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1.
Arch Virol ; 166(10): 2865-2868, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34292374

RESUMO

A putative new virus with sequence similarity to members of the genus Cavemovirus in the family Caulimoviridae was identified in wild chicory (Cichorium intybus) by next-generation sequencing (NGS). The putative new virus was tentatively named "chicory mosaic cavemovirus" (ChiMV), and its genome was determined to be 7,775 nucleotides (nt) long with the typical genome organization of cavemoviruses. ORF1 encodes a putative coat protein/movement polyprotein (1,278 aa), ORF2 encodes a putative replicase (650 aa), and ORF3 encodes a putative transactivator factor (384 aa). The first two putative proteins have 46.2% and 68.7% amino acid sequence identity to the CP/MP protein (YP_004347414) and replicase (YP_004347415), respectively, of sweet potato collusive virus (SPCV). ORF3 encodes a protein with 38.5% amino acid sequence identity to the putative transactivator factor (NP_056849) of cassava vein mosaic virus (CsVMV). The new putative viral genome and those of three cavemoviruses (epiphyllum virus 4 [EpV-4], SPCV, and CsVMV) differ by 24-27% in the nt sequence of the replicase gene, which exceeds the species demarcation cutoff (>20%) for the family.


Assuntos
Caulimoviridae/genética , Chicória/virologia , Sequência de Aminoácidos , Caulimoviridae/classificação , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/virologia , Folhas de Planta/virologia , RNA Viral/genética , Especificidade da Espécie , Proteínas Virais/genética
2.
Arch Virol ; 166(7): 1985-1990, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33881618

RESUMO

The genomes of three putative novel viruses, tentatively named "Bacopa monnieri virus 1" (BmV1), "Bacopa monnieri virus 2" (BmV2), and "Bacopa monnieri virus 3" (BmV3) were identified in the transcriptome dataset of a medicinally important herb - water hyssop (Bacopa monnieri (L.) Wettst.). The BmV1 and BmV2 genomes resemble those of plant rhabdoviruses. The 13.3-kb-long BmV1 genome contains eight antisense ORFs in the order 3' l-N-P2'-P-P3-M-G-P6-L-t 5', with P2' ORF overlapping with P, while the 13.2-kb BmV2 genome contains six interspersed ORFs in the antisense orientation (3' l-N-P-P3-M-G-L-t 5'). The 8-kb BmV3 genome possesses five overlapping ORFs, with ORFs 2 to 5 being similar to those of solendoviruses. Based on genome organization, sequence similarity, and phylogeny, BmV1, BmV2, and BmV3 can be regarded as new members of the genera Cytorhabdovirus, Betanucleorhabdovirus, and Solendovirus, respectively.


Assuntos
Bacopa/genética , Bacopa/virologia , Caulimoviridae/genética , Genoma Viral/genética , Rhabdoviridae/genética , Transcriptoma/genética , Fases de Leitura Aberta/genética , Filogenia , Plantas Medicinais/genética
3.
J Gen Virol ; 101(10): 1025-1026, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32940596

RESUMO

Caulimoviridae is a family of non-enveloped reverse-transcribing plant viruses with non-covalently closed circular dsDNA genomes of 7.1-9.8 kbp in the order Ortervirales. They infect a wide range of monocots and dicots. Some viruses cause economically important diseases of tropical and subtropical crops. Transmission occurs through insect vectors (aphids, mealybugs, leafhoppers, lace bugs) and grafting. Activation of infectious endogenous viral elements occurs in Musa balbisiana, Petunia hybrida and Nicotiana edwardsonii. However, most endogenous caulimovirids are not infectious. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Caulimoviridae, which is available at ictv.global/report/caulimoviridae.


