EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes

Brenner, E. D., Katari, M. S., Stevenson, D. W., Rudd, S. A., Douglas, A. W., Moss, W. N., Twigg, R. W., Runko, S. J., Stellari, G. M., McCombie, W. R., Coruzzi, G. M. (2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics, 6. p. 143. ISSN 1471-2164

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URL: http://www.ncbi.nlm.nih.gov/pubmed/16225698
DOI: 10.1186/1471-2164-6-143

Abstract

Background: Ginkgo biloba L. is the only surviving member of one of the oldest living seed plant groups with medicinal, spiritual and horticultural importance worldwide. As an evolutionary relic, it displays many characters found in the early, extinct seed plants and extant cycads. To establish a molecular base to understand the evolution of seeds and pollen, we created a cDNA library and EST dataset from the reproductive structures of male (microsporangiate), female (megasporangiate), and vegetative organs (leaves) of Ginkgo biloba. Results: RNA from newly emerged male and female reproductive organs and immature leaves was used to create three distinct cDNA libraries from which 6,434 ESTs were generated. These 6,434 ESTs from Ginkgo biloba were clustered into 3,830 unigenes. A comparison of our Ginkgo unigene set against the fully annotated genomes of rice and Arabidopsis, and all available ESTs in Genbank revealed that 256 Ginkgo unigenes match only genes among the gymnosperms and non-seed plants - many with multiple matches to genes in non-angiosperm plants. Conversely, another group of unigenes in Gingko had highly significant homology to transcription factors in angiosperms involved in development, including MADS box genes as well as post-transcriptional regulators. Several of the conserved developmental genes found in Ginkgo had top BLAST homology to cycad genes. We also note here the presence of ESTs in G. biloba similar to genes that to date have only been found in gymnosperms and an additional 22 Ginkgo genes common only to genes from cycads. Conclusion: Our analysis of an EST dataset from G. biloba revealed genes potentially unique to gymnosperms. Many of these genes showed homology to fully sequenced clones from our cycad EST dataset found in common only with gymnosperms. Other Ginkgo ESTs are similar to developmental regulators in higher plants. This work sets the stage for future studies on Ginkgo to better understand seed and pollen evolution, and to resolve the ambiguous phylogenetic relationship of G. biloba among the gymnosperms.

Item Type: Paper
Uncontrolled Keywords: SEED PLANT PHYLOGENY seed plant phylogeny MADS-BOX GENES MADS-Box genes MADS box genes EXTANT GYMNOSPERMS extand gymnosperms COP9 SIGNALOSOME signalosome ARABIDOPSIS arabidopsis EXPRESSION EVOLUTION FAMILY PROTEINS PHOTOMORPHOGENESIS photomorphogenesis microsporangiate megasporangiate
Subjects: bioinformatics > genomics and proteomics > databases > database construction
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
bioinformatics > genomics and proteomics > databases > databases
CSHL Authors:
Communities: CSHL labs > McCombie lab
Depositing User: CSHL Librarian
Date Deposited: 13 Jan 2012 19:27
Last Modified: 11 Apr 2013 19:50
PMCID: PMC1285361
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22542

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