RESUMEN
Bracoviruses (BVs) are endogenized nudiviruses in parasitoid wasps of the microgastroid complex (family Braconidae). Microgastroid wasps have coopted nudivirus genes to produce replication-defective virions that females use to transfer virulence genes to parasitized hosts. The microgastroid complex further consists of six subfamilies and â¼50,000 species but current understanding of BV gene inventories and organization primarily derives from analysis of two wasp species in the subfamily Microgastrinae (Microplitis demolitor and Cotesia congregata) that produce M. demolitor BV (MdBV) and C. congregata BV (CcBV). Notably, several genomic features of MdBV and CcBV remain conserved since divergence of M. demolitor and C. congregata â¼53 million years ago (MYA). However, it is unknown whether these conserved traits more broadly reflect BV evolution, because no complete genomes exist for any microgastroid wasps outside the Microgastrinae. In this regard, the subfamily Cheloninae is of greatest interest because it diverged earliest from the Microgastrinae (â¼85 MYA) after endogenization of the nudivirus ancestor. Here, we present the complete genome of Chelonus insularis, which is an egg-larval parasitoid in the Cheloninae that produces C. insularis BV (CinsBV). We report that the inventory of nudivirus genes in C. insularis is conserved but are dissimilarly organized compared to M. demolitor and C. congregata. Reciprocally, CinsBV proviral segments share organizational features with MdBV and CcBV but virulence gene inventories exhibit almost no overlap. Altogether, our results point to the functional importance of a conserved inventory of nudivirus genes and a dynamic set of virulence genes for the successful parasitism of hosts. Our results also suggest organizational features previously identified in MdBV and CcBV are likely not essential for BV virion formation. IMPORTANCE Bracoviruses are a remarkable example of virus endogenization, because large sets of genes from a nudivirus ancestor continue to produce virions that thousands of wasp species rely upon to parasitize hosts. Understanding how these genes interact and have been coopted by wasps for novel functions is of broad interest in the study of virus evolution. This work characterizes bracovirus genome components in the parasitoid wasp Chelonus insularis, which together with existing wasp genomes captures a large portion of the diversity among wasp species that produce bracoviruses. Results provide new information about how bracovirus genome components are organized in different wasps while also providing additional insights on key features required for function.
Asunto(s)
Genoma de los Insectos , Polydnaviridae , Avispas , Animales , Femenino , Componentes Genómicos/genética , Genoma de los Insectos/genética , Nudiviridae/genética , Polydnaviridae/genética , Polydnaviridae/patogenicidad , Provirus/genética , Factores de Virulencia/genética , Avispas/clasificación , Avispas/genética , Avispas/virologíaRESUMEN
Reorganization of topologically associated domain (TAD) is considered to be a novel mechanism for cell fate transitions. Here, we present a protocol to manipulate TAD via abscisic acid (ABA)-dependent genome linking. We use this protocol to merge two adjacent TADs and evaluate the influence on cell fate transitions. The advantages are that the manipulation does not change the genome and is reversible by withdrawing ABA. The major challenge is how to select linking loci for efficient TAD reorganization. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).
Asunto(s)
Diferenciación Celular/genética , Técnicas Citológicas/métodos , Componentes Genómicos , Genómica/métodos , Ácido Abscísico/farmacología , Animales , Línea Celular , Genoma/efectos de los fármacos , Genoma/genética , Componentes Genómicos/efectos de los fármacos , Componentes Genómicos/genética , Humanos , RatonesRESUMEN
Within-species variation in genome size has been documented in many animals and plants. Despite its importance for understanding eukaryotic genome diversity, there is only sparse knowledge about how individual-level processes mediate genome size variation in populations. Here, we study a natural population of the rotifer Brachionus asplanchnoidis whose members differ up to 1.9-fold in diploid genome size, but were still able to interbreed and produce viable offspring. We show that genome size is highly heritable and can be artificially selected up or down, but not below a certain basal diploid genome size for this species. Analyses of segregation patterns in haploid males reveal that large genomic elements (several megabases in size) provide the substrate of genome size variation. These elements, and their segregation patterns, explain the generation of new genome size variants, the short-term evolutionary potential of genome size change in populations, and some seemingly paradoxical patterns, like an increase in genome size variation among highly inbred lines. Our study suggests that a conceptual model involving only two variables, 1) a basal genome size of the population, and 2) a vector containing information on additional elements that may increase genome size in this population (size, number, and meiotic segregation behavior), can effectively address most scenarios of short-term evolutionary change of genome size in a population.
