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United States Department of Agriculture

Agricultural Research Service

Title: Bioinformatic Analysis of the Rehydration Transcriptome of Turtula Ruralis a Desiccation Tolerant Bryophyte

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

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: July 20, 2004
Publication Date: July 20, 2004
Citation: Oliver, M.J., Dowd, S.E., Zaragoza, J., Mauget, S.A., Payton, P.R. 2004. Bioinformatic analysis of the rehydration transcriptome of turtula ruralis a desiccation tolerant bryophyte [abstract]. American Society of Plant Biologists Annual Meeting. Paper No. 156.

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. To assess the transcriptome in the crucial phases of recovery from desiccation we isolated 10,368 cDNA clones from a non-normalized rehydration library (representative of the transcriptomes of a large population of individual gametophytes). The 10,368 clones form the basis of an EST collection following high-throughput 5' directional sequencing. Of the original 10,368 clones, 9,159 sequences were generated that passed quality control parameters representing some 5,934,527 nucleotides of the Tortula transcriptome. These ESTs generated 5,563 contigs (derived from identical transcripts), which in turn form 4,901 clusters (members may derive from the same gene yet represent different transcripts or alleles). Of the 5,563 contigs 3,321 matched known sequences in Genbank whilst the remaining 2,242 or 40.3% did not. Functional classification was achieved by using an InterProScan protocol to place the 3,321 matched Tortula contigs into the Gene Ontology (GO) hierarchy. 2,203 generate GO mappings for the Tortula contigs. The contigs were also functionally characterized to the KEGG biochemical pathways. These analyses are key to our understanding of the processes involved in the recovery from desiccation and their role in desiccation tolerance.

Last Modified: 7/30/2014
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