scholarly journals Pineapple bacilliform CO virus: Diversity, Detection, Distribution, and Transmission

Plant Disease ◽  
2012 ◽  
Vol 96 (12) ◽  
pp. 1798-1804 ◽  
Author(s):  
D. M. Sether ◽  
M. J. Melzer ◽  
W. B. Borth ◽  
J. S. Hu
Keyword(s):  
Reverse Transcriptase ◽  
Movement Protein ◽  
Rnase H ◽  
Open Reading Frames ◽  
Ananas Comosus ◽  
Genomic Variants ◽  
Virus Diversity ◽  
Putative Movement Protein ◽  
Dysmicoccus Neobrevipes ◽  
Reading Frames

Members of the genus Badnavirus (family Caulimovirdae) have been identified in dicots and monocots worldwide. The genome of a pineapple badnavirus, designated Pineapple bacilliform CO virus-HI1 (PBCOV-HI1), and nine genomic variants (A through H) were isolated and sequenced from pineapple, Ananas comosus, in Hawaii. The 7,451-nucleotide genome of PBCOV-HI1 possesses three open reading frames (ORFs) encoding putative proteins of 20 (ORF1), 15 (ORF2), and 211 (ORF3) kDa. ORF3 encodes a polyprotein that includes a putative movement protein and viral aspartyl proteinase, reverse transcriptase, and RNase H regions. Three distinct groups of putative endogenous pineapple pararetroviral sequences and Metaviridae-like retrotransposons encoding long terminal repeat, reverse-transcriptase, RNase H, and integrase regions were also identified from the pineapple genome. Detection assays were developed to distinguish PBCOV-HI1 and genomic variants, putative endogenous pararetrovirus sequences, and Ananas Metaviridae sequences also identified in pineapple. PBCOV-HI1 incidences in two commercially grown pineapple hybrids, PRI 73-114 and PRI 73-50, was 34 to 68%. PBCOV-HI1 was transmitted by gray pineapple mealybugs, Dysmicoccus neobrevipes, to pineapple.

RNA3 nucleotide sequence analyses ofpeanut stunt virusMi strain

2005 ◽  
Vol 2 (1) ◽  
pp. 33-38
Author(s):  
Xu Ze-Yong ◽  
Yan Li-Ying ◽  
Chen Kun-Rong ◽  
Marcel Prins
Keyword(s):  
Nucleotide Sequence ◽  
Movement Protein ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Sequence Analyses ◽  
Tomato Aspermy Virus ◽  
Subgroup Ii ◽  
Putative Movement Protein ◽  
Peanut Stunt Virus ◽  
Reading Frames

AbstractNucleotide sequence of full-length cDNA ofpeanut stunt virus(PSV) Mi strain RNA3 was determined and compared with those of PSV-ER and -J (subgroup I) and PSV-W (subgroup II), strains ofcucumber mosaic virus(CMV) andtomato aspermy virus(TAV). PSV-Mi RNA3 consists of 2170 nt and has two open reading frames, encoding a putative movement protein (3a protein) and a coat protein (CP). PSV-Mi RNA3 is 77.7% and 78.5% identical to those of PSV-ER and -J, whereas it shares 76.6% identity with PSV-W. Nucleotide identity of3aandcpgenes between PSV strains Mi and ER, J and W was 78.3–79.3% and 74.4–77.8%, respectively. Amino acid identity of 3a and CP between PSV-Mi and -ER, -J and -W was 73.9–77.4% and 64.8–77.5%, respectively. RNA3 of PSV-Mi (GenBank accession no. AY775057) had a varied intercistronic and 5′-untranslated region compared with those of PSV strains ER, J and W. Results indicate that PSV-Mi represents a new PSV subgroup from China, designated as subgroup III.

scholarly journals An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae.

1994 ◽  
Vol 14 (7) ◽  
pp. 4485-4492 ◽  
Author(s):  
B A Dombroski ◽  
Q Feng ◽  
S L Mathias ◽  
D M Sassaman ◽  
A F Scott ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Consensus Sequence ◽  
Unknown Origin ◽  
Open Reading Frames ◽  
Long Terminal Repeats ◽  
Base Pairs ◽  
In Vivo Assay ◽  
Reading Frames

L1 elements constitute a highly repetitive human DNA family (50,000 to 100,000 copies) lacking long terminal repeats and ending in a poly(A) tail. Some L1 elements are capable of retrotransposition in the human genome (Kazazian, H. H., Jr., C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips, and S.E. Antonarakis, Nature (London) 332:164-166, 1988). Although most are 5' truncated, a consensus sequence of complete L1 elements is 6 kb long and contains two open reading frames (ORFs) (Scott, A. F., B. J. Schmeckpeper, M. Abdelrazik, C. T. Comey, B. O'Hara, J. P. Rossiter, T. Cooley, P. Health, K. D. Smith, and L. Margolet, Genomics 1:113-125, 1987). The protein encoded by ORF2 has reverse transcriptase (RT) activity in vitro (Mathias, S. L., A. F. Scott, H. H. Kazazian, Jr., J. D. Boeke, and A. Gabriel, Science 254:1808-1810, 1991). Because L1 elements are so numerous, efficient methods for identifying active copies are required. We have developed a simple in vivo assay for the activity of L1 RT based on the system developed by Derr et al. (Derr, L. K., J. N. Strathern, and D. J. Garfinkel, Cell 67:355-364, 1991) for yeast HIS3 pseudogene formation. L1 ORF2 displays an in vivo RT activity similar to that of yeast Ty1 RT in this system and generates pseudogenes with unusual structures. Like the HIS3 pseudogenes whose formation depends on Ty1 RT, the HIS3 pseudogenes generated by L1 RT are joined to Ty1 sequences and often are part of complex arrays of Ty1 elements, multiple HIS3 pseudogenes, and hybrid Ty1/L1 elements. These pseudogenes differ from those previously described in that there are base pairs of unknown origin inserted at several of the junctions. In two of three HIS3 pseudogenes studied, the L1 RT appears to have jumped from the 5' end of a Ty1/L1 transcript to the poly(A) tract of the HIS3 RNA.

scholarly journals Genome of Staphylococcal Phage K: a New Lineage of Myoviridae Infecting Gram-Positive Bacteria with a Low G+C Content

2004 ◽  
Vol 186 (9) ◽  
pp. 2862-2871 ◽  
Author(s):  
S. O'Flaherty ◽  
A. Coffey ◽  
R. Edwards ◽  
W. Meaney ◽  
G. F. Fitzgerald ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Rnase H ◽  
Open Reading Frames ◽  
The Other ◽  
Gram Positive Bacteria ◽  
Acid Protein ◽  
Wide Range ◽  
Highly Virulent ◽  
Reading Frames ◽  
Amino Acid Protein

ABSTRACT Phage K is a polyvalent phage of the Myoviridae family which is active against a wide range of staphylococci. Phage genome sequencing revealed a linear DNA genome of 127,395 bp, which carries 118 putative open reading frames. The genome is organized in a modular form, encoding modules for lysis, structural proteins, DNA replication, and transcription. Interestingly, the structural module shows high homology to the structural module from Listeria phage A511, suggesting intergenus horizontal transfer. In addition, phage K exhibits the potential to encode proteins necessary for its own replisome, including DNA ligase, primase, helicase, polymerase, RNase H, and DNA binding proteins. Phage K has a complete absence of GATC sites, making it insensitive to restriction enzymes which cleave this sequence. Three introns (lys-I1, pol-I2, and pol-I3) encoding putative endonucleases were located in the genome. Two of these (pol-I2 and pol-I3) were found to interrupt the DNA polymerase gene, while the other (lys-I1) interrupts the lysin gene. Two of the introns encode putative proteins with homology to HNH endonucleases, whereas the other encodes a 270-amino-acid protein which contains two zinc fingers (CX2CX22CX2C and CX2CX23CX2C). The availability of the genome of this highly virulent phage, which is active against infective staphylococci, should provide new insights into the biology and evolution of large broad-spectrum polyvalent phages.

scholarly journals Reverse transcriptase-related enzymes are associated with horizontal chromosome transfer in an asexual pathogen

2015 ◽  
Author(s):  
Xiaoqiu Huang ◽  
Anindya Das ◽  
Binod B Sahu ◽  
Subodh K Srivastava ◽  
Leonor F Leandro ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Root Rot ◽  
Supernumerary Chromosome ◽  
Open Reading Frames ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Chromosome Transfer ◽  
Supernumerary Chromosomes ◽  
The Mean ◽  
Reading Frames

Supernumerary chromosomes have been shown to transfer horizontally from one isolate to another. However, the mechanism by which horizontal chromosome transfer (HCT) occurs is unknown. In this study, we compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and detected numerous instances of HCT in supernumerary chromosomes. We also identified a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs) in the supernumerary chromosomes between isolates of the asexual pathogen F. virguliforme. Supernumerary chromosomes carried reverse transcriptase-related genes (RVT); the presence of long RVT open reading frames (ORFs) in the supernumerary chromosome was correlated with the presence of two or more chromosome copies with a significant number of SNPs between them. Our results suggest that supernumerary chromosomes transfer horizontally via an RNA intermediate. Understanding the mechanism by which HCT occurs will have a profound impact on understanding evolution and applying biotechnology as well as accepting HCT as a natural source of genetic variation.

scholarly journals Reverse transcriptase-related enzymes are associated with horizontal chromosome transfer in an asexual pathogen

2015 ◽  
Author(s):  
Xiaoqiu Huang ◽  
Anindya Das ◽  
Binod B Sahu ◽  
Subodh K Srivastava ◽  
Leonor F Leandro ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Root Rot ◽  
Supernumerary Chromosome ◽  
Open Reading Frames ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Chromosome Transfer ◽  
Supernumerary Chromosomes ◽  
The Mean ◽  
Reading Frames

Supernumerary chromosomes have been shown to transfer horizontally from one isolate to another. However, the mechanism by which horizontal chromosome transfer (HCT) occurs is unknown. In this study, we compared the genomes of 11 isolates comprising six Fusarium species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and detected numerous instances of HCT in supernumerary chromosomes. We also identified a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs) in the supernumerary chromosomes between isolates of the asexual pathogen F. virguliforme. Supernumerary chromosomes carried reverse transcriptase-related genes (RVT); the presence of long RVT open reading frames (ORFs) in the supernumerary chromosome was correlated with the presence of two or more chromosome copies with a significant number of SNPs between them. Our results suggest that supernumerary chromosomes transfer horizontally via an RNA intermediate. Understanding the mechanism by which HCT occurs will have a profound impact on understanding evolution and applying biotechnology as well as accepting HCT as a natural source of genetic variation.

scholarly journals Complete Genome Sequence of Two Isolates of Spiraea Yellow Leafspot Virus (Genus: Badnavirus) From Spiraea x Bumalda ‘Anthony Waterer’

2021 ◽  
Author(s):  
Robert Alexander Alvarez-Quinto ◽  
Joana Serrano ◽  
Neil E Olszewski ◽  
Samuel Grinstead ◽  
Dimitre Mollov ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Virus Isolate ◽  
Rnase H ◽  
Open Reading Frames ◽  
Pairwise Comparisons ◽  
Nucleotide Level ◽  
Leaf Deformation ◽  
Reading Frames

Abstract Isolates of spiraea yellow leafspot virus (SYLSV) were collected from Spiraea (Spiraea x bumalda) ‘Anthony Waterer’ plants showing virus-like symptoms including yellow spotting and leaf deformation in Minnesota and Maryland. The complete genome sequence of SYLSV-MN (Minnesota) and SYLSV-MD (Maryland) was 8,017bp in length. The sequences share 95% of identity at the nucleotide level. Both isolates have the same genome organization containing three open reading frames (ORFs), with ORF3 being the largest encoding the putative polyprotein of 232 kDa with conserved domains including Zinc finger, pepsin-like aspartate protease, reverse transcriptase (RT), and RNase H. Pairwise comparisons between members of the genus badnavirus showed that Gooseberry vein banding associated virus GB1 (HQ852248) and Rubus yellow net virus isolate Baumforth's Seedling A (KM078034) were the closest related virus sequences to SYLSV sharing 73% of identity at the nucleotide level. Bacilliform virions with dimensions of 150 nm x 30 nm were observed in virus preparations from symptomatic but not in asymptomatic plants.