Asunto(s)
Tamaño del Genoma/genética , Genoma de los Helmintos/genética , Rotíferos/genética , Animales , Evolución Molecular , Femenino , Variación Genética , Genética de Población , Componentes Genómicos/genética , Masculino , Meiosis , Rotíferos/citologíaRESUMEN
Several general principles of global 3D genome organization have recently been established, including non-random positioning of chromosomes and genes in the cell nucleus, distinct chromatin compartments, and topologically associating domains (TADs). However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are still poorly characterized. Here, we systematically probe heterogeneity in genome organization. High-throughput optical mapping of several hundred intra-chromosomal interactions in individual human fibroblasts demonstrates low association frequencies, which are determined by genomic distance, higher-order chromatin architecture, and chromatin environment. The structure of TADs is variable between individual cells, and inter-TAD associations are common. Furthermore, single-cell analysis reveals independent behavior of individual alleles in single nuclei. Our observations reveal extensive variability and heterogeneity in genome organization at the level of individual alleles and demonstrate the coexistence of a broad spectrum of genome configurations in a cell population.
Asunto(s)
Ensamble y Desensamble de Cromatina/fisiología , Cromatina/genética , Componentes Genómicos/fisiología , Línea Celular , Núcleo Celular/genética , Cromosomas , Fibroblastos/fisiología , Genoma/genética , Componentes Genómicos/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Masculino , Análisis de la Célula IndividualRESUMEN
Two novel HLA class II alleles, DRB4*03:01N and DQB1*03:276N, containing large deletions were identified during routine typing. Extraction of DNA encompassing the deletions was carried out with a panel of capture oligonucleotides followed by whole genome amplification. Next generation DNA sequencing was then used to characterize the sequences. DRB4*03:01N has a 16 kilobase pair deletion stretching upstream from intron 2 toward centromeric DRB8. DQB1*03:276N has two deletions separated by 844 nucleotides. The first deletion (3.7 kilobase pairs) is upstream of intron 1 and the second deletion removes 3.3 kilobase pairs further upstream towards centromeric DQA2.
Asunto(s)
Alelos , Genotipo , Cadenas beta de HLA-DQ/genética , Cadenas HLA-DRB4/genética , Eliminación de Secuencia/genética , Cartilla de ADN/genética , Genoma , Componentes Genómicos/genética , Prueba de Histocompatibilidad , Humanos , Intrones/genética , Polimorfismo GenéticoRESUMEN
It has been known for over a century that chromatin is not randomly distributed within the nucleus. However, the question of how DNA is folded and the influence of such folding on nuclear processes remain topics of intensive current research. A longstanding, unanswered question is whether nuclear organization is simply a reflection of nuclear processes such as transcription and replication, or whether chromatin is folded by independent mechanisms and this per se encodes function? Evidence is emerging that both may be true. Here, using the α-globin gene cluster as an illustrative model, we provide an overview of the most recent insights into the layers of genome organization across different scales and how this relates to gene activity.
Asunto(s)
Componentes Genómicos/genética , Genoma/genética , Genoma/fisiología , Animales , Núcleo Celular/genética , Núcleo Celular/fisiología , Cromatina/genética , Cromatina/fisiología , ADN/genética , Replicación del ADN/genética , Humanos , Familia de Multigenes/genética , Conformación de Ácido Nucleico , Transcripción Genética/genética , Transcripción Genética/fisiología , Globinas alfa/genéticaRESUMEN
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat.
Asunto(s)
Mapeo Cromosómico/métodos , Marcadores Genéticos/genética , Genoma/genética , Ensayos Analíticos de Alto Rendimiento/métodos , ARN de Transferencia Aminoácido-Específico/genética , Aminoacil-ARN de Transferencia/genética , Algoritmos , Componentes Genómicos/genética , SelenocisteínaRESUMEN
The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation. Moreover, our data suggest that CTCF-dependent boundary function can be modulated by competing forces, such as the self-assembly of polycomb domains within the nucleus. Therefore, CTCF boundaries are not merely static structural components of the genome but instead are locally dynamic regulatory structures that control gene expression during development.
