Infected Ipomoea batatas with SPFMV and SPV2 rep2 - SRA

SRX796076: Infected Ipomoea batatas with SPFMV and SPV2 rep2
1 ILLUMINA (Illumina HiSeq 2000) run: 25.3M spots, 5.1G bases, 3.3Gb downloads

Design: A marketable commercial sweet potato (Ipomea batatas) root acquired in Barcelona was planted on soil to produce fresh tissue that was further propagated through cuttings at CRAG facilities. Presence of Sweet potato feathery mottle virus (SPFMV) in the original plant was confirmed by specific RT-PCR and sequencing of several genome fragments, including the complete P1 coding region where the existence of an embedded PISPO region was also confirmed. To boost accumulation of the potyvirus in the sweet potato plant, co-infection with an isolate of the crinivirus Sweet potato chlorotic stunt virus (SPCSV) was achieved by inoculation with 50 viroliferous Bemisia tabaci whiteflies, using 48 h acquisition and inoculation periods 1 . The Spanish isolate of SPCSV was kindly provided by Dr. Jesús Navas-Castillo (IHSM La Mayora, CSIC-UMA, Málaga, Spain) in an Ipomea setosa plant, also propagated through cuttings. Sweet potato virus C (SPVC) was found to be co-infecting the sweet potato plant after deep sequencing analysis. Symptomatic tissues of infected plants were collected for RNA extraction with Trizol reagent, following the provider instructions. Contaminating DNA from RNA extractions was removed with Turbo DNase (Ambion) and RNA was further purified using the RNeasy Mini kit (Quiagen).RNA libraries were constructed with the ScripSeq Complete Kit (epicentre) including barcoding elements to identify the different samples, according to provider protocols. Libraries were submitted to BGI for Illumina-Sequencing.

Submitted by: (CNB-CSIC)

Study: Variant analysis of several viruses infecting Ipomoeba batata and Nicotiana benthamiana

PRJNA268141 • SRP050522 • All experiments • All runs

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Project to analyze several virus infecting Ipomoeba batata and Nicotiana benthamiana, the virus are Sweet potato mild mottle virus, Sweet potato feathery mottle virus, Sweet potato virus 2, Sweet potato virus C, Sweet potato chlorotic stunt virus, Tobacco etch virus and there is control construction with SPFMV P1+T7 polymerase.

Sample: Plant sample from infected Ipomoea batatas rep2

SAMN03203479 • SRS779546 • All experiments • All runs

Organism: Ipomoea batatas

Library:

Name: SP2

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Runs: 1 run, 25.3M spots, 5.1G bases, 3.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR1693363	25,321,380	5.1G	3.3Gb	2015-11-21

ID:: 1139607

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