scholarly journals Identification of a Gene Encoding a Functional Reverse Transcriptase within a Highly Variable Locus in the P2-Like Coliphages

2006 ◽  
Vol 188 (4) ◽  
pp. 1643-1647 ◽  
Author(s):  
Richard Odegrip ◽  
Anders S. Nilsson ◽  
Elisabeth Haggård-Ljungquist
Keyword(s):  
Reverse Transcriptase ◽  
Reverse Transcriptase Activity ◽  
Open Reading Frames ◽  
Structural Genes ◽  
Gene Encoding ◽  
Transcriptase Activity ◽  
Reading Frames

ABSTRACT The P2-like coliphages are highly similar; the structural genes show at least 96% identity. However, at two loci they have genes believed to be horizontally transferred. We show that the genetic content at the second loci, the TO region, contains six completely different sequences with high AT contents and with different open reading frames. The product of one of them exhibits reverse transcriptase activity and blocks infection of phage T5.

scholarly journals Endogenous D-Type (HERV-K) Related Sequences Are Packaged into Retroviral Particles in the Placenta and Possess Open Reading Frames for Reverse Transcriptase

Virology ◽  
1996 ◽  
Vol 222 (2) ◽  
pp. 451-456 ◽  
Author(s):  
Guy R. Simpson ◽  
Clive Patience ◽  
Roswitha Löwer ◽  
Ralf.R. Tönjes ◽  
Harry D.M. Moore ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Open Reading Frames ◽  
Reading Frames

An in vivo assay for the reverse transcriptase of human retrotransposon L1 in Saccharomyces cerevisiae

1994 ◽  
Vol 14 (7) ◽  
pp. 4485-4492
Author(s):  
B A Dombroski ◽  
Q Feng ◽  
S L Mathias ◽  
D M Sassaman ◽  
A F Scott ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Consensus Sequence ◽  
Unknown Origin ◽  
Open Reading Frames ◽  
Long Terminal Repeats ◽  
Base Pairs ◽  
In Vivo Assay ◽  
Reading Frames

L1 elements constitute a highly repetitive human DNA family (50,000 to 100,000 copies) lacking long terminal repeats and ending in a poly(A) tail. Some L1 elements are capable of retrotransposition in the human genome (Kazazian, H. H., Jr., C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips, and S.E. Antonarakis, Nature (London) 332:164-166, 1988). Although most are 5' truncated, a consensus sequence of complete L1 elements is 6 kb long and contains two open reading frames (ORFs) (Scott, A. F., B. J. Schmeckpeper, M. Abdelrazik, C. T. Comey, B. O'Hara, J. P. Rossiter, T. Cooley, P. Health, K. D. Smith, and L. Margolet, Genomics 1:113-125, 1987). The protein encoded by ORF2 has reverse transcriptase (RT) activity in vitro (Mathias, S. L., A. F. Scott, H. H. Kazazian, Jr., J. D. Boeke, and A. Gabriel, Science 254:1808-1810, 1991). Because L1 elements are so numerous, efficient methods for identifying active copies are required. We have developed a simple in vivo assay for the activity of L1 RT based on the system developed by Derr et al. (Derr, L. K., J. N. Strathern, and D. J. Garfinkel, Cell 67:355-364, 1991) for yeast HIS3 pseudogene formation. L1 ORF2 displays an in vivo RT activity similar to that of yeast Ty1 RT in this system and generates pseudogenes with unusual structures. Like the HIS3 pseudogenes whose formation depends on Ty1 RT, the HIS3 pseudogenes generated by L1 RT are joined to Ty1 sequences and often are part of complex arrays of Ty1 elements, multiple HIS3 pseudogenes, and hybrid Ty1/L1 elements. These pseudogenes differ from those previously described in that there are base pairs of unknown origin inserted at several of the junctions. In two of three HIS3 pseudogenes studied, the L1 RT appears to have jumped from the 5' end of a Ty1/L1 transcript to the poly(A) tract of the HIS3 RNA.

Sign in / Sign up

Export Citation Format

Share Document