Asunto(s)
Diferenciación Celular/genética , Regulación del Desarrollo de la Expresión Génica/genética , Componentes Genómicos/genética , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Animales , Tipificación del Cuerpo/genética , Factor de Unión a CCCTC , Células Cultivadas , Células Madre Embrionarias , Eliminación de Gen , Proteínas de Homeodominio/genética , Proteínas de Homeodominio/metabolismo , Ratones , Dominios ProteicosRESUMEN
The complete mitochondrial genome of the intertidal barnacle Tetraclita serrata Darwin, 1854 (Crustacea: Maxillopoda: Sessilia) is presented. The genome is a circular molecule of 15,200 bp, which encodes 13 PCGs, 2 ribosomal RNA genes, and 22 transfer RNA genes. All non-coding regions are 591 bp in length, with the longest one speculated as the control region (389 bp), which is located between srRNA and trnK. The overall A+T content of the mitochondrial genome of T. serrata is 65.4%, which is lowest among all the eight mitochondrial genomes reported from sessile barnacles. There are variations of initiation and stop codons in the reported sessile barnacle mitochondrial genomes. Large-scale gene rearrangements are found in these genomes as compared to the pancrustacean ground pattern. ML and Bayesian analyses of all 15 complete mitochondrial genomes available from Maxillopoda lead to identical phylogenies. The phylogenetic tree based on mitochondrial PCGs shows that Argulus americanus (Branchiura) cluster with Armillifer armillatus (Pentastomida), distinct from all ten species from Cirripedia. Within the order Sessilia, Amphibalanus amphitrite (Balanidae) clusters with Striatobalanus amaryllis (Archaeobalanidae), and Nobia grandis (Pyrgomatidae). However, the two Megabalanus (Balanidae) are separated from the above grouping, resulting in non-monophyly of the family Balanidae. Moreover, the two Megabalanus have large-scale rearrangements as compared to the gene order shared by former three species. Therefore, both phylogenetic analysis using PCG sequences and gene order comparison suggest that Balanidae is not a monophyletic group. Given the limited taxa and moderate support values of the internal branches, the non-monophyly of the family Balanidae requires further verification.
Asunto(s)
Orden Génico/genética , Componentes Genómicos/genética , Genoma Mitocondrial/genética , Filogenia , Thoracica/genética , Animales , Composición de Base , Secuencia de Bases , Teorema de Bayes , Cartilla de ADN/genética , Funciones de Verosimilitud , Modelos Genéticos , Datos de Secuencia Molecular , Análisis de Secuencia de ADN , Thoracica/clasificaciónRESUMEN
Clostridium sulfidigenes 113A is a strictly anaerobic, rod shaped, gram positive bacterium isolated from sub-seafloor sediments associated with methane hydrates. Here, we report the first draft genome of C. sulfidigenes strain 113A, which comprises 3,717,420 bp in 96 contigs with the G+C content of 30.1%. A total of 3148 protein coding sequences were predicted. The genome annotation revealed that 113A could play an important role in biogeochemical cycles and have potential biotechnological applications such as production of organic acids and butanol.
Asunto(s)
Clostridium/genética , Componentes Genómicos/genética , Genoma Bacteriano/genética , Sedimentos Geológicos/microbiología , Composición de Base , Secuencia de Bases , Sedimentos Geológicos/química , Metano/análisis , Datos de Secuencia Molecular , Análisis de Secuencia de ADNRESUMEN
vB_DshP-R2C, a lytic phage that infects the marine bacterium Dinoroseobacter shibae DFL12(T), one of the model organisms of the Roseobacter clade, was isolated. Here we report the overall genome architecture of R2C. Genome analysis revealed that R2C is an N4-like phage with a 74.8 kb genome that contains 85 putative gene products.
Asunto(s)
Componentes Genómicos/genética , Genoma Viral/genética , Podoviridae/genética , Rhodobacteraceae/virología , Secuencia de Bases , Biología Marina , Datos de Secuencia Molecular , Análisis de Secuencia de ADNRESUMEN
Tumor necrosis factor (TNF) and its superfamily (TNFSF) members are important inflammatory cytokines. Although fish have fourteen TNFSF genes, their genomic location and existence are yet to be described and confirmed in the Japanese pufferfish (Fugu) (Takifugu rubripes). Therefore, we conducted in silico identification, synteny analysis of TNFSF genes from Fugu with that of zebrafish and human TNFSF loci and their expression analysis in various tissues. We identified ten novel TNFSF genes, viz. TNFSF5 (CD40L), TNFSF6 (FasL), three TNFSF10 (TRAIL) (-1, 2 and 3), TNFSF11 (RANKlg), TNFSF12 (TWEAK), two TNFSF13B (BAFF) (1 and 2) and TNFSF14 (LIGHT) belonging to seven TNFSFs in Fugu. Several features such as existence of TNF family signature, conservation of genes in TNF loci with human and zebrafish chromosomes and phylogenetic clustering with other teleost TNFSF orthologs confirmed their identity. Fugu TNFSF genes were constitutively expressed in all eight different tissues with most of them expressed highly in liver. Fugu TNFSF10 gene has three homologs present on chromosomes 10 (TNFSF10-1), 8 (TNFSF10-2) and 2 (TNFSF10-3). Moreover, a phylogenetic analysis containing all available vertebrate (mammals, birds, reptiles, amphibians and fish) TNFSF10 orthologs showed that Fugu TNFSF10-1 and 10-3 are present in all vertebrates, whereas TNFSF10-2 was not related to any mammalian and avian orthologs. Viral double-stranded RNA mimic poly (I:C) caused an elevated expression of three Fugu TNFSF10 genes in head kidney cells at 4h indicating probable role of these genes to induce apoptosis in virus-infected cells. In conclusion, Fugu possesses genes belonging to nine TNFSFs including the newly identified seven and previously reported two, TNFSF New (TNF-N) and TNFSF2 (TNF-α). Our findings would add up information to TNFSF evolution among vertebrates.
