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SRX4554090: GSM3333354: Medium leaf - Biorep 1; Vitis riparia; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 27.4M spots, 2.7G bases, 1.8Gb downloads

Submitted by: NCBI (GEO)
Study: A galling insect activates plant reproductive programs during gall development
show Abstracthide Abstract
Some insects can redirect plant development to form unique organs called galls, which provide these insects with unique, enhanced food and protection from enemies and the elements. Many galls resemble flowers or fruits, suggesting that elements of reproductive development may be involved. We addressed this possibility using RNA sequencing (RNAseq) to quantify the transcriptional responses of wild grapevine (Vitis riparia Michx.) leaves to a galling parasite, phylloxera (Daktulosphaira vitifoliae (Fitch 1855)). If development of reproductive structures is part of gall formation, we expected to find significantly elevated expression of genes involved in flower and/or fruit development in developing galls as opposed to ungalled leaves. We found that reproductive gene ontology classes were significantly enriched in developing galls, and that expression of many putative genes involved in flower formation was significantly increased, particularly in later gall stages. The patterns of gene expression found in galls suggest that phylloxera exploits vascular cambium to provide meristematic tissue and redirects leaf development towards formation of carpels. The phylloxera leaf gall, and perhaps other similar galls, appears to be phenotypically and transcriptionally convergent on the plant carpel. Overall design: Comparison of 4 gall developmental stages (1-4) with 3 ungalled control leaves (small, medium, large)
Sample: Medium leaf - Biorep 1
SAMN09837299 • SRS3671098 • All experiments • All runs
Organism: Vitis riparia
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Samples were dissected on ice, and flash frozen in liquid nitrogen. RNA was extracted and DNase1 treated, on column, using the Spectrum Plant Total RNA Kit (Sigma #STRN50-1KT; Sigma-Aldrich, St. Louis, MO, USA; protocol A and Appendix). The resulting RNA was further purified and concentrated with the RNeasy MinElute Cleanup Kit (Qiagen #74204; Qiagen, Hilden, Germany) and eluted with pure water. The quality of the resulting RNA was assessed using the Agilent 2100 BioAnalyzer (www.genomics.agilent.com; Agilent, Santa Clara, CA, USA), and all RNA integrity number values were found to be above 8. The Illumina libraries were constructed using the RNA TruSeq Kit (Illumina, Inc., San Diego, CA, USA), barcoded (TACT ungalled; GTAT galled), and sequenced single-end with 100bp reads on the Illumina HiSeq-2000 platform at the University of Missouri DNA core (http://dnacore.missouri.edu ).
Experiment attributes:
GEO Accession: GSM3333354
Links:
Runs: 1 run, 27.4M spots, 2.7G bases, 1.8Gb
Run# of Spots# of BasesSizePublished
SRR769575727,448,1782.7G1.8Gb2018-09-25

ID:
6162896

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