An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

Genomic and Morphological Features of a Banchine Polydnavirus: Comparison with Bracoviruses and Ichnoviruses

Journal of Virology ◽

10.1128/jvi.02702-06 ◽

2007 ◽

Vol 81 (12) ◽

pp. 6491-6501 ◽

Cited By ~ 66

Author(s):

Renée Lapointe ◽

Kohjiro Tanaka ◽

Walter E. Barney ◽

James B. Whitfield ◽

Jonathan C. Banks ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genome Size ◽

Genome Sequence ◽

Protein Tyrosine Phosphatase ◽

Size Range ◽

Tyrosine Phosphatase ◽

Gene Families ◽

Open Reading Frames ◽

Genomic Features ◽

ABSTRACT Many ichneumonid and braconid endoparasitoids inject a polydnavirus (PDV) into their caterpillar hosts during oviposition. The viral entities carried by wasps of these families are referred to as “ichnoviruses” (IVs) and “bracoviruses” (BVs), respectively. All IV genomes characterized to date are found in wasps of the subfamily Campopleginae; consequently, little is known about PDVs found in wasps of the subfamily Banchinae, the only other ichneumonid taxon thus far shown to carry these viruses. Here we report on the genome sequence and virion morphology of a PDV carried by the banchine parasitoid Glypta fumiferanae. With an aggregate genome size of ∼290 kb and 105 genome segments, this virus displays a degree of genome segmentation far greater than that reported for BVs or IVs. The size range of its genome segments is also lower than those in the latter two groups. As reported for other PDVs, the predicted open reading frames of this virus cluster into gene families, including the protein tyrosine phosphatase (PTP) and viral ankyrin (ank) families, but phylogenetic analysis indicates that ank genes of the G. fumiferanae virus are not embedded within the IV lineage, while its PTPs and those of BVs form distinct clusters. The banchine PDV genome also encodes a novel family of NTPase-like proteins displaying a pox-D5 domain. The unique genomic features of the first banchine virus examined, along with the morphological singularities of its virions (IV-like nucleocapsids, but enveloped in groups like some of the BVs), suggest that they could have an origin distinct from those of IVs and BVs.

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 ◽

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.

Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽

10.1093/genetics/143.2.777 ◽

1996 ◽

Vol 143 (2) ◽

pp. 777-788 ◽

Cited By ~ 2

Author(s):

Carole H Sellem ◽

Yves d'Aubenton-Carafa ◽

Michèle Rossignol ◽

Léon Belcour

Keyword(s):

Mitochondrial Genome ◽

Open Reading Frames ◽

Nucleotide Substitutions ◽

Sequence Comparisons ◽

Modular Evolution ◽

Group I ◽

Sequence Variations ◽

Type Strains ◽

Reading Frames ◽

Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

Bias between the Left and Right Inverted Repeats during IS911 Targeted Insertion

Journal of Bacteriology ◽

10.1128/jb.00452-08 ◽

2008 ◽

Vol 190 (18) ◽

pp. 6111-6118 ◽

Cited By ~ 5

Author(s):

P. Rousseau ◽

C. Loot ◽

C. Turlan ◽

S. Nolivos ◽

M. Chandler

Keyword(s):

Insertion Sequence ◽

Regulatory Protein ◽

Open Reading Frames ◽

Inverted Repeats ◽

Functional Differences ◽

Left And Right ◽

Ordered Assembly ◽

ABSTRACT IS911 is a bacterial insertion sequence composed of two consecutive overlapping open reading frames (ORFs [orfA and orfB]) encoding the transposase (OrfAB) as well as a regulatory protein (OrfA). These ORFs are bordered by terminal left and right inverted repeats (IRL and IRR, respectively) with several differences in nucleotide sequence. IS911 transposition is asymmetric: each end is cleaved on one strand to generate a free 3′-OH, which is then used as the nucleophile in attacking the opposite insertion sequence (IS) end to generate a free IS circle. This will be inserted into a new target site. We show here that the ends exhibit functional differences which, in vivo, may favor the use of one compared to the other during transposition. Electromobility shift assays showed that a truncated form of the transposase [OrfAB(1-149)] exhibits higher affinity for IRR than for IRL. While there was no detectable difference in IR activities during the early steps of transposition, IRR was more efficient during the final insertion steps. We show here that the differential activities between the two IRs correlate with the different affinities of OrfAB(1-149) for the IRs during assembly of the nucleoprotein complexes leading to transposition. We conclude that the two inverted repeats are not equivalent during IS911 transposition and that this asymmetry may intervene to determine the ordered assembly of the different protein-DNA complexes involved in the reaction.

