Dataset Information

Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete Cucurbit aphid-borne yellows virus Genome.

ABSTRACT: Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of Cucurbit aphid-borne yellows virus (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118.

SUBMITTER: Maina S

PROVIDER: S-EPMC5427211 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete <i>Cucurbit aphid-borne yellows virus</i> Genome.

Maina Solomon S Edwards Owain R OR de Almeida Luis L Ximenes Abel A Jones Roger A C RAC

Genome announcements 20170511 19

Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of <i>Cucurbit aphid-borne yellows virus</i> (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118. ...[more]

PMID: 28495776

Similar Datasets

Project description:Background:Cucurbit aphid-borne yellows virus (CABYV) is among the most important yellowing viruses on cucurbits in Iran. The presence of CABYV has been previously reported from the major cucurbit growing areas in Iran, however, there are few studies concerning the detection of the different strains of this virus in the grower's fields, and especially, there is no report of the weed host plants near crop fields. Objectives: This study was done in order to detect the new strains of the CABYV polerovirus in cucurbits and the weed plants in the Lorestan province, Iran, as an introductory investigation for initiating a program of the breeding for resistance. Material and Methods: During a survey carried out in 2013-2014 in Lorestan province; Iran, 189 cucurbit and 261 weed samples were investigated for the presence of CABYV using RT-PCR. In addition, the phylogeny and nucleotide similarities were discussed on the basis of the partial nucleotide sequence of RNA dependent RNA polymerase (RdRP) gene. Results: The RT-PCR carried out on leaf samples revealed the infection with the CABYV in 43 cucumber and 12 weed samples. RT-PCR using strain specific primers detected the presence of the both common (C) and recombinant (R) strains of CABYV in the tested samples. On the basis of the phylogenetic analyses, the CABYV-C isolates from Iran were clustered into two distinct sub-populations (CI and CII), such that all the weed samples with two sequenced cucumber isolates were clustered in the CI sub-population. Meanwhile, a distinct sub-population of the isolates was clustered in the CABYV-R group showed a shared sequence identity of 97% to a Taiwanese isolate (JQ700306). Conclusions: This study has indicated the incidence of CABYV-R in the Southwest Asia; Iran for the first time. We were also able to show CABYV occurrence in Sysimbrium irio and Citrullus colocynthis from this area of the world. Identification of cucurbit infecting viruses and studying their distribution and potential reservoir hosts are important for developing successful control programs for virus disease management.

Dataset Information

Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete Cucurbit aphid-borne yellows virus Genome.

Publications

Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete <i>Cucurbit aphid-borne yellows virus</i> Genome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets