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1.
Arch Virol ; 164(10): 2641-2644, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31375908

RESUMO

We report the complete genome sequence of a novel nucleorhabdovirus, apple rootstock virus A (ApRVA), isolated from Malus spp. in South Korea. ApRVA has a 14,043-nt single-stranded negative-sense RNA genome. In the antigenome sense, it contains seven open reading frames, encoding the putative nucleocapsid protein, phosphoprotein, cell-to-cell movement protein, matrix protein, glycoprotein, RNA-dependent RNA polymerase, and an additional hypothetical protein, the gene for which is located between the genes for the matrix protein and glycoprotein. The complete genome sequence of ApRVA showed 47.45% nucleotide sequence identity to that of black currant-associated rhabdovirus 1. The genome organization, phylogenetic relationships, and sequence similarities to other nucleorhabdoviruses suggest that ApRVA is a new member of the genus Nucleorhabdovirus.


Assuntos
Genoma Viral , Malus/virologia , Raízes de Plantas/virologia , Rhabdoviridae/classificação , Rhabdoviridae/genética , Análise de Sequência de DNA , Ordem dos Genes , Fases de Leitura Aberta , Filogenia , RNA Viral/genética , República da Coreia , Rhabdoviridae/isolamento & purificação , Homologia de Sequência do Ácido Nucleico , Proteínas Virais/genética
2.
Arch Virol ; 164(10): 2609-2611, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31312966

RESUMO

A new virus belonging to the genus Vitivirus in the family Betaflexiviridae was identified by next-generation sequencing of a blueberry plant showing green mosaic symptoms. The genome organization of the virus, which is tentatively named "blueberry green mosaic-associated virus" (BGMaV), is typical of vitiviruses, with five open reading frames (ORFs) and a polyadenylated 3' terminus. The ORFs code for the viral replicase, a 16K protein of unknown function, a movement protein, a coat protein (CP), and a nucleic acid binding protein. Phylogenetic analyses based on the deduced amino acid sequence of the CP and conserved motifs of the RNA-dependent RNA polymerase confirmed the taxonomic placement of BGMaV in the genus Vitivirus.


Assuntos
Mirtilos Azuis (Planta)/virologia , Flexiviridae/classificação , Flexiviridae/isolamento & purificação , Filogenia , Doenças das Plantas/virologia , Ordem dos Genes , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Fases de Leitura Aberta , RNA Mensageiro , RNA Viral/genética , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Proteínas Virais/genética
3.
Arch Virol ; 164(10): 2621-2625, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31350613

RESUMO

Porcine epidemic diarrhea virus (PEDV) is a deadly epizootic swine coronavirus that is of importance to the world pork industry. Since the re-emergence of the virulent genotype 2b (G2b) in 2014, Jeju Island in South Korea has faced periodic outbreaks, leading to the occurrence of endemics in provincial herds. In this study, we examined the complete genome sequences and molecular characteristics of novel G2b PEDV variants with a two-amino-acid deletion in the neutralizing epitope of the spike (S) gene, which were concurrently identified on a re-infected farm and its neighboring farm on Jeju Island. Whole-genome sequencing of the Jeju S-DEL isolates KNU-1829 and KNU-1830 revealed the presence of a continuous 9-nucleotide deletion within the nonstructural protein coding region. Their genomes were 28,023 nucleotides in length, 15 nucleotides shorter than those of the classical G2b PEDV strains. The two S-DEL isolates had 96.4-99.2% and 98.3-99.7% identity at the S-gene and full-genome level, respectively, to other global G2b PEDV strains. Genetic and antigenic analyses indicated that the S-DEL isolates are most closely related to the primary strain identified from the initial exposure at the same farm, but the virus appears to undergo continuous evolution, possibly leading to antigenic drift under recurrent or endemic pressure. This study provides important information about the antigenic diversity of PEDV circulating in the endemic areas, which arises from continuous non-lethal mutations to ensure viral fitness in the host environment.


