We examined more than 700 DNA sequences (full length chromosomes and plasmids) for stretches of purines (R) or pyrimidines (Y) and alternating YR stretches; such regions will likely adopt structures ...which are different from the canonical B-form. Since one turn of the DNA helix is roughly 10 bp, we measured the fraction of each genome which contains purine (or pyrimidine) tracts of lengths of 10 bp or longer (hereafter referred to as ‘purine tracts’), as well as stretches of alternating pyrimidines/purine (‘pyr/pur tracts’) of the same length. Using this criteria, a random sequence would be expected to contain 1.0% of purine tracts and also 1.0% of the alternating pyr/pur tracts. In the vast majority of cases, there are more purine tracts than would be expected from a random sequence, with an average of 3.5%, significantly larger than the expectation value. The fraction of the chromosomes containing pyr/pur tracts was slightly less than expected, with an average of 0.8%. One of the most surprising findings is a clear difference in the length distributions of the regions studied between prokaryotes and eukaryotes. Whereas short-range correlations can explain the length distributions in prokaryotes, in eukaryotes there is an abundance of long stretches of purines or alternating purine/pyrimidine tracts, which cannot be explained in this way; these sequences are likely to play an important role in eukaryotic chromosome organisation.
•A novel Enterobacter cloacae bacteriophage, PZJ0206, was isolated in this study.•Phage PZJ0206 is the novel member within autographiviridae that can lyse E. cloacae.•Our findings may promote further ...understanding of the evolution of Berlinvirus.
Enterobacter cloacae is an opportunistic pathogen that widely distributes in various environments, often causing hospital and community-acquired infections. The limited phage resources and poor genomic data hinder the understanding of the lysis mechanism of Enterobacter cloacae phages. In the present study, we characterized a newly discovered lytic phage PZJ0206 that infects an E. cloacae strain isolated from sewage water into the Pearl River in Guangdong, China. The morphological characteristics of the icosahedral head and short tail of PZJ0206 were observed by transmission electron microscopy. The one-step growth curve showed that PZJ0206 has a relatively short latent period and an average burst size of approximately 124 PFU (plaque forming unit)/infected cell at an MOI of 0.1. The genome of phage PZJ0206 consists of 40,526 bp with a GC content of 48.62% and contains 45 putative open reading frames (ORFs). Based on genomic characteristics, comparative genomics and phylogenetic analysis, it was strongly demonstrated that PZJ0206 is a novel member of the genus Berlinvirus in the family Autographiviridae. Our work provides basic information on Enterobacter cloacae phage PZJ0206 and lays the foundation for the further study of the evolution of phage PZJ0206 and interactions between the phage and its host.
Enteropathies are a serious concern in racing pigeons as they significantly impair performance in races and their training, and viruses are suspected to be one of the main factors. Astroviruses are ...well-known to be responsible for causing enteric disease in humans and various other animals including birds, although their prevalence and pathogenicity in pigeons is poorly understood. In this study, we investigated two groups of young racing pigeons (sick – study group and healthy – control group) to assess the correlation between the number of astrovirus genome copies in cloacal swabs and the occurrence of enteropathy. To determine this, we developed a novel TaqMan quantitative PCR (qPCR) and digital droplet PCR (ddPCR) methods for astrovirus detection and absolute quantitative analysis. We also performed high-throughput sequencing to obtain the complete genome sequences and establish the genetic similarity of the obtained strains to known astroviruses of poultry and other avian species. Two new complete genome sequences of pigeon astroviruses in the Avastrovirus genus were identified, representing two new species. These were found most closely related to astroviruses identified in Columbidae species and chickens. They share an average of 75.8% genome-wide pairwise identity and 57.6% and 64.6% capsid protein sequence identity with other unclassified columbid avastrovirus sequences in GenBank. Although the difference in prevalence of astrovirus in the study and control group was found statistically insignificant, there was a significant difference between the number of genome copies in positive samples from both groups. These unambiguous results leave the role of astroviruses as enteropathogenic factors in pigeons still undetermined.
Sathuperi virus (SATV) and Shamonda virus (SHAV) (family Peribunyaviridae, genus Orthobunyavirus, species Schmallenberg orthobunyavirus) have been suggested to cause congenital abnormalities in ...ruminants. In this study, we determined the complete genome sequences of SATV KSB-6/C/02 and SHAV KSB-2/C/08 strains, which were obtained from Culicoides biting midges in Japan, by next-generation sequencing and Sanger sequencing. The 3’- and 5’-untranslated region sequences of the M segment of SHAV KSB-2/C/08 strains are distinctly different from those of SATV KSB-6/C/02 and Schmallenberg viruses. This study provides the genome characterization of Japanese strains of SATV and SHAV and presented the genetic variation in the untranslated regions of Schmallenberg orthobunyavirus M segments.
Isolated from intertidal sediment of the Yellow Sea, China, Bremerella sp. P1 putatively represents a novel species within the genus Bremerella of the family Pirellulaceae in the phylum ...Planctomycetota. The complete genome of strain P1 comprises a single circular chromosome with a size of 6,955,728 bp and a GC content of 55.26%. The genome contains 5772 protein-coding genes, 80 tRNA and 6 rRNA genes. A total of 147 CAZymes and 128 sulfatases have been identified from the genome of strain P1, indicating that the strain has the capability to degrade a wide range of polysaccharides. Moreover, a gene cluster related to bacterial microcompartments (BMCs) formation containing genes encoding the shell proteins and related enzymes to metabolize fucose or rhamnose is also found in the genome of strain P1. The genome of strain P1 represents the second complete one in the genus Bremerella, expanding the understanding of the physiological and metabolic characteristics, interspecies diversity, and ecological functions of the genus.