Assuntos
Caulimoviridae , Caulimoviridae/classificação , Caulimoviridae/fisiologia , Caulimoviridae/ultraestrutura , Genoma Viral , Plantas/virologia , Replicação Viral
4.
Cytogenet Genome Res ; 160(6): 329-334, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32683370

RESUMO

Rubus yellow net virus (RYNV) infects Rubus spp., causing a severe decline when present in mixed infections with other viruses. RYNV belongs to the family Caulimoviridae, also known as plant pararetroviruses, which can exist as episomal or integrated elements (endogenous). Most of integrated pararetroviruses are noninfectious; however, a few cases have been reported where they excised from the plant genome and formed infectious particles. Graft transmission onto indicator plants R. occidentalis "Munger" has been the standard test method for RYNV detection in certification programs. Previously, it was noticed that some RYNV PCR-positive plants did not induce symptoms on "Munger", suggesting an integration event. In this study, bio-indexing and different molecular techniques were employed to differentiate between integrated and episomal RYNV sequences. Reverse transcription-PCR using RYNV-specific oligonucleotides after DNase treatment generated positive results for the virus in graft transmissible isolates (episomal) only. To confirm these results, rolling circle amplification on DNA preparations from the same samples resulted in amplicons identified as RYNV only from plants with graft transmissible RYNV. High-throughput sequencing was used to identify the RYNV-like sequences present in the host DNA. These results indicate the integration of RYNV into the red raspberry genome and highlight the necessity to recognize this phenomenon (integration) in future Rubus quarantine and certification programs.


Assuntos
Caulimoviridae/genética , Genoma de Planta/genética , Vírus de Plantas/genética , Rubus/genética , Rubus/virologia , Integração Viral/genética , Caulimoviridae/isolamento & purificação , Doenças das Plantas/genética , Doenças das Plantas/prevenção & controle , Doenças das Plantas/virologia , Vírus de Plantas/isolamento & purificação , Plasmídeos/genética
5.
Arch Virol ; 165(9): 2083-2086, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32524261

RESUMO

A new virus with sequence similarities to members of the genus Cavemovirus in the family Caulimoviridae was identified in an Epiphyllum hybrid. The complete genome of the virus, tentatively named "epiphyllum virus 4" (EpV-4), was determined to be 7,296 nucleotides long. Its circular genome organization is typical of cavemoviruses, containing four open reading frames. This virus and the two known cavemoviruses share 67-69% and 72-75% overall nucleotide sequence identity in the replicase gene. Phylogenetic analysis placed EpV-4 in a same cluster with the two recognized cavemoviruses. Thus, EpV-4 should be considered a representative of a third species of the genus Cavemovirus. The virus was transmitted by grafting.


Assuntos
Cactaceae/virologia , Caulimoviridae/isolamento & purificação , Doenças das Plantas/virologia , Caulimoviridae/classificação , Caulimoviridae/genética , Genoma Viral , Fases de Leitura Aberta , Filogenia , Proteínas Virais/genética
6.
Plant J ; 103(2): 497-511, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32100385

RESUMO

White areas of star-type bicolour petals of petunia (Petunia hybrida) are caused by post-transcriptional gene silencing (PTGS) of the key enzyme of anthocyanin biosynthesis. We observed blotched flowers and a vein-clearing symptom in aged petunia plants. To determine the cause of blotched flowers, we focused on an endogenous pararetrovirus, petunia vein clearing virus (PVCV), because this virus may have a suppressor of PTGS (VSR). Transcripts and episomal DNAs derived from proviral PVCVs accumulated in aged plants, indicating that PVCV was activated as the host plant aged. Furthermore, DNA methylation of CG and CHG sites in the promoter region of proviral PVCV decreased in aged plants, suggesting that poor maintenance of DNA methylation activates PVCV. In parallel, de novo DNA methylation of CHH sites in its promoter region was also detected. Therefore, both activation and inactivation of PVCV occurred in aged plants. The accumulation of PVCV transcripts and episomal DNAs in blotched regions and the detection of VSR activity support a mechanism in which suppression of PTGS by PVCV causes blotched flowers.


Assuntos
Caulimoviridae/metabolismo , Flores/virologia , Petunia/virologia , Caulimoviridae/genética , Cor , Metilação de DNA , DNA Viral/genética , Flores/anatomia & histologia , Regulação da Expressão Gênica de Plantas , Petunia/anatomia & histologia , Provírus/genética , Interferência de RNA , Reação em Cadeia da Polimerase em Tempo Real
7.
Virus Genes ; 56(1): 78-86, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31705264