Assuntos
Infecções por Coronavirus/veterinária , Surtos de Doenças , Genoma Viral , Vírus da Diarreia Epidêmica Suína/genética , Deleção de Sequência , Glicoproteína da Espícula de Coronavírus/genética , Doenças dos Suínos/virologia , Animais , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Fazendas , Ordem dos Genes , Ilhas/epidemiologia , Filogenia , Vírus da Diarreia Epidêmica Suína/classificação , Vírus da Diarreia Epidêmica Suína/isolamento & purificação , RNA Viral/genética , República da Coreia/epidemiologia , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico , Suínos , Doenças dos Suínos/epidemiologia , Proteínas não Estruturais Virais/genética
4.
Gene ; 706: 146-153, 2019 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-31077734

RESUMO

Necrophagous Dermestes species have high forensic importance in relation to the estimation of elapsed time since death or death season. To further supplement the genome-level features for related species, the complete mitochondrial genome (mitogenome) of Dermestes species D. essellatocollis, D. frischii and D. coarctatus are amplified, sequenced, annotated, analyzed, and compared with other twelve species of the infraorder Bostrichoidea. The mitochondrial genomes were typical circular molecules with 16,218, 15,873 and 15,873 bp in length, respectively. They included 13 protein coding genes, two rRNAs, and 22 tRNAs, as well as the putative control region. The gene orders and orientations are identical to those of other recorded bostrichiformian species and had the ancestral insect gene composition. Furthermore, phylogenetic analyses based on all the mitochondrial protein coding genes for 13 Bostrichoidea and 16 outgroup taxa were performed using Bayesian and Maximum Likelihood analyses. The inferred trees indicate that the genus Dermestes is monophyletic. The monophyly of infraorder Bostrichiformia is not supported. This study provides genomic data for mitochondrial genome library of the genus Dermestes to investigate evolutionary and systematic studies.


Assuntos
Besouros/genética , Genoma Mitocondrial/genética , Mitocôndrias/genética , Animais , Composição de Bases/genética , Sequência de Bases , Ciências Forenses/métodos , Ordem dos Genes/genética , Filogenia , RNA Ribossômico/genética , RNA de Transferência/genética
5.
Fungal Biol ; 123(5): 351-363, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31053324

RESUMO

The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.


Assuntos
Ascomicetos/genética , Genoma Fúngico , Doenças das Plantas/microbiologia , Árvores/microbiologia , África , Biologia Computacional , Evolução Molecular , Ordem dos Genes , Variação Genética , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Sequências Repetitivas Dispersas , Sintenia
6.
Parasitol Int ; 71: 99-105, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30946896

RESUMO

Despite the highly divergent morphology, pathogenicity and worldwide distribution of digenean parasites belonging to one of the largest families, the Plagiorchiidae, there are no complete mitochondrial (mt) genomes published to date for plagiorchiids. In this study, we obtained nuclear ribosomal DNA (ITS region and 28S rDNA) sequences and the complete mt genome sequences of Plagiorchis maculosus (Rudolphi 1802) Braun, 1902, and assessed its phylogenetic relationship with other xiphidiates, based on the mtDNA sequences. The obtained ITS and 28S rDNA sequences were identical to the corresponding sequences of P. maculosus available in GenBank. The complete mitochondrial genome of P. maculosus (14,124 bp) contained 36 genes (atp8 is absent) and a long non-coding region (NCR) with two sets of repeated sequences of 283 nucleotides each. The phylogenetic tree resulting from Bayesian inference (BI) analyses based on concatenated nucleotide sequences of all 36 genes of P. maculosus and other xiphidiates mitochondrial genomes, indicated that P. maculosus (and the Plagiorchiidae) is phylogenetically closest to the Brachycladiidae and Paragonimidae. The present study describes the first mitochondrial genome from the type genus of the family Plagiorchiidae. The overall gene arrangement, nucleotide composition, A + T contents, AT and GC skew and codon usage with relative synonymous codon usage (RSCU) for 12 PCGs are described. Characterization of mitochondrial genomes from additional plagiorchiid taxa is necessary to make further progress in phylogenetic and epidemiological studies of these digeneans as well as accurate diagnostics of these parasites including those parasitic in humans.


