Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.

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Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽

10.1515/hf-2017-0065 ◽

2018 ◽

Vol 72 (4) ◽

pp. 337-345 ◽

Cited By ~ 9

Author(s):

Yu Song ◽

Xin Yao ◽

Bing Liu ◽

Yunhong Tan ◽

Richard T. Corlett

Keyword(s):

Type Species ◽

Phylogenetic Analyses ◽

Comparative Genomic ◽

Inverted Repeats ◽

Genome Sequences ◽

Complete Chloroplast Genome ◽

Tropical Asia ◽

Length Difference ◽

The Family ◽

Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

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Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000347 ◽

2015 ◽

Vol 65 (Pt_9) ◽

pp. 3203-3215 ◽

Cited By ~ 61

Author(s):

Chantal Campbell ◽

Mobolaji Adeolu ◽

Radhey S. Gupta

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Trees ◽

Core Protein ◽

Phylogenetic Analyses ◽

Comparative Genomic ◽

Rrna Gene ◽

Conserved Signature Indels ◽

The Family ◽

Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

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ICTV Virus Taxonomy Profile: Roniviridae

Journal of General Virology ◽

10.1099/jgv.0.001514 ◽

2020 ◽

Author(s):

Walker P. J. ◽

Cowley J. A. ◽

Dong X. ◽

Huang J. ◽

Moody N. ◽

...

Keyword(s):

International Committee ◽

Open Reading Frames ◽

Virus Taxonomy ◽

Highly Pathogenic ◽

Ribosomal Frameshifting ◽

Yellow Head Virus ◽

The Family ◽

Positive Sense ◽

Membrane Spanning ◽

Reading Frames

The family Roniviridae includes the genus Okavirus for three species of viruses with enveloped, rod-shaped virions. The monopartite, positive-sense ssRNA genome (26–27 kb) contains five canonical long open reading frames (ORFs). ORF1a encodes polyprotein pp1a containing proteinase domains. ORF1b is expressed as a large polyprotein pp1ab by ribosomal frameshifting from ORF1a and encodes replication enzymes. ORF2 encodes the nucleoprotein. ORF3 encodes two envelope glycoproteins. ORFX encodes a putative double membrane-spanning protein. Roniviruses infect shrimp but only yellow head virus is highly pathogenic. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Roniviridae, which is available at ictv.global/report/roniviridae.

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Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽

10.1093/genetics/159.3.1103 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1103-1115 ◽

Cited By ~ 1

Author(s):

Hongguang Shao ◽

Zhijian Tu

Keyword(s):

Phylogenetic Analyses ◽

Mosquito Species ◽

Open Reading Frames ◽

Inverted Repeats ◽

Sequence Comparisons ◽

Wide Range ◽

Multiple Copies ◽

Catalytic Motif ◽

Open The Doors ◽

Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses

Journal of Virology ◽

10.1128/jvi.76.7.3382-3387.2002 ◽

2002 ◽

Vol 76 (7) ◽

pp. 3382-3387 ◽

Cited By ~ 155

Author(s):

Marilyn J. Roossinck

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Virus Isolate ◽

Phylogenetic Analyses ◽

Open Reading Frames ◽

Broad Host Range ◽

Nontranslated Region ◽

History Of ◽

Evolutionary Success ◽

Reading Frames

ABSTRACT Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5′ nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3′ NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3′ NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

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Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

10.21203/rs.3.rs-520549/v1 ◽

2021 ◽

Author(s):

Yang Sun ◽

Yan qiong Li ◽

Wen han Dong ◽

Ai li Sun ◽

Ning wei Chen ◽

...

Keyword(s):

Rhizoctonia Solani ◽

Rna Virus ◽

Dsrna Virus ◽

Open Reading Frames ◽

The Family ◽

Significant Amino Acid Sequence ◽

Overlapping Open Reading Frames ◽

Significant Amino Acid ◽

Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

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YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

F1000Research ◽

10.12688/f1000research.6617.2 ◽

2015 ◽

Vol 4 ◽

pp. 155 ◽

Cited By ~ 17

Author(s):

Sandeep Chakraborty ◽

Monica Britton ◽

Jill Wegrzyn ◽

Timothy Butterfield ◽

Pedro José Martínez-García ◽

...