RESUMO

Petunia plants are used for urban landscaping in many parts of the world, including South Korea. In this study, we aimed to investigate the occurrence of petunia vein clearing virus (PVCV) infection in petunia plants in Seoul, South Korea. PVCV was detected from 23 of 79 petunia samples collected from Seoul. We obtained the complete genome sequences of the Korean isolates in this study (called PVCV-Kr, Kr2, and Kr3), which were compared with the genome sequence of the USA isolate of the virus (PVCV-USA). The genomic DNA of the three PVCV isolates was found to comprise 7210-7267 nucleotides (nts), which is 4-15 nts longer than the PVCV-USA genome. The genomes of the Kr and Kr2 isolates encode a large polyprotein of 252 kDa (2180 amino acids (aa)). The genome of the Kr3 isolate encodes a large polyprotein of 255 kDa (2203 aa). The polyprotein has six protein domains: a movement protein (MP; 72 aa), a coiled-coil domain (CC; 33 aa), an RNA-binding domain (RB; 18 aa), a protease (PR; 21 aa), a reverse transcriptase (RT; 196 aa), and an RNase H (RH; 121 aa). The large polyprotein and six domains of the three isolates showed 93.9-100.0% sequence homology with those of PVCV-USA. Furthermore, the polymerase polyprotein gene (PR, RT, and RH) of the four PVCV isolates containing the USA isolate grouped with those of Rice tungro bacilliform virus and Soybean chlorotic mottle virus, which belong to the same family (Caulimoviridae). Our findings suggested that the Korean isolates represent a new isolate of PVCV. To our knowledge, this is the first report of PVCV detection in South Korea.


Assuntos
Caulimoviridae/genética , Doenças das Plantas/virologia , Sequência de Bases , Caulimoviridae/química , Caulimoviridae/classificação , Caulimoviridae/isolamento & purificação , Variação Genética , Genoma Viral , Fases de Leitura Aberta , Petunia/virologia , Domínios Proteicos , República da Coreia , Estados Unidos , Proteínas Virais/química , Proteínas Virais/genética
8.
BMC Plant Biol ; 19(1): 159, 2019 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-31023231

RESUMO

BACKGROUND: A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. High throughput sequencing of small RNA (sRNA) combined with bioinformatics, and molecular identification based on PCR detection with virus-specific primers and DNA sequencing is a desirable approach to identify an unknown infectious agent. In this study, we employed this approach to identify viral sequences in water chestnut plants and to explore the molecular interaction of the identified viral pathogen and its natural plant host. RESULTS: Based on high throughput sequencing of virus-derived small RNAs (vsRNA), we identified the sequence a new-to-science double-strand DNA virus isolated from water chestnut cv. 'Tuanfeng' samples, a widely grown cultivar in Hubei province, China, and analyzed its genomic organization. The complete genomic sequence is 7535 base-pairs in length, and shares 42-52% nucleotide sequence identity with viruses in the Caulimoviridae family. The virus contains nine predicated open reading frames (ORFs) encoding nine hypothetical proteins, with conserved domains characteristic of caulimoviruses. Phylogenetic analyses at the nucleotide and amino acid levels indicated that the virus belongs to the genus Soymovirus. The virus is tentatively named Water chestnut soymovirus-1 (WCSV-1). Phylogenetic analysis of the putative viral polymerase protein suggested that WCSV-1 is distinct to other well established species in the Soymovirus genus. This conclusion was supported by phylogenetic analyses of the amino acid sequences encoded by ORFs I, IV, VI, or VII. The sRNA bioinformatics showed that the majority of the vsRNAs are 22-nt in length with a preference for U at the 5'-terminal nucleotide. The vsRNAs are unevenly distributed over both strands of the entire WCSV-1 circular genome, and are clustered into small defined regions. In addition, we detected WCSV-1 in asymptomatic and symptomatic water chestnut samples collected from different regions of China by using PCR. RNA-seq assays further confirmed the presence of WCSV-1-derived viral RNA in infected plants. CONCLUSIONS: This is the first discovery of a dsDNA virus in the genus Soymovirus infecting water chestnuts. Data presented also add new information towards a better understanding of the co-evolutionary mechanisms between the virus and its natural plant host.


