Project description:Gene copy number variation plays a large role in the evolution of genomes. In Rattus norvegicus and other rodent species, the Y-chromosome has accumulated multiple copies of Sry loci. These copy number variations have been previously linked with changes in phenotype of animal models such as the spontaneously hypertensive rat (SHR). This study characterizes the Y-chromosome in the Sry region of Rattus norvegicus, while addressing functional variations seen in the Sry protein products.Eleven Sry loci have been identified in the SHR with one (nonHMG Sry) containing a frame shift mutation. The nonHMGSry is found and conserved in the related WKY and SD rat strains. Three new, previously unidentified, Sry loci were identified in this study (Sry3BII, Sry4 and Sry4A) in both SHR and WKY. Repetitive element analysis revealed numerous LINE-L1 elements at regions where conservation is lost among the Sry copies. In addition we have identified a retrotransposed copy of Med14 originating from spliced mRNA, two autosomal genes (Ccdc110 and HMGB1) and a normal mammalian Y-chromosome gene (Zfy) in the Sry region of the rat Y-chromosome. Translation of the sequences of each Sry gene reveals eight proteins with amino acid differences leading to changes in nuclear localization and promoter activation of a Sry-responsive gene. Sry-? (coded by the Sry2 locus) has an increased cytoplasmic fraction due to alterations at amino acid 21. Sry-? has altered gene regulation of the Sry1 promoter due to changes at amino acid 76.The duplication of Sry on the Rattus norvegicus Y-chromosome has led to proteins with altered functional ability that may have been selected for functions in addition to testis determination. Additionally, several other genes not normally found on the Y-chromosome have duplicated new copies into the region around the Sry genes. These suggest a role of active transposable elements in the evolution of the mammalian Y-chromosome in species such as Rattus norvegicus.
Project description:<i>Hunnivirus</i> is a novel member of the family <i>Picornaviridae</i>. A single species, <i>Hunnivirus A</i>, is currently described. However, there is limited information on the identification of <i>Hunnivirus</i> to date, and thereby the circulation of <i>Hunnivirus</i> is not fully understood. Thus, the objective of this study was to investigate the prevalence, genomic characteristics, and evolution of rat hunnivirus in southern China. A total of 404 fecal samples were subjected to detection of <i>Hunnivirus</i> from urban rats (<i>Rattus norvegicus</i> and <i>Rattus tanezumi</i>) using PCR assay based on specific primers targeted to partial 3D regions, with the prevalence of 17.8% in <i>Rattus norvegicus</i> and 15.6% in <i>Rattus tanezumi</i>. An almost full-length rat hunnivirus sequence (RatHuV/YY12/CHN) and the genome structure were acquired in the present study. Phylogenetic analysis of the P1 coding regions suggested the RatHuV/YY12/CHN sequence was found to be within the genotype of <i>Hunnivirus A4</i>. The negative selection was further identified based on analysis of non-synonymous to synonymous substitution rates. The present findings suggest that hunniviruses are common in urban rats. Further research is needed for increased surveillance and awareness of potential risks to human health.
Project description:Invasive species are the primary driver of island taxa extinctions and, among them, those belonging to the genus <i>Rattus</i> are considered as the most damaging. The presence of black rat (<i>Rattus rattus</i>) on Cyprus has long been established, while that of brown rat (<i>Rattus norvegicus</i>) is dubious. This study is the first to provide molecular and morphological data to document the occurrence of <i>R. norvegicus</i> in the island of Cyprus. A total of 223 black rats and 14 brown rats were collected. Each sample was first taxonomically attributed on the basis of body measurements and cranial observations. Four of the specimens identified as <i>R. norvegicus</i> and one identified as <i>R. rattus</i> were subjected to molecular characterization in order to corroborate species identification. The analyses of the mitochondrial control region were consistent with morphological data, supporting the taxonomic identification of the samples. At least two maternal molecular lineages for <i>R. norvegicus</i> were found in Cyprus. The small number of brown rats collected in the island, as well as the large number of samples of black rats retrieved in the past years might be an indication that the distribution of <i>R. norvegicus</i> is still limited into three out of the six districts of Cyprus.
Project description:Recently, murine kobuvirus (MuKV), a novel member of the family <i>Picornaviridae</i>, was identified in faecal samples of <i>Rattus norvegicus</i> in China. The limited information on the circulation of MuKV in other murine rodent species prompted us to investigate its prevalence and conduct a genetic characterization of MuKV in <i>Rattus losea</i>, <i>Rattus tanezumi</i> and <i>Rattus norvegicus</i> in China. Between 2015 and 2017, 243 faecal samples of these three murine rodent species from three regions in southern China were screened for the presence of MuKV. The overall prevalence was 23.0% (56/243). Three complete MuKV polyprotein sequences were acquired, and the genome organization was determined. Phylogenetic analyses suggested that our sequences were closely related to Chinese strains and belong to the species <i>Aichivirus A</i> in the genus <i>Kobuvirus</i>. Additional studies are required to understand the true prevalence of MuKV in murine rodent populations in China.
