Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii

Weng, Jing-Ke, Tanurdzic, Milos and Chapple, Clint (2005) Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii. BMC Genomics, 6 85.1-85.13. doi:10.1186/1471-2164-6-85


Author Weng, Jing-Ke
Tanurdzic, Milos
Chapple, Clint
Title Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii
Formatted title
Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2005-06-01
Sub-type Article (original research)
DOI 10.1186/1471-2164-6-85
Open Access Status DOI
Volume 6
Start page 85.1
End page 85.13
Total pages 13
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
 The lycophyte Selaginella moellendorffii is a member of one of the oldest lineages of vascular plants on Earth. Fossil records show that the lycophyte clade arose 400 million years ago, 150-200 million years earlier than angiosperms, a group of plants that includes the well-studied flowering plant Arabidopsis thaliana. S. moellendorffii has a genome size of approximately 100 Mbp, as small or smaller than that of A. thaliana. S. moellendorffii has the potential to provide significant comparative information to better understand the evolution of vascular plants. We sequenced 2181 Expressed Sequence Tags (ESTs) from a S. moellendorffii cDNA library. One thousand three hundred and one non-redundant sequences were assembled, containing 291 contigs and 1010 singletons. Approximately 75% of the ESTs matched proteins in the non-redundant protein database. Among 1301 clusters, 343 were categorized according to Gene Ontology (GO) hierarchy and were compared to the GO mapping of A. thaliana tentative consensus sequences. We compared S. moellendorffii ESTs to the A. thaliana and Physcomitrella patens EST databases, using the tBLASTX algorithm. Approximately 60% of the ESTs exhibited similarity with both A. thaliana and P. patens ESTs; whereas, 13% and 1% of the ESTs had exclusive similarity with A. thaliana and P. patens ESTs, respectively. A substantial proportion of the ESTs (26%) had no match with A. thaliana or P. patens ESTs. We discovered 1301 putative unigenes in S. moellendorffii. These results give an initial insight into its transcriptome that will aid in the study of the S. moellendorffii genome in the near future.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Biological Sciences Publications
 
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Created: Tue, 09 Apr 2013, 08:08:50 EST by Gail Walter on behalf of School of Biological Sciences