondrial sequences in future study.

Genomic factors shaping codon usage across the Saccharomycotina subphylum.

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy greater than 90% using a machine-learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

Genome microsatellite signature analysis in Adenoviridae family of viruses

Simple sequence repeats (SSRs) are present across both coding & non-coding regions of the genomes of all organisms with diversity in incidence, complexity, and repetition. The present study is focused on Adenoviridae which are non-enveloped viruses consisting of linear double-stranded DNA genome. The members of Adenoviridae are known to cause respiratory illnesses like the common cold (cough, runny nose, mild fever), pneumonia (occasionally), keratoconjunctivitis (infection in the eye known as pink eye), croup and cystitis (inflammation of the bladder). Our investigation aims to extract and analyse SSRs from 68 Adenoviridae genomes. Virus genome sequences were retrieved from NCBI and SSRs extracted from MISA. ETE3 and iTOL were used for the phylogenetic tree construction, annotation and visualization. The genome length of Adenoviridae genomes ranged from 26163 bp to 45667 bp while GC content varied from 33.6 % to 66.9 %. Genome wide analysis revealed a total incidence of 9861 SSRs and 793 cSSRs. The minimum and maximum range of SSR incidence is 112 (A67) to 203 (A61) respectively. The most prevalent mono, di and tri-SSR motif is “A”, “GC/CG” and “GAG/CTC” comprised of 1177, 1859 and 201 occurrences respectively. About 78 % SSRs are present in the coding region in the studied genomes. In terms of protein specific distribution, DNA polymerase enzyme had the highest incidence of 485 SSRs. The presence of mono-SSRs in the A/T region is a marker for host determination and divergence. The average mono-SSRs present in A/T region is 67.14 % and it ranged from 16.22 % to 99.11 %. The high prevalence of mono-SSRs in the A/T region was associated with human and related species as hosts. Further, the clustering of viruses as per their hosts was observed in the phylogenetic tree suggesting the role of host in viral evolution. The presence of unique and conserved cSSRs as genome markers has also been highlighted.

First identification and genomic features of multidrug-resistant Citrobacter freundii ST669 strain isolated from a domesticated duck in Bangladesh

ObjectivesCitrobacter freundii is a prevalent source of nosocomial infections and a well-known cause of diarrheal diseases. In recent years, it has also become increasingly resistant to various antimicrobials. In this study, we screened and characterized a multidrug-resistant (MDR) C. freundii isolate obtained from a domesticated diseased duck to better understand the genetic features, molecular epidemiology, and underlying factors linked to the antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) of the isolate. MethodsThe C. freundii BAU_TM8 strain was isolated using culturing, staining, biochemical, polymerase chain reaction, and Matrix-assisted laser desorption/ionization-time of flight methods. The MDR properties of the strain were determined by a disk diffusion test. The genomic sequence of C. freundii BAU_TM8 was performed using the Illumina NextSeq2000 platform. The ARGs, VFGs, and genomic functional characteristics of the C. freundii BAU_TM8 strain were identified using several open-source databases. ResultsThe sequence type of this strain was ST669, and the pathogenicity index of the strain was 0.919. Moreover, the strain had an estimated genome length of 5,797,806 bp, harboring 62 contigs, a G + C content of 54.32 %, and five contig L50s with an N50 value of 443,947 bp. Using phylogenetic analysis, this strain was closely related to two strains isolated from human and environmental samples in the USA and China despite huge geographical distances. The C. freundii BAU_TM8 strain consisted of 40 AGRs encoding resistance to 19 antimicrobial categories, e.g., fluoroquinolones, macrolides, folate pathway antagonists, aminoglycosides, tetracyclines, cephalosporins, and others. According to the phenotypic assay and genome sequence, the sensitivity and specificity of resistance profiles of the strain were 100 % and 20 %, respectively. Moreover, the virulence factor database detected 66 VFGs in this strain. This strain contained 1581 subsystems, having 33 % subsystem coverage and 2275 genes encoding amino acid derivatives, carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups, pigments, respiration, motility and chemotaxis, stress response, DNA metabolism, nucleosides and nucleotides, and others. ConclusionsTo the best of our knowledge, this is the first WGS report of C. freundii from a domesticated duck in Bangladesh. The ubiquitous occurrence of ARGs and VFGs in the C. freundii BAU_TM8 strain detected in this study highlights the growing concern about antimicrobial resistance in humans, animals, and environments.

Genome characterization of BI2 subcluster Streptomyces scabiei bacteriophages GoblinVoyage and Doxi13.

We present the bacteriophages GoblinVoyage and Doxi13, siphoviruses isolated on Streptomyces scabiei RL-34. They belong to the BI2 cluster and have genomes consisting of 60.9% GC content with identical 3' end sticky overhangs. The genome lengths of GoblinVoyage and Doxi13 are 43,540 bp and 43,696 bp, respectively.