scholarly journals Complete Nucleotide Sequence of a French Isolate of Maize rough dwarf virus , a Fijivirus Member in the Family Reoviridae

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
L. Svanella-Dumas ◽  
A. Marais ◽  
C. Faure ◽  
S. Theil ◽  
J. B. Thibord ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Complete Sequence ◽  
Dwarf Virus ◽  
Maize Rough Dwarf Virus ◽  
Online Databases ◽  
The Family ◽  
French Isolate ◽  
Generation Sequencing

The complete nucleotide sequence of a French isolate of Maize rough dwarf virus (MRDV) was determined by next-generation sequencing and compared with the single available complete sequence and with the partial sequences of two additional isolates available in online databases.

scholarly journals Complete Nucleotide Sequence of an Isolate of Grapevine Satellite Virus and Evidence for the Presence of Multimeric Forms in an Infected Grapevine

2017 ◽  
Vol 5 (16) ◽  
Author(s):  
T. Candresse ◽  
A. Marais ◽  
S. Theil ◽  
C. Faure ◽  
T. Lacombe ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Complete Sequence ◽  
Next Generation ◽  
Satellite Virus ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Infected Grapevine ◽  
Generation Sequencing

ABSTRACT The complete nucleotide sequence of an isolate of grapevine satellite virus (GV-Sat) was determined by next-generation sequencing (NGS) and compared with the single available complete sequence. The NGS data unexpectedly provided evidence for the existence of multimeric forms of GV-Sat, which were experimentally confirmed, allowing the redefinition of GV-Sat genomic ends.

scholarly journals The Complete Nucleotide Sequence and Biotype Variability of Papaya leaf distortion mosaic virus

2005 ◽  
Vol 95 (2) ◽  
pp. 128-135 ◽  
Author(s):  
Tetsuo Maoka ◽  
Tatsuji Hataya
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Mosaic Virus ◽  
Complete Nucleotide Sequence ◽  
Distinct Species ◽  
Cleavage Sites ◽  
Reading Frame ◽  
The Family ◽  
Evolutionary Event ◽  
Leaf Distortion

The complete nucleotide sequence of the genome of Papaya leaf distortion mosaic virus (PLDMV) was determined. The viral RNA genome of strain LDM (leaf distortion mosaic) comprised 10,153 nucleotides, excluding the poly(A) tail, and contained one long open reading frame encoding a polyprotein of 3,269 amino acids (molecular weight 373,347). The polyprotein contained nine putative proteolytic cleavage sites and some motifs conserved in other potyviral polyproteins with 44 to 50% identities, indicating that PLDMV is a distinct species in the genus Potyvirus. Like the W biotype of Papaya ringspot virus (PRSV), the non-papaya-infecting biotype of PLDMV (PLDMV-C) was found in plants of the family Cucurbitaceae. The coat protein (CP) sequence of PLDMV-C in naturally infected-Trichosanthes bracteata was compared with those of three strains of the P biotype (PLDMV-P), LDM and two additional strains M (mosaic) and YM (yellow mosaic), which are biologically different from each other. The CP sequences of three strains of PLDMV-P share high identities of 95 to 97%, while they share lower identities of 88 to 89% with that of PLDMV-C. Significant changes in hydrophobicity and a deletion of two amino acids at the N-terminal region of the CP of PLDMV-C were observed. The finding of two biotypes of PLDMV implies the possibility that the papaya-infecting biotype evolved from the cucurbitaceae-infecting potyvirus, as has been previously suggested for PRSV. In addition, a similar evolutionary event acquiring infectivity to papaya may arise frequently in viruses in the family Cucurbitaceae.

Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology

Weed Science ◽  
2009 ◽  
Vol 57 (5) ◽  
pp. 463-469 ◽  
Author(s):  
Ryan M. Lee ◽  
Jyothi Thimmapuram ◽  
Kate A. Thinglum ◽  
George Gong ◽  
Alvaro G. Hernandez ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Ecological Model ◽  
Average Length ◽  
Science Research ◽  
Complete Sequence ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Sequencing Technologies ◽  
Generation Sequencing

Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.

Amelogenesis Imperfecta

2016 ◽  
Vol 95 (13) ◽  
pp. 1457-1463 ◽  
Author(s):  
M.K. Prasad ◽  
S. Laouina ◽  
M. El Alloussi ◽  
H. Dollfus ◽  
A. Bloch-Zupan
Keyword(s):  
Next Generation Sequencing ◽  
Nonsense Mutation ◽  
Amelogenesis Imperfecta ◽  
Consanguineous Family ◽  
Novel Mutations ◽  
Enamel Defects ◽  
Targeted Next Generation Sequencing ◽  
The Family ◽  
Moroccan Family ◽  
Generation Sequencing

Amelogenesis imperfecta (AI) is a clinically and genetically heterogeneous group of diseases characterized by enamel defects. The authors have identified a large consanguineous Moroccan family segregating different clinical subtypes of hypoplastic and hypomineralized AI in different individuals within the family. Using targeted next-generation sequencing, the authors identified a novel heterozygous nonsense mutation in COL17A1 (c.1873C>T, p.R625*) segregating with hypoplastic AI and a novel homozygous 8-bp deletion in C4orf26 (c.39_46del, p.Cys14Glyfs*18) segregating with hypomineralized-hypoplastic AI in this family. This study highlights the phenotypic and genotypic heterogeneity of AI that can exist even within a single consanguineous family. Furthermore, the identification of novel mutations in COL17A1 and C4orf26 and their correlation with distinct AI phenotypes can contribute to a better understanding of the pathophysiology of AI and the contribution of these genes to amelogenesis.

Complete nucleotide sequence of rice gall dwarf virus genome segment S7

2007 ◽  
Vol 152 (6) ◽  
pp. 1233-1235 ◽  
Author(s):  
F. X. Liu ◽  
X. L. Ruan ◽  
Y. W. He ◽  
H. P. Li ◽  
J. S. Hu
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Virus Genome ◽  
Genome Segment ◽  
Dwarf Virus ◽  
Rice Gall Dwarf Virus

Complete nucleotide sequence of clematis chlorotic mottle virus, a new member of the family Tombusviridae

2017 ◽  
Vol 162 (5) ◽  
pp. 1373-1379 ◽  
Author(s):  
Margaret McLaughlin ◽  
Ben Lockhart ◽  
Ramon Jordan ◽  
Geoff Denton ◽  
Dimitre Mollov
Keyword(s):  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Mottle Virus ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle ◽  
The Family

scholarly journals Whole-Genome Sequencing of Six Borrelia miyamotoi Clinical Strains Isolated in Russia

2018 ◽  
Vol 6 (1) ◽  
Author(s):  
Konstantin V. Kuleshov ◽  
Joris Koetsveld ◽  
Irina A. Goptar ◽  
Mikhail L. Markelov ◽  
Nadezhda M. Kolyasnikova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
Russian Federation ◽  
Complete Sequence ◽  
Whole Genome Sequence ◽  
Borrelia Miyamotoi ◽  
Whole Genome ◽  
The Russian Federation ◽  
Sequencing Platforms ◽  
Generation Sequencing

ABSTRACT Here, we report the whole-genome sequence of six clinical Borrelia miyamotoi isolates from the Russian Federation. Using two independent next-generation sequencing platforms, we determined the complete sequence of the chromosome and several plasmids. All strains have an Asian genotype with 99.8% chromosome nucleotide similarity with B. miyamotoi strain FR64b.

scholarly journals Arenavirus Coinfections Are Common in Snakes with Boid Inclusion Body Disease

2015 ◽  
Vol 89 (16) ◽  
pp. 8657-8660 ◽  
Author(s):  
J. Hepojoki ◽  
P. Salmenperä ◽  
T. Sironen ◽  
U. Hetzel ◽  
Y. Korzyukov ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Inclusion Body ◽  
New Genus ◽  
De Novo ◽  
Sequence Assembly ◽  
Next Generation ◽  
Content Type ◽  
The Family ◽  
Inclusion Body Disease ◽  
Generation Sequencing

Recently, novel arenaviruses were found in snakes with boid inclusion body disease (BIBD); these form the new genusReptarenaviruswithin the familyArenaviridae. We used next-generation sequencing andde novosequence assembly to investigate reptarenavirus isolates from our previous study. Four of the six isolates and all of the samples from snakes with BIBD contained at least two reptarenavirus species. The viruses sequenced comprise four novel reptarenavirus species and a representative of a new arenavirus genus.

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