Assuntos
Caulimoviridae/fisiologia , Eleocharis/virologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Sequência de Bases , Caulimoviridae/genética , China , Biologia Computacional , Sequência Conservada , Eleocharis/genética , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , RNA Viral/genética , Transcriptoma/genética , Proteínas Virais/química
9.
J Virol Methods ; 262: 48-55, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30236898

RESUMO

Recent metagenomic surveys have provided unprecedented amounts of data that have revolutionized our understanding of virus evolution and diversity. Infectious clones are powerful tools to aid the biological characterization of viruses. We recently described the pLX vectors, a set of mini binary T-DNA vectors (∼3 kb) that includes strong bacterial terminators and a minimal replicon from the broad-host-range plasmid pBBR1, which replicate autonomously in both Escherichia coli and Agrobacterium. In this study, a workflow that encompassed pLX binary vectors, overlap-based assembly strategies, and sequencing-by-synthesis verification steps is described and applied for the streamlined generation of infectious clones suitable for Agrobacterium-mediated delivery. The pLX-based vectors herein assembled include the first infectious clone of Wasabi mottle virus, a crucifer-infecting tobamovirus, as well as binary vectors of positive-single-stranded RNA and single- and double-stranded DNA viruses from the Potyviridae, Geminiviridae and Caulimoviridae families, respectively. Finally, the clones generated were used to agro-inoculate the model plant Arabidopsis thaliana and infections were confirmed by a multiplex RT-PCR assay. This workflow facilitated the rapid generation of infectious clones which, together with agro-infection scalability, would allow the pursuit of systematic insights into virus biology and physiology of plant infections and the design of novel biotechnological applications.


Assuntos
Vetores Genéticos , Vírus de Plantas/genética , Virologia/métodos , Agricultura , Arabidopsis/virologia , Biotecnologia/métodos , Caulimoviridae/genética , Geminiviridae/genética , Genoma Viral , Potyviridae/genética
10.
PLoS One ; 13(9): e0203038, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30208072

RESUMO

We have characterized the complete genome of a novel circular double-stranded DNA virus, tentatively named Dioscorea nummularia-associated virus (DNUaV), infecting Dioscorea nummularia originating from Samoa. The genome of DNUaV comprised 8139 bp and contained four putative open reading frames (ORFs). ORFs 1 and 2 had no identifiable conserved domains, while ORF 3 had conserved motifs typical of viruses within the family Caulimoviridae including coat protein, movement protein, aspartic protease, reverse transcriptase and ribonuclease H. A transactivator domain, similar to that present in members of several caulimoviridae genera, was also identified in the putative ORF 4. The genome size, organization, and presence of conserved amino acid domains are similar to other viruses in the family Caulimoviridae. However, based on nucleotide sequence similarity and phylogenetic analysis, DNUaV appears to be a distinct novel member of the family and may represent a new genus.


Assuntos
Caulimoviridae/classificação , Caulimoviridae/fisiologia , Dioscorea/virologia , Sequência de Aminoácidos , Caulimoviridae/genética , Genômica , Fases de Leitura Aberta/genética , Oceano Pacífico , Filogenia , Proteínas Virais/química , Proteínas Virais/genética
12.
J Virol ; 92(10)2018 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-29491164

RESUMO

Endogenous viral elements (paleoviruses) provide "molecular fossils" for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms, but little is known about EPRVs in earlier-branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as Caulimoviridae). We uncover an unprecedented and unappreciated diversity of EPRVs within the genomes of gymnosperms and ferns. The known angiosperm viruses constitute only a minor part of the Caulimoviridae diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of Caulimoviridae, raising the possibility that many exogenous Caulimoviridae remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs might define a unique group of repetitive elements and represent important components of euphyllophyte genomes. Evolutionary analyses suggest an ancient origin of Caulimoviridae and at least three independent origins of Caulimoviridae in angiosperms. Our findings reveal the remarkable diversity of Caulimoviridae and have important implications for understanding the origin and macroevolution of plant pararetroviruses.IMPORTANCE Few viruses have been documented in plants outside angiosperms. Viruses can occasionally integrate into host genomes, forming endogenous viral elements (EVEs). Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms. In this study, we performed comprehensive comparative and phylogenetic analyses of EPRVs and found that EPRVs are present in the genomes of gymnosperms and ferns. We identified numerous EPRVs in gymnosperm and fern genomes, revealing an unprecedented depth in the diversity of plant pararetroviruses. Plant pararetroviruses mainly underwent cross-species transmission, and angiosperm pararetroviruses arose at least three times. Our study provides novel insights into the diversity and macroevolution of plant pararetroviruses.