Assuntos
DNA Mitocondrial/genética , Genoma Mitocondrial , Filogenia , Trematódeos/genética , Animais , Sequência de Bases , Aves/parasitologia , Códon , DNA Ribossômico/genética , Ordem dos Genes , Intestinos/parasitologia , Análise de Sequência de DNA
7.
Appl Microbiol Biotechnol ; 103(10): 4089-4102, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30937499

RESUMO

Teicoplanin is a frontline glycopeptide antibiotic produced by Actinoplanes teichomyceticus. It is used to treat complicated cases of infection, including pediatric ones, caused by Gram-positive pathogens. There is a steady interest in elucidating the genetic mechanisms determining teicoplanin production, as they would help overproduce known teicoplanins and discover novel glycopeptides. Herein, we investigate the transcriptional organization of the tei biosynthetic gene cluster and the roles of the cluster-situated regulatory genes in controlling teicoplanin production and self-resistance in A. teichomyceticus. We demonstrate that the tei cluster is organized into nine polygenic and nine monogenic transcriptional units. Most of tei biosynthetic genes are subjected to StrR-like Tei15* control, which, in turn, appears to be regulated by LuxR-type Tei16*. Expression of the genes conferring teicoplanin self-resistance in A. teichomyceticus is not co-regulated with antibiotic production. The gene tei31*, coding for a putative DNA binding protein, is not expressed under teicoplanin producing conditions and is dispensable for antibiotic production. Finally, phylogenesis reconstruction of the glycopeptide cluster-encoded regulators reveals two main clades of StrR-like regulators. Tei15* and close orthologues form one of these clades; the second clade is composed by orthologues of Bbr and Dbv4, governing the biosynthesis of balhimycin and teicoplanin-like A40926, respectively. In addition, the LuxR-type Tei16* appears unrelated to the LuxR-like Dbv3, which is controlling A40926 biosynthesis. Our results shed new light on teicoplanin biosynthesis regulation and on the evolution of novel and old glycopeptide biosynthetic gene clusters.


Assuntos
Antibacterianos/biossíntese , Vias Biossintéticas/genética , Regulação Bacteriana da Expressão Gênica , Genes Reguladores , Micromonosporaceae/genética , Micromonosporaceae/metabolismo , Teicoplanina/biossíntese , Farmacorresistência Bacteriana , Perfilação da Expressão Gênica , Ordem dos Genes , Óperon
8.
Int J Mol Sci ; 20(7)2019 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-30974837

RESUMO

Trentepohliales is an aerial order of Chlorophyta with approximately 80 species distributed mainly in tropical and subtropical regions. The taxonomy of this genus is quite difficult and presents a challenge for many phycologists. Although plentiful molecular data is available, most of the sequences are not identified at the species level. In the present study, we described a new specimen with detailed morphological data and identified it as Trentepohlia odorata. A phylogenetic analysis showed T. odorata as a novel lineage in Trentepohliales. T. odorata has the closest relationship with T. annulata, which is expected since sporangia of both species are without stalk cell and with dorsal pore. Species with such morphological characteristics may represent deep lineages in Trentepohliales. Although an increasing number of chloroplast genomes of Ulvophyceae have been reported in recent years, the whole plastome of Trentepohliales has not yet been reported. Thus, the chloroplast genome of Trentepohlia odorata was reported in the present study. The whole plastome was 399,372 bp in length, with 63 predicted protein-coding genes, 31 tRNAs, and 3 rRNAs. Additionally, we annotated 95 free-standing open reading frames, of which seven were annotated with plastid origins, 16 with eukaryotic genome origins, and 33 with bacterial genome origins. Four rpo genes (rpoA, rpoB, rpoC1, and rpoC2) were annotated within ORF clusters. These four genes were fragmented into several (partial) ORFs by in-frame stop codons. Additionally, we detected a frame shift mutation in the rpoB gene. The phylogenetic analysis supported that Trentepohliales clustered with Dasycladales and nested into the BDT clade (Bryopsidales, Dasycladales and Trentepohliales). Our results present the first whole chloroplast genome of a species of Trentepohliales and provided new data for understanding the evolution of the chloroplast genome in Ulvophyceae.


Assuntos
Clorófitas , DNA de Cloroplastos/genética , Evolução Molecular , Genoma de Cloroplastos , Filogenia , Clorófitas/classificação , Clorófitas/genética , Ordem dos Genes , Fases de Leitura Aberta
9.
Biomed Res Int ; 2019: 5046958, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31016191

RESUMO

Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among Sorghum species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying Sorghum species. In this study, we sequenced the complete chloroplast genomes of Sorghum sudanense and S. propinquum and analyzed the published chloroplast genomes of S. bicolor and S. timorense to retrieve valuable chloroplast molecular resources for Sorghum. The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (rps16-trnQ, trnG-trnM, rbcL-psaI, and rps15-ndhF), which were suitable for phylogenetic and species identification, were detected in the Sorghum chloroplast genomes. A phylogenetic analysis strongly supported that Sorghum is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in Sorghum.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos/genética , Sorghum/genética , Composição de Bases/genética , DNA de Cloroplastos/genética , Ordem dos Genes/genética , Marcadores Genéticos/genética , Genômica/métodos , Filogenia , Poaceae/genética , Análise de Sequência de DNA/métodos
10.
MBio ; 10(2)2019 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-30940697

RESUMO

Hepatitis D virus (HDV) forms the genus Deltavirus unassigned to any virus family. HDV is a satellite virus and needs hepatitis B virus (HBV) to make infectious particles. Deltaviruses are thought to have evolved in humans, since for a long time, they had not been identified elsewhere. Herein we report, prompted by the recent discovery of an HDV-like agent in birds, the identification of a deltavirus in snakes (Boa constrictor) designated snake HDV (sHDV). The circular 1,711-nt RNA genome of sHDV resembles human HDV (hHDV) in its coding strategy and size. We discovered sHDV during a metatranscriptomic study of brain samples of a Boa constrictor breeding pair with central nervous system signs. Applying next-generation sequencing (NGS) to brain, blood, and liver samples from both snakes, we did not find reads matching hepadnaviruses. Sequence comparison showed the snake delta antigen (sHDAg) to be 55% and 37% identical to its human and avian counterparts. Antiserum raised against recombinant sHDAg was used in immunohistology and demonstrated a broad viral target cell spectrum, including neurons, epithelial cells, and leukocytes. Using RT-PCR, we also detected sHDV RNA in two juvenile offspring and in a water python (Liasis mackloti savuensis) in the same snake colony, potentially indicating vertical and horizontal transmission. Screening of 20 randomly selected boas from another breeder by RT-PCR revealed sHDV infection in three additional snakes. The observed broad tissue tropism and the failure to detect accompanying hepadnavirus suggest that sHDV could be a satellite virus of a currently unknown enveloped virus.IMPORTANCE So far, the only known example of deltaviruses is the hepatitis delta virus (HDV). HDV is speculated to have evolved in humans, since deltaviruses were until very recently found only in humans. Using a metatranscriptomic sequencing approach, we found a circular RNA, which resembles that of HDV in size and coding strategy, in a snake. The identification of similar deltaviruses in distantly related species other than humans indicates that the previously suggested hypotheses on the origins of deltaviruses need to be updated. It is still possible that the ancestor of deltaviruses emerged from cellular RNAs; however, it likely would have happened much earlier in evolution than previously thought. These findings open up completely new avenues in evolution and pathogenesis studies of deltaviruses.


Assuntos
Boidae/virologia , Hepatite D/veterinária , Vírus Delta da Hepatite/classificação , Vírus Delta da Hepatite/isolamento & purificação , Estruturas Animais/virologia , Animais , Encéfalo/virologia , Transmissão de Doença Infecciosa , Perfilação da Expressão Gênica , Ordem dos Genes , Hepatite D/transmissão , Hepatite D/virologia , Vírus Delta da Hepatite/genética , Sequenciamento de Nucleotídeos em Larga Escala , Imuno-Histoquímica , Filogenia , RNA/genética , RNA Viral/genética , Homologia de Sequência , Tropismo Viral
11.
Exp Oncol ; 41(1): 7-13, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30932401

RESUMO

AIM: Placenta-specific 1 (PLAC1) is among recently-discovered placental antigens which exerts fundamental role in placental function and development. Increasing body of literature shows that PLAC1 is frequently activated and expressed in a wide variety of human cancers and promote cancer progression. However, no data is available regarding the expression of mouse orthologue, plac1, in murine cancer cell lines. Materials and Methods: We investigated the expression of plac1 in a series of murine cell lines from different histological origins, mammary carcinoma (4T1), melanoma (B16F10), colorectal carcinoma (CT26), renal carcinoma (Renca), glioma (GL26), B-cell lymphoma (A20 and BCL1) and also two fibroblast cell lines (NIH3T3 and L929), using RT-PCR, Western blotting and flow cytometry. Results: Our data demonstrated that plac1 transcript and plac1 protein were expressed in all examined cell lines, as judged by RT-PCR and Western blot, respectively. The molecular weight of mouse plac1 was experimentally observed to be approximately 24 kD. Flow cytometric analysis showed surface expression of plac1 in aforesaid cell lines ranging from 2% to 42.5%. Conclusion: Based on the ubiquitous expression of plac1, the investigated cancer cell lines or immortalized cell lines can be used to examine the role of plac1 in the process of immortalization.


