Literature DB >> 33026576

Date palm virus A: first plant virus found in date palm trees.

Ayoub Maachi1, Tatsuya Nagata2, João Marcos Fagundes Silva3.   

Abstract

In this work, a novel ssRNA (+) viral genomic sequence with gene organization typical of members of the subfamily Quinvirinae (family Betaflexiviridae) was identified using high- throughput sequencing data of date palm obtained from the Sequence Read Archive database. The viral genome sequence consists of 7860 nucleotides and contains five ORFs encoding for the replication protein (Rep), triple gene block proteins 1, 2, 3 (TGB 1, 2, and 3), and coat protein (CP). Phylogenetic analysis based on the Rep and the CP amino acid sequences showed the closest relationship to garlic yellow mosaic-associated virus (GYMaV). Based on the demarcation criteria of the family Betaflexiviridae, this new virus, provisionally named date palm virus A (DPVA), could constitute a member of a novel genus. However, considering that DPVA and GYMaV share the same genomic organization and that they cluster together on the Rep phylogenetic analysis, they could also constitute a novel genus together, highlighting the necessity of a revision of the taxonomic criteria of the family Betaflexiviridae.

Entities:  

Keywords:  Betaflexiviridae; Date palm virus A; High-throughput sequencing; New genus; New species

Mesh:

Substances:

Year:  2020        PMID: 33026576     DOI: 10.1007/s11262-020-01801-0

Source DB:  PubMed          Journal:  Virus Genes        ISSN: 0920-8569            Impact factor:   2.332


  9 in total

Review 1.  Triple gene block: modular design of a multifunctional machine for plant virus movement.

Authors:  Sergey Yu Morozov; Andrey G Solovyev
Journal:  J Gen Virol       Date:  2003-06       Impact factor: 3.891

2.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Authors:  Dinghua Li; Chi-Man Liu; Ruibang Luo; Kunihiko Sadakane; Tak-Wah Lam
Journal:  Bioinformatics       Date:  2015-01-20       Impact factor: 6.937

3.  MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies.

Authors:  Jonathan Seguin; Patricia Otten; Loïc Baerlocher; Laurent Farinelli; Mikhail M Pooggin
Journal:  J Virol Methods       Date:  2016-03-16       Impact factor: 2.014

4.  Sensitive high-performance liquid chromatographic determination of ionic drugs in biological fluids with short-wavelength ultraviolet detection using column switching combined with ion-pair chromatography: application to basic compounds.

Authors:  K Yamashita; M Motohashi; T Yashiki
Journal:  J Chromatogr       Date:  1989-02-24

5.  Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

Authors:  Matthew Kearse; Richard Moir; Amy Wilson; Steven Stones-Havas; Matthew Cheung; Shane Sturrock; Simon Buxton; Alex Cooper; Sidney Markowitz; Chris Duran; Tobias Thierer; Bruce Ashton; Peter Meintjes; Alexei Drummond
Journal:  Bioinformatics       Date:  2012-04-27       Impact factor: 6.937

6.  DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data.

Authors:  Junko Tsuji; Zhiping Weng
Journal:  PLoS One       Date:  2016-10-13       Impact factor: 3.240

Review 7.  Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization.

Authors:  Mikhail M Pooggin
Journal:  Front Microbiol       Date:  2018-11-20       Impact factor: 5.640

8.  A new virus found in garlic virus complex is a member of possible novel genus of the family Betaflexiviridae (order Tymovirales).

Authors:  Leonardo A Da Silva; Athos S Oliveira; Fernando L Melo; Daniel M P Ardisson-Araújo; Francisco V Resende; Renato O Resende; Bergmann M Ribeiro
Journal:  PeerJ       Date:  2019-01-16       Impact factor: 2.984

9.  Fast and accurate short read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2009-05-18       Impact factor: 6.937

  9 in total
  1 in total

1.  Exploring the tymovirales landscape through metatranscriptomics data.

Authors:  Nicolás Bejerman; Humberto Debat
Journal:  Arch Virol       Date:  2022-06-16       Impact factor: 2.685

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.