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Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii
BACKGROUND: 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 flowe...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2005
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184070/ https://www.ncbi.nlm.nih.gov/pubmed/15938755 http://dx.doi.org/10.1186/1471-2164-6-85 |
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author | Weng, Jing-Ke Tanurdzic, Milos Chapple, Clint |
author_facet | Weng, Jing-Ke Tanurdzic, Milos Chapple, Clint |
author_sort | Weng, Jing-Ke |
collection | PubMed |
description | BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. |
format | Text |
id | pubmed-1184070 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-11840702005-08-11 Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii Weng, Jing-Ke Tanurdzic, Milos Chapple, Clint BMC Genomics Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. BioMed Central 2005-06-06 /pmc/articles/PMC1184070/ /pubmed/15938755 http://dx.doi.org/10.1186/1471-2164-6-85 Text en Copyright © 2005 Weng et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Weng, Jing-Ke Tanurdzic, Milos Chapple, Clint Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii |
title | Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii |
title_full | Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii |
title_fullStr | Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii |
title_full_unstemmed | Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii |
title_short | Functional analysis and comparative genomics of expressed sequence tags from the lycophyte Selaginella moellendorffii |
title_sort | functional analysis and comparative genomics of expressed sequence tags from the lycophyte selaginella moellendorffii |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1184070/ https://www.ncbi.nlm.nih.gov/pubmed/15938755 http://dx.doi.org/10.1186/1471-2164-6-85 |
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