Asunto(s)
Evolución Molecular , Regulación de la Expresión Génica/genética , Componentes Genómicos/genética , Genoma/genética , Familia de Multigenes/genética , Takifugu/genética , Factor de Necrosis Tumoral alfa/genética , Secuencia de Aminoácidos , Animales , Secuencia de Bases , Análisis por Conglomerados , Cartilla de ADN/genética , Riñón Cefálico/citología , Riñón Cefálico/metabolismo , Datos de Secuencia Molecular , Filogenia , Poli I-C , Análisis de Secuencia de ADN , Homología de SecuenciaRESUMEN
Bacillus sp. A053, isolated from the Arctic seawater, shows strong antifungal activity against plant pathogenic fungi. Here, we report the draft sequence of the approximately 4.1-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Bacillus strain isolated from the Arctic seawater with antifungal activity. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compound in this strain.
Asunto(s)
Bacillus/genética , Componentes Genómicos/genética , Genoma Bacteriano/genética , Agua de Mar/microbiología , Antifúngicos/análisis , Regiones Árticas , Bacillus/química , Bacillus/patogenicidad , Secuencia de Bases , Mapeo Cromosómico , Datos de Secuencia Molecular , Océanos y Mares , Análisis de Secuencia de ADNRESUMEN
The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.
Asunto(s)
Carpas/genética , Evolución Molecular , Variación Genética , Genoma/genética , Animales , Secuencia de Bases , Mapeo Cromosómico , Perfilación de la Expresión Génica , Componentes Genómicos/genética , Datos de Secuencia Molecular , Análisis de Secuencia de ADN , Piel/metabolismo , Especificidad de la EspecieRESUMEN
Brevibacillus agri strain 5-2 was isolated from the formation water of a deep oil reservoir in Changqing Oilfield, China. This bacterium was found to have a capacity for degrading tetradecane, hexadecane and alkanesulfonate. To gain insights into its efficient metabolic pathway for degrading hydrocarbon and organosulfur compounds, here, we report the high quality draft genome of this strain. Two putative alkane 1-monooxygenases, one putative alkanesulfonate monooxygenase, one putative alkanesulfonate transporter, one putative sulfate permease and five putative sulfate transporters were identified in the draft genome. The genomic data of strain 5-2 may provide insights into the mechanism of microorganisms adapt to the petroleum reservoir after chemical flooding.
Asunto(s)
Adaptación Biológica/genética , Brevibacillus/genética , Genoma Bacteriano/genética , Agua Subterránea/microbiología , Redes y Vías Metabólicas/genética , Yacimiento de Petróleo y Gas/microbiología , Alcanos/metabolismo , Secuencia de Bases , Brevibacillus/metabolismo , China , Cartilla de ADN/genética , Componentes Genómicos/genética , Datos de Secuencia Molecular , Análisis de Secuencia de ADN , Especificidad de la EspecieRESUMEN
The complete mitochondrial (mt) DNA sequence of the rhodophyte Kappaphycus striatus ("Green Sacol" variety) was determined. The mtDNA is circular, 25,242 bases long (A+T content: 69.94%), and contains 50 densely packed genes comprising 93.22% of the mitochondrial genome, with genes encoded on both strands. Through comparative analysis, the overall sequence, genome structure, and organization of K. striatus mtDNA were seen to be highly similar with other fully sequenced mitochondrial genomes of the class Florideophyceae. On the other hand, certain degrees of genome rearrangements and greater sequence dissimilarities were observed for the mtDNAs of other evolutionarily distant red algae, such as those from the class Bangiophyceae and Cyanidiophyceae, compared to that of K. striatus. Furthermore, a trend was observed wherein the red algal mtDNAs tend to encode lesser number of protein-coding genes, albeit not necessarily shorter, as the organism becomes more morphologically complex. This trend is supported by the phylogenetic tree inferred from the concatenated amino acid sequences of the deduced protein products of cytochrome c oxidase subunit genes (cox1, 2, and 3).