Assuntos
Caulimoviridae/classificação , Caulimoviridae/genética , Cycadopsida/virologia , Gleiquênias/virologia , Genoma de Planta/genética , Magnoliopsida/virologia , Vírus de Plantas/genética , Cycadopsida/genética , Variações do Número de Cópias de DNA/genética , Elementos de DNA Transponíveis/genética , Retrovirus Endógenos/genética , Evolução Molecular , Gleiquênias/genética , Interações Hospedeiro-Patógeno/genética , Magnoliopsida/genética , Filogenia
13.
Sci Rep ; 8(1): 572, 2018 01 12.
Artigo em Inglês | MEDLINE | ID: mdl-29330451

RESUMO

Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.


Assuntos
Caulimoviridae/genética , DNA Viral/genética , Análise de Sequência de DNA/métodos , Traqueófitas/genética , Evolução Molecular , Genoma de Planta , Interações Hospedeiro-Patógeno , Filogenia , Traqueófitas/virologia
14.
Arch Virol ; 162(10): 3221-3224, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28612117

RESUMO

We report a new circular DNA virus identified from a Chinese jujube tree showing mosaic-like symptoms. The genome of this virus is 7194 bp in length and contains five putative open reading frames (ORFs), all on the plus-strand of the genome. The genomic organization, primer binding sites and the sizes of the ORFs were similar to those reported for other badnaviruses (family Caulimoviridae), except for ORF3, which was split into ORF3a and ORF3b with a 70-nt intergenic region. Furthermore, this new virus shares low nucleotide sequence identity (<50%) with other members of the family Caulimoviridae. Consequently, we propose this virus as a new member of the family Caulimoviridae and refer to it as jujube mosaic-associated virus (JuMaV).


Assuntos
Caulimoviridae/genética , Genoma Viral , Vírus do Mosaico/genética , Ziziphus/virologia , Filogenia
15.
Virus Res ; 241: 62-67, 2017 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-28559100

RESUMO

A disease of Rudbeckia hirta (Black-eyed Susan), characterized by severe flower deformation, was observed in Minnesota during 2010-2016. A previously undescribed virus species, named Rudbeckia flower distortion virus (RuFDV, family Caulimoviridae, genus unassigned), was determined to be the causal agent of the disease. Symptoms induced by RuFDV infection resemble those characteristic of phytoplasma-induced diseases, but no phytoplasmas were detected in RuFDV-infected R. hirta. The virus, and the disease were transmitted readily by mechanical inoculation and by the aphid Myzus persicae, but only to R. hirta. Virions of RuFDV are icosahedral, 42-45nm in diameter, and contain a circular 8222bp dsDNA genome containing seven open reading frames (ORFs). The ORFs 2-6 have 28-52% amino acid sequence identity to the movement protein (MP), coat protein (CP), aspartic protease (AP), reverse transcriptase (RT) and RNase H, and translational transactivator (TA) domains of known caulimoviruses. The two remaining ORFs (1 and 7) have no significant amino acid sequence similarity to known viruses. Although the RuFDV ORF 6 is significantly truncated relative to those of other known caulimoviruses, neither this nor the concomitant absence of characteristic virus-encoded cytoplasmic inclusion bodies appears to adversely affect aphid transmission of this virus. Phylogenetic analysis based on the sequence of the RT region revealed no close relationship to known members of the family Caulimoviridae. Based on sequence similarity, genome organization and phylogenetic relatedness, RuFDV appears to be distinct from any currently recognized taxonomic grouping in the family Caulimoviridae.


Assuntos
Caulimoviridae/classificação , Caulimoviridae/genética , Flores/virologia , Doenças das Plantas/virologia , Rudbeckia/virologia , Sequência de Aminoácidos , Animais , Afídeos/virologia , Ácido Aspártico Proteases/genética , Proteínas do Capsídeo/genética , Insetos Vetores/virologia , Proteínas do Movimento Viral em Plantas/genética , DNA Polimerase Dirigida por RNA/genética , Ribonuclease H/genética , Homologia de Sequência de Aminoácidos
16.
Mol Genet Genomics ; 292(5): 1051-1067, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28601922

RESUMO

Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae, and Copia lineages. Most of the Musa-related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation, and evolutionary dynamics in the Musa genome.


Assuntos
Genoma de Planta/genética , Musa/genética , Retroelementos/genética , Sequências Repetidas Terminais/genética , Sequência de Bases , Caulimoviridae/genética , Cromossomos Artificiais Bacterianos/genética , DNA de Plantas/genética , Filogenia , Análise de Sequência de DNA
17.
Viruses ; 7(4): 1685-99, 2015 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-25855242

RESUMO

Here, we report the genome sequence and evidence for transcriptional activity of a virus-like element in the native Chilean berry tree Aristotelia chilensis. We propose to name the endogenous sequence as Aristotelia chilensis Virus 1 (AcV1). High-throughput sequencing of the genome of this tree uncovered an endogenous viral element, with a size of 7122 bp, corresponding to the complete genome of AcV1. Its sequence contains three open reading frames (ORFs): ORFs 1 and 2 shares 66%-73% amino acid similarity with members of the Caulimoviridae virus family, especially the Petunia vein clearing virus (PVCV), Petuvirus genus. ORF1 encodes a movement protein (MP); ORF2 a Reverse Transcriptase (RT) and a Ribonuclease H (RNase H) domain; and ORF3 showed no amino acid sequence similarity with any other known virus proteins. Analogous to other known endogenous pararetrovirus sequences (EPRVs), AcV1 is integrated in the genome of Maqui Berry and showed low viral transcriptional activity, which was detected by deep sequencing technology (DNA and RNA-seq). Phylogenetic analysis of AcV1 and other pararetroviruses revealed a closer resemblance with Petuvirus. Overall, our data suggests that AcV1 could be a new member of Caulimoviridae family, genus Petuvirus, and the first evidence of this kind of virus in a fruit plant.


Assuntos
Caulimoviridae/classificação , Caulimoviridae/isolamento & purificação , Elaeocarpaceae/virologia , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala , Caulimoviridae/genética , Análise por Conglomerados , Dados de Sequência Molecular , Fases de Leitura Aberta , Filogenia , Proteínas do Movimento Viral em Plantas/genética , DNA Polimerase Dirigida por RNA/genética , Ribonuclease H/genética , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Transcrição Genética , Integração Viral
18.
J Gen Virol ; 96(Pt 1): 165-169, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25281563

RESUMO

Grapevine vein clearing virus (GVCV) is a recently discovered DNA virus in grapevine that is closely associated with the grapevine vein clearing syndrome observed in vineyards in Missouri and surrounding states. The genome sequence of GVCV indicates that it belongs to the genus Badnavirus in the family Caulimoviridae. To identify the GVCV promoter, we cloned portions of the GVCV large intergenic region in front of a GFP gene present in an Agrobacterium tumefaciens binary vector. GFP expression was assessed by ELISA 3 days after agroinfiltration of Nicotiana benthamiana leaves. We found that the GVCV DNA segment between nts 7332 and 7672 directed expression of GFP and this expression was stronger than expression using the Cauliflower mosaic virus 35S promoter. It was revealed by 5' and 3' RACE that transcription was initiated predominantly at nt 7571 and terminated at nt 7676.


Assuntos
Caulimoviridae/genética , Vírus de DNA/genética , Doenças das Plantas/virologia , Regiões Promotoras Genéticas/genética , Vitis/virologia , Agrobacterium tumefaciens/virologia , Caulimovirus/genética , DNA Viral/genética , Missouri , Folhas de Planta/virologia , Tabaco/virologia
19.
Virology ; 471-473: 141-52, 2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25461539

RESUMO

Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy.


Assuntos
Evolução Molecular , Especiação Genética , Genoma de Planta/genética , Oryza/genética , Vírus de Plantas/genética , Caulimoviridae/classificação , Caulimoviridae/genética , Hepadnaviridae/classificação , Hepadnaviridae/genética , Oryza/virologia , Filogenia , Vírus de Plantas/classificação
20.
Nat Commun ; 5: 5269, 2014 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-25381880

RESUMO

The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called 'Florendovirus', members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20-34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.


Assuntos
Caulimoviridae/genética , Evolução Molecular , Genoma de Planta/genética , Oryza/virologia , Filogenia , Dosagem de Genes/genética , Loci Gênicos/genética , Íntrons/genética , Repetições de Microssatélites/genética , Replicação Viral/genética
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