Project description:Bartonella rattimassiliensis is a facultative intracellular bacterium isolated from the blood of Rattus norvegicus in Marseille. The present study reports the draft genome of B. rattimassiliensis strain 15908 (CIP 107705(T)).
Project description:Natural infection with larval Echinococcus multilocularis was recognized in one of eight Norway rats, Rattus norvegicus, caught indoors in 2009 in Ebetsu, Hokkaido, northern Japan. Cystic lesions were found in the right median and lateral lobes of the liver, with numerous alveolar cysts in the periphery of the lesions. Protoscolices were formed within large cysts. The laminated layers of the cysts were positive for PAS staining. Nested PCR using the primers specific for Taenia mitochondrial 12S rDNA yielded a 250-bp product, and the sequence of the PCR product matched that of E. multilocularis isolates from Hokkaido and Germany. This is the third natural alveolar hydatidosis in R. norvegicus in Japan.
Project description:BACKGROUND:Murine kobuviruses (MuKV) are newly recognized picornaviruses first detected in murine rodents in the USA in 2011. Little information on MuKV epidemiology in murine rodents is available. Therefore, we conducted a survey of the prevalence and genomic characteristics of rat kobuvirus in Guangdong, China. RESULTS:Fecal samples from 223 rats (Rattus norvegicus) were collected from Guangdong and kobuviruses were detected in 12.6% (28) of samples. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions showed that rat kobuvirus obtained in this study were genetically closely related to those of rat/mouse kobuvirus reported in other geographical areas. Two near full-length rat kobuvirus genomes (MM33, GZ85) were acquired and phylogenetic analysis of these revealed that they shared very high nucleotide/amino acids identity with one another (95.4%/99.4%) and a sewage-derived sequence (86.9%/93.5% and 87.5%/93.7%, respectively). Comparison with original Aichivirus A strains, such human kobuvirus, revealed amino acid identity values of approximately 80%. CONCLUSION:Our findings indicate that rat kobuvirus have distinctive genetic characteristics from other Aichivirus A viruses. Additionally, rat kobuvirus may spread via sewage.
Project description:GRASP65 and GRASP55 were classified as Golgi reassembly stacking proteins which play crucial and complementary roles in the stacking of Golgi cisternae. They also participate in vesicle tethering, mitotic progression, the disassembly and reassembly of the Golgi apparatus during mitosis and unconventional secretory pathway regulation. In this study, the expression, crystallization and preliminary crystallographic analysis of the GRASP65 GRASP domain from Rattus norvegicus are presented. The crystals diffracted to 2.0 Å resolution and belonged to space group P21212, with unit-cell parameters a = 44.99, b = 104.29, c = 37.93 Å, ? = ? = ? = 90°. Furthermore, molecular replacement was employed to determine the structure of the GRASP65 GRASP domain from R. norvegicus.
Project description:BACKGROUND AND OBJECTIVES:Widespread use of antibiotics has resulted in selection pressure on genes that make bacteria non-responsive to antibiotics. These antibiotic-resistant bacteria are currently a major threat to global health. There are various possibilities for the transfer of antibiotic resistance genes. It has been argued that animal vectors such as Rattus norvegicus (R. norvegicus) living in hospital sewage systems are ideal for carrying pathogens responsible for fatal diseases in humans. METHODOLOGY:Using a metagenomic sequencing approach, we investigated faecal samples of R. norvegicus from three major cities for the presence of antibiotic resistance genes. RESULTS:We show that despite the shared resistome within samples from the same geographic locations, samples from hospital area carry significantly abundant vancomycin resistance genes. CONCLUSIONS AND IMPLICATIONS:The observed pattern is consistent with a selection for vancomycin genes in the R. norvegicus microbiome, potentially driven by the outflow of antibiotics and antibiotic-resistant bacteria into the wastewater systems. Carriage of vancomycin resistance may suggest that R. norvegicus is acting as a reservoir for possible transmission to the human population.
Project description:The brown rat, Rattus norvegicus, is both a notorious pest and a frequently used model in biomedical research. By analyzing genome sequences of 12 wild-caught brown rats from their presumed ancestral range in NE China, along with the sequence of a black rat, Rattus rattus, we investigate the selective and demographic forces shaping variation in the genome. We estimate that the recent effective population size (Ne) of this species = [Formula: see text], based on silent site diversity. We compare patterns of diversity in these genomes with patterns in multiple genome sequences of the house mouse (Mus musculus castaneus), which has a much larger Ne. This reveals an important role for variation in the strength of genetic drift in mammalian genome evolution. By a Pairwise Sequentially Markovian Coalescent analysis of demographic history, we infer that there has been a recent population size bottleneck in wild rats, which we date to approximately 20,000 years ago. Consistent with this, wild rat populations have experienced an increased flux of mildly deleterious mutations, which segregate at higher frequencies in protein-coding genes and conserved noncoding elements. This leads to negative estimates of the rate of adaptive evolution (?) in proteins and conserved noncoding elements, a result which we discuss in relation to the strongly positive estimates observed in wild house mice. As a consequence of the population bottleneck, wild rats also show a markedly slower decay of linkage disequilibrium with physical distance than wild house mice.