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Authors: Manju Yadav 1 ; Suresh Babu 2 and Gitanjali Yadav 1

Affiliations: 1 National Institute of Plant Genome Research, India ; 2 Ambedkar University of Delhi, India

ISBN: 978-989-758-070-3

Keyword(s): Codon Bias, Molecular Evolution, Biostatistics, Organellar Genomics.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Genomics and Proteomics ; Pattern Recognition, Clustering and Classification ; Sequence Analysis

Abstract: Basal angiosperms are the first flowering plants that diverged from ancestral angiosperms, while magnoliids represent the oldest known angiosperms and are considered to retain the characteristics of more primitive angiosperms. Availability of the plastidial genomes from several members of both these classes of plants provides an opportunity to identify and understand large-scale genomic patterns in organelles of early angiosperms. In this work, chloroplast genomes from nine AT-rich basal angiosperm and magnoliid species were analyzed to unearth patterns, if any, in terms of codon bias and to identify factors responsible for the detected patterns. We were able to distinguish nine optimal codons in basal angiosperm chloroplasts and 18 in case of magnoliids. Our findings suggest mutational bias as the most predominant factor shaping codon usage patterns among the genomes examined, while gene expression, hydrophobicity and aromaticity, were found to have a limited but important effect on pattern determination. (More)

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Paper citation in several formats:
Yadav, M.; Babu, S. and Yadav, G. (2015). Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide Insights into Evolution.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 144-149. DOI: 10.5220/0005246301440149

@conference{bioinformatics15,
author={Manju Yadav. and Suresh Babu. and Gitanjali Yadav.},
title={Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide Insights into Evolution},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={144-149},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005246301440149},
isbn={978-989-758-070-3},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide Insights into Evolution
SN - 978-989-758-070-3
AU - Yadav, M.
AU - Babu, S.
AU - Yadav, G.
PY - 2015
SP - 144
EP - 149
DO - 10.5220/0005246301440149

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