Summary
Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a ...near‐complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong‐read sequencing and Hi‐C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near‐complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.
Antibiotic-resistant bacteria, especially multi-antibiotic-resistant bacteria (MARBs), greatly threaten environmental safety and human health. However, studies on the phenotypic resistance and ...complete genotypic characterization of MARB in aquatic environments are lacking. In this study, a multi-resistant superbug (TR3) was screened by the selective pressure of multi-antibiotics from the activated sludge of the aeration tanks of urban wastewater treatment plants (WWTPs) in 5 different regions of China. Based on the 16 S rDNA sequence alignment it was found that the sequence similarity between strain TR3 and Aeromonas was as high as 99.50%. The genome-wide sequence showed that the base content of the chromosome of strain TR3 is 4,521,851 bp. It contains a plasmid with a length of 9182 bp. All antibiotic resistance genes (ARGs) of strain TR3 are located on the chromosome, which means that it has passage stability. There are multiple types of resistance genes in the genome and plasmid of strain TR3, enduing it with resistance to 5 antibiotics (ciprofloxacin, tetracycline, ampicillin, clarithromycin, and kanamycin), accompanied by the strongest resistance to kanamycin (aminoglycosides) and the worst resistance to clarithromycin (quinolones). From the perspective of gene expression, we show the resistance mechanism of strain TR3 to different types of antibiotics. In addition, the potential pathogenicity of strain TR3 is also discussed. Chlorine and ultraviolet (UV) sterilization on strain TR3 showed that UV is ineffective at low intensity, and it is easy to be revived by light. A low concentration of hypochlorous acid is effective for sterilization, but it can cause the release of DNA, becoming a potential source of ARGs discharged from WWTPs to environmental water bodies.
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•A multi-antibiotic resistant bacteria (MARB) was found in different WWTPs.•The genome-wide map and genotypic characteristics was provided.•Low-intensity UV sterilization is not enough for WWTP effluent.
Four molluscum contagiosum virus (MOCV) genotypes (MOCV1-4) and four subtype variants (MOCV1p, MOCV1va, MOCV1vb, and MOCV1vc) were partially characterized using restriction enzyme profiling in the ...early 1980s/1990s. However, complete genome sequences of only MOCV1 and MOCV2 are available. The evolutionary pathways of MOCV genotypes and subtype variants with unavailable sequences remain unclear, and also whether all MOCV genotypes/subtype variants can be reliably detected and appropriately categorized using available PCR-based protocols. We
fully characterized and functionally annotated 47 complete MOCV genomes, including two putative non-MOCV1/2 isolates, expanding the number of fully characterized MOCV genomes to 66. To ascertain the placement of any putative novel MOCV sequence into the restriction profiling typing scheme, we developed an original framework for extracting complete MOCV genome sequence-based restriction profiles and matching them with reference restriction profiles. We confirmed that two putative non-MOCV1/2 isolates represent the first complete genomes of MOCV3. Comprehensive phylogenomic, recombination, and restriction enzyme recognition site analysis of all 66 currently available MOCV genomes showed that they can be agglomerated into six phylogenetic subgroups (PG1-6), corresponding to the subtype variants from the pioneering studies. PG5 was a novel subtype variant of MOCV2, but no PGs corresponded to the subtype variants MOCV1vb or MOCV4. We showed that the phylogenetic subgroups may have diverged from the prototype MOCV genotype lineages following large-scale recombination events and hinted at partial sequence content of MOCV4 and direction of recombinant transfer in the events that spawned PG5 and the yet undetected subtype variant MOCV1vb.IMPORTANCEFour molluscum contagiosum virus (MOCV) genotypes (MOCV1-4) and four subtype variants were partially characterized using restriction enzyme profiling in the 1980s/1990s, but complete genome sequences of only MOCV1 and MOCV2 are available. The evolutionary pathways whereby genotypes/subtype variants with unavailable sequences emerged and whether all MOCVs can be detected using current diagnostic approaches remain unclear. We fully characterized 47 novel complete MOCV genomes, including the first complete MOCV3 genome, expanding the number of fully characterized genomes to 66. For reliably classifying the novel non-MOCV1/2 genomes, we developed and validated a framework for matching sequence-derived restriction maps with those defining MOCV subtypes in pioneering studies. Six phylogenetic subgroups (PG1-6) were identified, PG5 representing a novel MOCV2 subtype. The phylogenetic subgroups diverged from the prototype lineages following large-scale recombination events and hinted at partial sequence content of MOCV4 and direction of recombinant transfer in the events spawning PG5 and yet undetected MOCV1vb variant.
The general features and genome characteristics of the alginolytic Psychroserpens sp. NJDZ02 isolated from macroalgae collected from King George Island, Antarctica, are described. The sequenced ...genome is composed of a 4,319,537 bp circular chromosome containing 3699 coding genes including 49 tRNAs and 6 rRNA operons as 16S-23S-5S rRNA. The NJDZ02 genome contains several alginate lyases, which correlate with the high capacity of the strain to degrade sodium alginate. Genome sequencing of NJDZ02 revealed gene candidates of potential interest for use in enzymatic industries or applications in the field of polysaccharide degradation.