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 ◽

Significant Amino Acid ◽

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.

Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

Applied and Environmental Microbiology ◽

10.1128/aem.00128-11 ◽

2011 ◽

Vol 77 (10) ◽

pp. 3443-3450 ◽

Cited By ~ 35

Author(s):

Evelien M. Adriaenssens ◽

Pieter-Jan Ceyssens ◽

Vincent Dunon ◽

Hans-Wolfgang Ackermann ◽

Johan Van Vaerenbergh ◽

...

Keyword(s):

Soil Samples ◽

Pantoea Agglomerans ◽

Open Reading Frames ◽

Human Pathogen ◽

Content Type ◽

Host Diversity ◽

Double Stranded Dna ◽

Opportunistic Human Pathogen ◽

ABSTRACTPantoea agglomeransis a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight ofP. agglomeransare lytic phages, isolated from soil samples, belonging to thePodoviridaeand are the firstPantoeaphages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of theAutographivirinae, within the genus of the “phiKMV-like viruses.” Phylogenetic analysis of all the sequenced members of theAutographivirinaesupports the classification of phages LIMElight and LIMEzero as members of the “phiKMV-like viruses” and corroborates the subdivision into the different genera. These data expand the knowledge ofPantoeaphages and illustrate the wide host diversity of phages within the “phiKMV-like viruses.”

Genome Sequences of Two Dual-Serotype-Specific Echovirus 20 Strains from Nigeria

Microbiology Resource Announcements ◽

10.1128/mra.00894-19 ◽

2019 ◽

Vol 8 (43) ◽

Author(s):

T. O. C. Faleye ◽

O. M. Adewumi ◽

D. Klapsa ◽

M. Majumdar ◽

J. Martin ◽

...

Keyword(s):

Amino Acids ◽

Complete Genome ◽

Neutralization Assay ◽

Open Reading Frames ◽

Genome Sequences ◽

Here, we describe nearly complete genome sequences (7,361 nucleotides [nt] and 6,893 nt) of two echovirus 20 (E20) isolates from Nigeria that were simultaneously typed as CVB and E20 (dual serotype) by neutralization assay. Both include two overlapping open reading frames (ORFs) of 67 and 2,183 amino acids that encoded a recently described gut infection-facilitating protein and the classic enterovirus proteins, respectively.

Complete genome sequence of GII.9 norovirus

Archives of Virology ◽

10.1007/s00705-021-05257-x ◽

2021 ◽

Author(s):

Zilong Zhang ◽

Danlei Liu ◽

Zilei Zhang ◽

Peng Tian ◽

Shenwei Li ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

High Throughput Sequencing ◽

Open Reading Frames ◽

Viral Sequence ◽

Sequence Comparisons ◽

Rapid Amplification ◽

Genome Level ◽

AbstractNorovirus is recognized as one of the leading causes of acute gastroenteritis outbreaks. Genotype GII.9 was first detected in Norfolk, VA, USA, in 1997. However, the complete genome sequence of this genotype has not yet been determined. In this study, a complete genome sequence of GII.9[P7] norovirus, SCD1878_GII.9[P7], from a patient was determined using high-throughput sequencing and rapid amplification of cDNA ends (RACE) technology. The complete genome sequence of SCD1878_GII.9[P7] is 7544 nucleotides (nt) in length with a 3’ poly(A) tail and contains three open reading frames. Sequence comparisons indicated that SCD1878_GII.9[P7] shares 92.1%-92.3% nucleotide sequence identity with GII.P7 (AB258331 and AB039777) and 96.7%-97.4% identity with GII.9 (AY038599 and DQ379715). The results suggested that SCD1878_GII.9[P7] is a member of P genotype GII.P7 and G genotype GII.9. This viral sequence fills a gap at the whole-genome level for the GII.9 genotype.

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 ◽

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.