Asunto(s)
Componentes Genómicos/genética , Genoma Mitocondrial/genética , Genoma de Planta/genética , Filogenia , Rhodophyta/genética , Secuencia de Aminoácidos , Composición de Base , Secuencia de Bases , Mapeo Contig , Cartilla de ADN/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Datos de Secuencia Molecular , Especificidad de la EspecieRESUMEN
Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species.
Asunto(s)
Ascomicetos/genética , Bromus/microbiología , Componentes Genómicos/genética , Genoma Fúngico/genética , Secuencia de Bases , ADN Complementario/genética , Idaho , Datos de Secuencia Molecular , Oligonucleótidos/genética , Análisis de Secuencia de ADNRESUMEN
BACKGROUND: The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine. METHODOLOGY/PRINCIPAL FINDINGS: Eighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis 'Shang-24' revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses. CONCLUSION: The results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop.
Asunto(s)
Componentes Genómicos/genética , Genoma de Planta/genética , MicroARNs/genética , Familia de Multigenes/genética , Filogenia , Factores de Transcripción/genética , Vitis/genética , Secuencia de Aminoácidos , Secuencia de Bases , Mapeo Cromosómico , Análisis por Conglomerados , ADN Complementario/genética , Perfilación de la Expresión Génica , Datos de Secuencia Molecular , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , Alineación de Secuencia , Análisis de Secuencia de ADN , Especificidad de la Especie , Sintenía/genéticaRESUMEN
Mycoplasma bovis pneumonia in cattle has been epidemic in China since 2008. To investigate M. bovis pathogenesis, we completed genome sequencing of strain HB0801 isolated from a lesioned bovine lung from Hubei, China. The genomic plasticity was determined by comparing HB0801 with M. bovis strain ATCC® 25523™/PG45 from cow mastitis milk, Chinese strain Hubei-1 from lesioned lung tissue, and 16 other Mycoplasmas species. Compared to PG45, the genome size of HB0801 was reduced by 11.7 kb. Furthermore, a large chromosome inversion (580 kb) was confirmed in all Chinese isolates including HB0801, HB1007, a strain from cow mastitis milk, and Hubei-1. In addition, the variable surface lipoproteins (vsp) gene cluster existed in HB0801, but contained less than half of the genes, and had poor identity to that in PG45, but they had conserved structures. Further inter-strain comparisons revealed other mechanisms of gene acquisition and loss in HB0801 that primarily involved insertion sequence (IS) elements, integrative conjugative element, restriction and modification systems, and some lipoproteins and transmembrane proteins. Subsequently, PG45 and HB0801 virulence in cattle was compared. Results indicated that both strains were pathogenic to cattle. The scores of gross pathological assessment for the control group, and the PG45- and HB0801-infected groups were 3, 13 and 9, respectively. Meanwhile the scores of lung lesion for these three groups were 36, 70, and 69, respectively. In addition, immunohistochemistry detection demonstrated that both strains were similarly distributed in lungs and lymph nodes. Although PG45 showed slightly higher virulence in calves than HB0801, there was no statistical difference between the strains (P>0.05). Compared to Hubei-1, a total of 122 SNP loci were disclosed in HB0801. In conclusion, although genomic plasticity was thought to be an evolutionary advantage, it did not apparently affect virulence of M. bovis strains in cattle.
Asunto(s)
Genoma Bacteriano/genética , Mycoplasma bovis/genética , Animales , Antígenos Bacterianos/genética , Proteínas de la Membrana Bacteriana Externa/genética , Secuencia de Bases , Bovinos , China , Inversión Cromosómica/genética , Transferencia de Gen Horizontal/genética , Componentes Genómicos/genética , Genómica , Familia de Multigenes/genética , Mycoplasma bovis/aislamiento & purificación , Mycoplasma bovis/patogenicidad , Especificidad de la EspecieRESUMEN
Erythromelagia is a condition characterized by attacks of burning pain and inflammation in the extremeties. An epidemic form of this syndrome occurs in secondary students in rural China and a virus referred to as erythromelalgia-associated poxvirus (ERPV) was reported to have been recovered from throat swabs in 1987. Studies performed at the time suggested that ERPV belongs to the orthopoxvirus genus and has similarities with ectromelia virus, the causative agent of mousepox. We have determined the complete genome sequence of ERPV and demonstrated that it has 99.8% identity to the Naval strain of ectromelia virus and a slighly lower identity to the Moscow strain. Small DNA deletions in the Naval genome that are absent from ERPV may suggest that the sequenced strain of Naval was not the immediate progenitor of ERPV.