Horizontal Transfer of Domains in ssrA gene Among Enterobacteriaceae

BackgroundThe tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene act as recognition sites for various integrases. Variations in ssrA genes were widely reported among the members of Enterobacteriaceae, but the functional relevance in the course of evolution are not well understood. In this study, we investigated the horizontal gene transfer of tmRNA among the members of Enterobacteriaceae. Methods and ResultsHorizontal gene transfer in tmRNA was found by predicting recombination signals in the tmRNA belong to Enterobacteriaceae using recombination detection program (RDP5). Our results revealed 7 recombination signals in tmRNA among different species. We further showed that the recombination signals was more in the domains present in the 3’ end than the domains in the 5’ end of tmRNA. Of note, the mRNA region, which codes for the peptide tag was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya, and Enterobacter were highly represented in the recombination signatures.Conclusions Taken together, our results revealed a high level of recombination among specific regions of tmRNA of Enterobacteriaceae and suggest the possible role of recombination in the diversification of SsrA function in proteolysis and other pathways.

Identification Sus scrofa and Mus musculus as potential hosts of SARS-CoV-2 via phylogenetic and homologous recombination analysis

Background: Previously, most studies focus on the wild animal being sold in the Wuhan Huanan seafood wholesale market, neglecting that the livestock living around other place could also be the original hosts. Methods: First, relative synonymous codon usage was utilized to analyze the potential hosts of SARS-CoV-2; Then cluster SARS-CoV-2 and related coronavirus through the phylogenetic tree. Next, we used Recombination Detection Program to identify the possible recombination region, as well as verifying via Simplot. Results: Related coronavirus from porcine or murine sources may faciliatate the evolution and reorganization of SARS-CoV-2. Conclusions: Overall, to our knowledge, this is the first paper to illustrate that swine and mice could be probable reservoirs for the SARS-CoV-2.

Identification Sus scrofa and Mus musculus as potential hosts of SARS-CoV-2 via phylogenetic and homologous recombination analysis

Background: Wuhan Huanan seafood wholesale market is highly suspected as the original place for the outbreak of SARS-CoV-2 previously. Most studies focus on the livestock being sold in the market, neglecting that the livestock living around the city of Wuhan could also be the original hosts. Methods: First, relative synonymous codon usage was utilized to analyze the potential hosts of SARS-CoV-2; Then cluster SARS-CoV-2 and related coronavirus through the phylogenetic tree. Next, we used Recombination Detection Program to identify the possible recombination region, as well as verifying via Simplot. Results: Related coronavirus from porcine or murine sources may faciliatate the evolution and reorganization of SARS-CoV-2. Conclusions: Overall, to our knowledge, this is the first paper to illustrate that swine and mice could be probable reservoirs for the SARS-CoV-2.

Sequence Analysis of Plum pox virus Strain C Isolates from Russia Revealed Prevalence of the D96E Mutation in the Universal Epitope and Interstrain Recombination Events

The understanding of genetic diversity, geographic distribution, and antigenic properties of Plum pox virus (PPV) is a prerequisite to improve control of sharka, the most detrimental viral disease of stone fruit crops worldwide. Forty new PPV strain C isolates were detected in sour cherry (Prunus cerasus) from three geographically distant (700–1100 km) regions of European Russia. Analysis of their 3’-terminal genomic sequences showed that nineteen isolates (47.5%) bear the D96E mutation in the universal epitope of the coat protein. Almost all of them cannot be detected by the monoclonal antibody 5B in triple antibody sandwich enzyme-linked immunosorbent assayand Western blot analysis that may potentially compromise serological PPV detection in cherries. Full-length genomes of seven PPV-C isolates were determined employing next-generation sequencing. Using the Recombination Detection Program (RDP4), the recombination event covering the region from (Cter)P1 to the middle of the HcPro gene was predicted in all the available PPV-C complete genomes. The isolates Tat-4, belonging to the strain CV, and RU-17sc (PPV-CR) were inferred as major and minor parents, respectively, suggesting possible pathways of evolution of the cherry-adapted strains. Downy cherry (P. tomentosa) was identified as the natural PPV-C host for the first time.

Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence

Human adenovirus type 53 (HAdV-53) has commonly been detected in samples from epidemic keratoconjunctivitis (EKC) patients in Japan since 1996. HAdV-53 is an intermediate virus, containing hexon-chimeric, penton base and fiber structures similar to HAdV-22 and -37, HAdV-37 and HAdV-8, respectively. HAdV-53-like intermediate strains were first isolated from EKC samples in Japan in the 1980s. Here, the complete genome sequences of three such HAdV-53-like intermediate strains (870006C, 880249C and 890357C) and four HAdV-53 strains were determined, and their relationships were analysed. The seven HAdV strains were classified into three groups, 870006C/880249C, 890357C and the four HAdV-53 strains, on the basis of phylogenetic analyses of the partial and complete genome sequences. HAdV strains within the same group showed the highest nucleotide identities (99.87–100.00 %). Like HAdV-53, the hexon loop 1 and 2 regions of 870006C, 880249C and 890357C showed the highest identity with HAdV-22. However, these strains did not show a hexon-chimeric structure similar to HAdV-22 and -37, or a penton base similar to HAdV-37. The fiber genes of 870006C and 880249C were identical to that of HAdV-37, but not HAdV-8. Thus, the three intermediate HAdVs isolated in the 1980s were similar to each other but not to HAdV-53. The recombination breakpoints were inferred by the Recombination Detection Program (rdp) using whole-genome sequences of these seven HAdV and of 12 HAdV-D strains from GenBank. HAdV-53 may have evolved from intermediate HAdVs circulating in the 1980s, and from HAdV-8, -22 and -37, by recombination of sections cut at the putative breakpoints.