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United States Department of Agriculture

Agricultural Research Service

Title: THE REHYDRATION TRANSCRIPTOME: TRANSLATOME OF TORTULA RURALIS: A COMBINED BIOINFORMATICS AND MICROARRAY APPROACH TO INVESTIGATE THE DESICCATION RESPONSE OF TOLERANT MOSSES.

Authors
item Oliver, Melvin
item Payton, Paxton
item Dowd, Scot
item Mauget, Steven

Submitted to: Annual International Meeting for Moss Research
Publication Type: Abstract Only
Publication Acceptance Date: September 11, 2004
Publication Date: September 15, 2004
Citation: Oliver, M.J., Payton, P.R., Dowd, S.E., Mauget, S.A. 2004. The rehydration transcriptome: translatome of tortula ruralis: a combined bioinformatics and microarray approach to investigate the desiccation response of tolerant mosses[Abstract]. Annual International Meeting for Moss Research.

Technical Abstract: Gene expression studies of desiccation-tolerant plants are limited to only a few species one of which is the desiccation-tolerant moss Tortula ruralis. From an evolutionary standpoint T. ruralis represents the primitive mechanism for tolerance of dehydration and thus an understanding of its genome level response has important implications for plant biology and agriculture. We have demonstrated that the alteration in gene expression in response to desiccation in this plant occurs following rehydration, in large part as the result of a change in translational controls. In addition, during drying certain transcripts, encoding rehydrins, are sequestered in messenger ribonucleoprotein particles (mRNPs) for storage in the dried state. To characterize the extent and importance of translational versus transcriptional events we have taken a combined genomics and bioinformatics approach to analyze gene expression in response to desiccation. A Tortula EST collection, 10,368 primary ESTs (9,159 passing quality controls), has been established and a total of 5.93 million nucleotides have been submitted to Genbank. The EST collection was established from a non-normalized 2h rehydrated gametophyte cDNA library, the non-normalized library was used in order to gain an appreciation of individual transcript abundance within the transcriptome. The 9,159 ESTs formed 7,272 contigs which in turn reduced to 5,563 clusters (a cluster is an assembly of ESTs that could represent transcripts from the same gene but either from separate alleles or alternate splice forms). Even though the ESTs derive from a non-normalized library 96.5% of the clusters still have 5 or fewer EST members. Consensus cluster sequences were subjected to a Blastx search and annotated according to the degree of similarity to known genes. Of he 5,563 clusters, 3,321 (59.7 %) could be matched to known sequences and 2,242 (40.3%) were categorized as unknowns. Functional classification of the Tortula rehydration transcripts were achieved using Gene Ontology (GO) and KEGG pathway mapping strategies. The results of these analyses will be discussed in context and are also available at our website, http://199.133.147.108/bryobase/. The 5,563 clusters formed the basis of a Tortula 'uni-cluster' cDNA microarray that we have used to complete a comprehensive expression profile for a desiccation:rehydration cycle. Using both total and polysomal mRNA transcripts for the source of cDNA probes we have evaluated the relative importance of transcript abundance and recruitment in the response for each represented gene. The data we will present, coupled with the bioinformatics, offers a unique picture of the transcriptome and translatome level response of T. ruralis to severe stress.

Last Modified: 7/25/2014
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