Keyword(s):

Transition Zone ◽

Transcript Abundance ◽

Black Walnut ◽

Open Reading Frames ◽

Rna Seq ◽

Reading Frame ◽

Homologous Genes ◽

Associated Proteins ◽

Molecular Components ◽

Reading Frames

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.

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Molecular Characterization and Geographic Distribution of a Mymonavirus in the Population of Botrytis cinerea

Viruses ◽

10.3390/v10080432 ◽

2018 ◽

Vol 10 (8) ◽

pp. 432 ◽

Cited By ~ 14

Author(s):

Fangmin Hao ◽

Mingde Wu ◽

Guoqing Li

Keyword(s):

Botrytis Cinerea ◽

Sclerotinia Sclerotiorum ◽

Cdna Sequence ◽

Rna Virus ◽

Open Reading Frames ◽

Phytopathogenic Fungus ◽

Rna Dependent Rna Polymerase ◽

Rdrp Domain ◽

The Family ◽

Reading Frames

Here, we characterized a negative single-stranded (−ss)RNA mycovirus, Botrytis cinerea mymonavirus 1 (BcMyV1), isolated from the phytopathogenic fungus Botrytis cinerea. The genome of BcMyV1 is 7863 nt in length, possessing three open reading frames (ORF1–3). The ORF1 encodes a large polypeptide containing a conserved mononegaviral RNA-dependent RNA polymerase (RdRp) domain showing homology to the protein L of mymonaviruses, whereas the possible functions of the remaining two ORFs are still unknown. The internal cDNA sequence (10-7829) of BcMyV1 was 97.9% identical to the full-length cDNA sequence of Sclerotinia sclerotiorum negative stranded RNA virus 7 (SsNSRV7), a virus-like contig obtained from Sclerotinia sclerotiorum metatranscriptomes, indicating BcMyV1 should be a strain of SsNSRV7. Phylogenetic analysis based on RdRp domains showed that BcMyV1 was clustered with the viruses in the family Mymonaviridae, suggesting it is a member of Mymonaviridae. BcMyV1 may be widely distributed in regions where B. cinerea occurs in China and even over the world, although it infected only 0.8% of tested B. cinerea strains.

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Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine

Genome Announcements ◽

10.1128/genomea.00995-17 ◽

2017 ◽

Vol 5 (37) ◽

Cited By ~ 9

Author(s):

Yeonhwa Jo ◽

Myung-Kyu Song ◽

Hoseong Choi ◽

Jae-Seong Park ◽

Jae-Wung Lee ◽

...

Keyword(s):

Genome Sequence ◽

Rna Virus ◽

Open Reading Frames ◽

Grapevine Virus ◽

The Family ◽

Putative Member ◽

Reading Frames

ABSTRACT Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae.

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Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease

Phytopathology ◽

10.1094/phyto-09-20-0420-r ◽

2020 ◽

Author(s):

Armelle Marais ◽

Sergio Murolo ◽

Chantal Faure ◽

Yoann Brans ◽

Clement Larue ◽

...

Keyword(s):

High Throughput Sequencing ◽

Molecular Detection ◽

Phylogenetic Analyses ◽

Epidemiological Studies ◽

Mosaic Disease ◽

Open Reading Frames ◽

Sequence Comparisons ◽

High Incidence ◽

The Usa ◽

Reading Frames

Although the chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not elucidated. Here, using classical approaches in combination with high throughput sequencing (HTS) techniques, we identify a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted and sequenced on an Illumina NextSeq500 (2x150 or 2x 75 nt). In each source, we identified a single contig of about 7.2 kilobases that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5% with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons show that this virus is a novel species for which we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak), as well in chestnut trees presenting typical ChMD symptoms in the field (100% and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut SRA transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the USA, as well as ChMV detection in C. dentata from the USA. Preliminary epidemiological studies, performed in France and in Central Eastern Italy, showed that ChMV has a high incidence in some commercial orchards, with a low within-orchard genetic diversity.

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