EST analysis in Ginkgo biloba

An assessment of conserved developmental regulators and gymnosperm specific genes

Eric D. Brenner, Manpreet S. Katari, Dennis W. Stevenson, Stephen A. Rudd, Andrew W. Douglas, Walter N. Moss, Richard W. Twigg, Suzan J. Runko, Giulia M. Stellari, Richard W. McCombie, Gloria M. Coruzzi

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number143
JournalBMC Genomics
Volume6
DOIs
StatePublished - Oct 15 2005

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Gymnosperms
Ginkgo biloba
Expressed Sequence Tags
Genes
Seeds
Pollen
Gene Library
Developmental Genes
Angiosperms
Nucleic Acid Databases
Arabidopsis

ASJC Scopus subject areas

  • Medicine(all)
  • Biotechnology
  • Genetics

Cite this

EST analysis in Ginkgo biloba : An assessment of conserved developmental regulators and gymnosperm specific genes. / Brenner, Eric D.; Katari, Manpreet S.; Stevenson, Dennis W.; Rudd, Stephen A.; Douglas, Andrew W.; Moss, Walter N.; Twigg, Richard W.; Runko, Suzan J.; Stellari, Giulia M.; McCombie, Richard W.; Coruzzi, Gloria M.

In: BMC Genomics, Vol. 6, 143, 15.10.2005.

Research output: Contribution to journalArticle

Brenner, ED, Katari, MS, Stevenson, DW, Rudd, SA, Douglas, AW, Moss, WN, Twigg, RW, Runko, SJ, Stellari, GM, McCombie, RW & Coruzzi, GM 2005, 'EST analysis in Ginkgo biloba: An assessment of conserved developmental regulators and gymnosperm specific genes', BMC Genomics, vol. 6, 143. https://doi.org/10.1186/1471-2164-6-143
Brenner, Eric D. ; Katari, Manpreet S. ; Stevenson, Dennis W. ; Rudd, Stephen A. ; Douglas, Andrew W. ; Moss, Walter N. ; Twigg, Richard W. ; Runko, Suzan J. ; Stellari, Giulia M. ; McCombie, Richard W. ; Coruzzi, Gloria M. / EST analysis in Ginkgo biloba : An assessment of conserved developmental regulators and gymnosperm specific genes. In: BMC Genomics. 2005 ; Vol. 6.
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