Assuntos
Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Proteínas da Gravidez/genética , Animais , Western Blotting , Linhagem Celular Tumoral , Ordem dos Genes , Loci Gênicos , Imunofenotipagem , Camundongos , Células NIH 3T3 , Proteínas da Gravidez/metabolismo
13.
PLoS Genet ; 15(4): e1008103, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30998688

RESUMO

The ribosomal RNA genes (rDNA) comprise a highly repetitive gene cluster. The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome. DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase, which triggers unequal sister chromatid recombination. However, the precise mechanisms by which such DNA double-strand breaks (DSBs) are repaired is not well understood. Here, we demonstrate that the conserved protein kinase Tel1 maintains rDNA stability after replication fork arrest. We show that rDNA associates with nuclear pores, which is dependent on DNA damage checkpoint kinases Mec1/Tel1 and replisome component Tof1. These findings suggest that rDNA-nuclear pore association is due to a replication fork block and subsequent DSB. Indeed, quantitative microscopy revealed that rDNA is relocated to the nuclear periphery upon induction of a DSB. Finally, rDNA stability was reduced in strains where this association with the nuclear envelope was prevented, which suggests its importance for avoiding improper recombination repair that could induce repeat instability.


Assuntos
Dano ao DNA , Genes de RNAr , Poro Nuclear/metabolismo , Quebras de DNA de Cadeia Dupla , Replicação do DNA , DNA Fúngico , DNA Ribossômico/genética , Proteínas de Ligação a DNA/metabolismo , Ordem dos Genes , Mutação , Recombinação Genética , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
14.
Molecules ; 24(6)2019 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-30875988

RESUMO

The genus Angelica (Apiaceae) comprises valuable herbal medicines. In this study, we determined the complete chloroplast (CP) genome sequence of A. polymorpha and compared it with that of Ligusticum officinale (GenBank accession no. NC039760). The CP genomes of A. polymorpha and L. officinale were 148,430 and 147,127 bp in length, respectively, with 37.6% GC content. Both CP genomes harbored 113 unique functional genes, including 79 protein-coding, four rRNA, and 30 tRNA genes. Comparative analysis of the two CP genomes revealed conserved genome structure, gene content, and gene order. However, highly variable regions, sufficient to distinguish between A. polymorpha and L. officinale, were identified in hypothetical chloroplast open reading frame1 (ycf1) and ycf2 genic regions. Nucleotide diversity (Pi) analysis indicated that ycf4⁻chloroplast envelope membrane protein (cemA) intergenic region was highly variable between the two species. Phylogenetic analysis revealed that A. polymorpha and L. officinale were well clustered at family Apiaceae. The ycf4-cemA intergenic region in A. polymorpha carried a 418 bp deletion compared with L. officinale. This region was used for the development of a novel indel marker, LYCE, which successfully discriminated between A. polymorpha and L. officinale accessions. Our results provide important taxonomic and phylogenetic information on herbal medicines and facilitate their authentication using the indel marker.


Assuntos
Angelica/classificação , Genoma de Cloroplastos , Ligusticum/classificação , Sequenciamento Completo do Genoma/métodos , Angelica/genética , Composição de Bases , Cloroplastos/genética , DNA Intergênico , Evolução Molecular , Ordem dos Genes , Tamanho do Genoma , Mutação INDEL , Ligusticum/genética , Fases de Leitura Aberta , Filogenia
15.
Int J Biol Macromol ; 131: 176-183, 2019 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-30836184

RESUMO

The domestication of domestic silkworm Bombyx mori, the only truly domesticated insect, is a distinctive event in agricultural history. The domestication and origin of domestic silkworm remains unclear, although it has connected with human for ~5500 years. In the present study, we would like to highlight our evidence from whole mitochondrial genome for the presence of two genetically distinctive subtypes in Chinese B. mandarina populations, corresponding to northern Chinese B. mandarina and southern Chinese B. mandarina, respectively. The mitochondrial genomes and mitochondrial phylogenetic tree provide a solid molecular evidence that the true wild ancestor of domestic silkworm is northern Chinese B. mandarina, rather than southern Chinese B. mandarina, thus implying that the early domestication event may have occurred in northern China. Our finding provides new insights into the origin and evolution of domestic silkworm.


