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Title: An expressed sequence tag (EST) set from Citrus sinensis L. Osbeck whole seedings and the implications of further perennial source investigations

item Bausher, Michael
item Shatters, Robert - Bob
item Dang, Phat
item Chaparro, Jose
item Hunter, Wayne
item Niedz, Randall

Submitted to: Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2003
Publication Date: 7/1/2003
Citation: Bausher,M.G., Shatters,R.G., Dang,P.M., Chaparro,J.X., Hunter,W.B., Niedz,R.P. 2003. An express sequence tag (EST) set from Citrus sinensis L. Osbeck whole seedlings and the implications of further perennial source investigations. Plant Science. 165(2):415-422.

Interpretive Summary: This report describes the largest study of sweet orange expressed sequence tags (EST) that has been publicly released thus far. ESTs are sequence information, which is a global representation of the transcription of RNA and the time the analysis, was made. A total of 3483 unique genes were found in a cDNA library made from Citrus sinensis (Ridge Pineapple sweet orange) whole seedling RNA. In this work we found that Citrus transcription is much different then other crops and even from other woody species such as grape and pine. Many of the most abundant genes identified matched with those from other woody species such as peach, pine and rubber trees. Sequence data was compared to known databases of sequence information from crop and non-crop plants. Of the information found over a third of the genes sequence represent possible gene entities, which are not known by comparison to the databases at The National Center for Biotechnology Information (NCBI). The results of this work have been release to the dbEST at NCBI for use by the community at large. We and other groups will use this data for comparisons of citrus plant reactions to environmental, insect and disease interactions on citrus production. This work will provide information for use in the development of diagnostics for new variety development using marker assisted selection and fingerprinting molecular changes which equate to changes in production practices and their probability of changing cropping efficiencies such as water, pesticide and nutrient management.

Technical Abstract: There are a number of large-scale single past cDNA sequencing entries from annual plants in the NCBI database. However, NCBI has very little information on perennial species. As of November 2002 of the 1,100,000 entries less than 5 percent of the publicly available sequence information represent these plants. Because perennials are unique in their ability to survive pathological and environmental onslaughts without the ability of short cycle reproduction as an escape mechanism, these plants represent a reservoirs of EST information most likely not found in annual species. Tree genomes, especially Citrus, contain genes that encode proteins involved in important traits including- essential oil production, fruit production, dormancy, apomixis, and evergreen and deciduous types. ESTs are an excellent tool to identify and catalog many of the genes responsible for these important metabolic pathways in perennial trees species like Citrus. We describe here a set of ESTs produced from mRNA isolated from 180-day-old whole immature sweet orange Citrus seedlings. From this library, 6758 were sequenced and using several bioinformatics programs producing 922 unique contig composite assemblies with 2561 unique singlets. Based on BLAST comparisons, the data contains genes involved in a number of biochemical pathways, but approximately 30 percent have no significant homology to current dbEST entries. The high level of novel sequences in this database set is evidence that perennial trees are an important source of genetic diversity not duplicated in typical annual model plant species.