Development of an Affymetrux dual species ( Neotyphodium lolii/Lolium perenne) Symbiosis GeneChip
DOI:
https://doi.org/10.33584/rps.13.2006.3136Abstract
The aim of this project was to undertake large scale transcript profiling of endophyte and plant genes during symbiosis, and to determine the impact of targeted endophyte gene deletions on expression of plant and endophyte genes. We have designed and developed an Affymetrix NimbleExpress™ GeneChip® representing expressed sequence tags (ESTs) of the fungal endophyte Neotyphodium lolii Lp19 and its ryegrass host, Lolium perenne. In total, 8511 genes were represented on the microarrays with approximately eleven 25 base pair oligonucleotides per gene. Experiments were conducted to analyse differential expression of genes from endophyte-infected and endophyte-free plant material, and from endophytes grown in culture. In some symbioses, endophytes had targeted mutations in genes involved in signalling, synthesis of secondary metabolites or in genes of unknown function. Here we describe the processes which guided design of the GeneChip®, the results of quality control assessments of hybridised arrays and considerations concerning statistical analyses of gene expression. Keywords: Affymetrix, GeneChip®, NimbleExpress, Neotyphodium lolii, Epichloë festucae, ryegrass, Lolium perenne, endophyte, symbiosis.
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