Assuntos
Bombyx/classificação , Bombyx/genética , Evolução Molecular , Genoma Mitocondrial , Sequência de Aminoácidos , Animais , China , Ordem dos Genes , Genômica/métodos , Haplótipos , Filogenia , Polimorfismo Genético , Seleção Genética , Alinhamento de Sequência
16.
Int J Biol Macromol ; 131: 925-932, 2019 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-30914370

RESUMO

Interferon-inducible transmembrane protein 3 (IFITM3) inhibits the replication of multiple pathogenic viruses by blocking their entry. In this study, we constructed a shuttle plasmid, harboring human IFITM3. Thereafter, recombinant adenovirus rAd5-IFITM3 was obtained by co-transfection of the linearized viral backbone vector pAd5 and the shuttle plasmid. The results showed that human IFITM3 did not affect the assembly and morphogenesis of progeny adenovirus. Human IFITM3 can be expressed in both A549 and MDCK cells in a time dependent manner. Furthermore, cells infected with rAd5-IFITM3 at a multiplicity of infection (MOI) of 100 for 24 h were challenged with avian influenza virus (AIV) H5N1 at an MOI of 1 for 6, 12 and 24 h. Rates of H5N1 infection in rAd5-IFITM3 cells were significantly decreased at 24 h post-infection (hpi), in a time dependent manner, compared with that of wild type wtAd5-infected cells. The expressions of viral genes were significantly inhibited at transcriptional and translational levels at 6 and 12 hpi. These results suggest that IFITM3 can suppress H5N1 replication in the early stage of the infection, which may be used as a promise agent against H5N1 infection in vivo.


Assuntos
Adenoviridae/genética , Clonagem Molecular , Expressão Gênica , Vetores Genéticos/genética , Proteínas de Membrana/genética , Proteínas de Ligação a RNA/genética , Adenoviridae/ultraestrutura , Animais , Linhagem Celular , Cães , Ordem dos Genes , Humanos , Virus da Influenza A Subtipo H5N1 , Células Madin Darby de Rim Canino , Proteínas de Membrana/metabolismo , Proteínas de Ligação a RNA/metabolismo
17.
Gene ; 699: 24-36, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-30849538

RESUMO

Watercress (Nasturtium officinale R. Br.), an aquatic leafy vegetable of the Brassicaceae family, is known as a nutritional powerhouse. Here, we de novo sequenced and assembled the complete chloroplast (cp) genome of watercress based on combined PacBio and Illumina data. The cp genome is 155,106 bp in length, exhibiting a typical quadripartite structure including a pair of inverted repeats (IRA and IRB) of 26,505 bp separated by a large single copy (LSC) region of 84,265 bp and a small single copy (SSC) region of 17,831 bp. The genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNAs and 4 rRNAs, with 20 duplicate in the IRs. Compared with the prior cp genome of watercress deposited in GenBank, 21 single nucleotide polymorphisms (SNPs) and 27 indels were identified, mainly located in noncoding sequences. A total of 49 repeat structures and 71 simple sequence repeats (SSRs) were detected. Codon usage showed a bias for A/T-ending codons in the cp genome of watercress. Moreover, 45 RNA editing sites were predicted in 16 genes, all for C-to-U transitions. A comparative plastome study with Cardamineae species revealed a conserved gene order and high similarity of protein-coding sequences. Analysis of the Ka/Ks ratios of Cardamineae suggested positive selection exerted on the ycf2 gene in watercress, which might reflect specific adaptations of watercress to its particular living environment. Phylogenetic analyses based on complete cp genomes and common protein-coding genes from 56 species showed that the genus Nasturtium was a sister to Cardamine in the Cardamineae tribe. Our study provides valuable resources for future evolution, population genetics and molecular biology studies of watercress.


Assuntos
Brassicaceae/genética , Cloroplastos/genética , Genes de Plantas/genética , Genoma de Cloroplastos/genética , Nasturtium/genética , Códon/genética , Evolução Molecular , Ordem dos Genes/genética , Repetições de Microssatélites/genética , Filogenia , Edição de RNA/genética , Análise de Sequência de DNA/métodos , Sequenciamento Completo do Genoma/métodos
18.
Mol Phylogenet Evol ; 135: 177-184, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30858078

RESUMO

Stylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bilineatum (Arionoidea: Philomycidae), a widespread land slug in East Asia. This is the first report on a mitogenome of the superfamily Arionoidea, and indeed on a terrestrial slug. The mitogenome of Meghimatium bilineatum comprises 13,972 bp and exhibits a novel, highly distinctive gene arrangement among the Stylommatophora. Phylogenetic reconstructions based on the sequences of all protein-coding genes consistently recovered Meghimatium bilineatum as sister-group of the Succineidae. A phylogenetic reconstruction based on gene order, however, suggested a highly divergent tree topology, which is less credible when taking into account prior knowledge of stylommatophoran relationships. Our CREx (Common interval Rearrangement Explorer) analysis suggested that three successive events of tandem duplication random loss (TDRL) best explain the evolutionary process of gene order rearrangement in Meghimatium bilineatum from an ancestral stylommatophoran mitogenome. The present example offers new insights into the mechanisms of mitogenome rearrangements in gastropods at large and into the usefulness of mitogenomic gene order as a phylogenetic marker.


Assuntos
Gastrópodes/genética , Rearranjo Gênico , Genoma Mitocondrial , Animais , Sequência de Bases , Mapeamento Cromossômico , Extremo Oriente , Ordem dos Genes , Mitocôndrias/genética , Filogenia
19.
Mol Genet Genomics ; 294(3): 715-727, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30848356

RESUMO

Among invertebrates, only a few groups still have uncertain phylogenetic position, Orthonectida, a small group of rare multi-cellular parasites of marine invertebrates, being one of them. Recent molecular and morphological findings suggest that orthonectids belong to Lophotrochozoa and are close to Annelida. Nevertheless, phylogenetic relationships between orthonectids and annelids are unclear, and the phylogeny within the group itself has never been studied. Sequencing of mitochondrial genomes is used here to clarify this issue. Complete mt genomes of the orthonectids Intoshia variabili and Rhopalura litoralis were characterized and compared with Intoshia linei mt genome. Our results show that Orthonectida mt genomes have undergone reduction and gene loss, and that they have complicated organization revealed in strand asymmetry in nucleotide composition, in some features of intergenic non-coding regions, tRNA duplication and folding. Moreover, all species of Orthonectida have a unique gene order with complicated rearrangement landscape. Significant differences in mitochondrial genomes in the three orthonectid species could be explained by the fact that their host species belong to different taxa (flat worms, nemertines and gastropods). Among the analyzed mt genomes of Orthonectida, I. linei possesses the closest gene order to the ancestral genome. All Orthonectida species are monophyletic, and in the phylogenetic tree are close to Pleistoannelida, and specifically, to Clitellata.


Assuntos
Evolução Molecular , Ordem dos Genes , Genes Mitocondriais/genética , Genoma Mitocondrial/genética , Invertebrados/genética , Animais , Composição de Bases/genética , DNA Mitocondrial/química , DNA Mitocondrial/genética , Gastrópodes/parasitologia , Helmintos/parasitologia , Interações Hospedeiro-Parasita , Invertebrados/classificação , Invertebrados/fisiologia , Filogenia , Análise de Sequência de DNA , Especificidade da Espécie
20.
Int J Antimicrob Agents ; 53(5): 694-697, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30878667

RESUMO

An emergent kanamycin-susceptible ST5 methicillin-resistant Staphylococcus aureus (MRSA) lineage has been identified in France. Whole-genome sequencing revealed a 40-kb staphylococcal cassette chromosome (SCC) composite island with a mosaic structure including three SCC elements: a ΨSCCcop/ars, a SCCLim88A with a ccrC recombinase, and a novel subtype of SCCmec type VI (VIb). This mosaic structure suggests a high recombination rate of SCC elements from distinct staphylococci species.


Assuntos
Cromossomos Bacterianos , Ordem dos Genes , Ilhas Genômicas , Staphylococcus aureus Resistente à Meticilina/genética , Idoso de 80 Anos ou mais , França , Genótipo , Humanos , Masculino , Staphylococcus aureus Resistente à Meticilina/classificação , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Recombinação Genética , Infecções Estafilocócicas/microbiologia , Sequenciamento Completo do Genoma
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