Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide Insights into Evolution

Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide Insights into Evolution

6 Pages · 2015 · 355 KB · English

Piper cenocladum,. Chloranthus spicatus and Illicium oligandrum. Details of these nine genomes are provided in. Table1. Only those sequences were .. (Grant No. BT/BI/04/069/2006). REFERENCES. Bernardi G, Berbardi G 1986 Compositional constraints and genome evolution. J Mol Evol 24:1-11.

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Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide Insights into Evolution Manju Yadav 1, Suresh Babu 2 and Gitanjali Yadav 1 1National Institute of Plant Genome Resear ch, Aruna Asaf Ali Marg, New Delhi, India 2School of Human Ecology, Ambedkar University of Delhi, New Delhi, India Keywords: Codon Bias, Molecular Evolution, Biostatistics, Organellar Genomics Abstract: Basal angiosperms are the first flowering plants that diverged from ancestral angiosperms, while magnoliids represent the oldest known angiosperms and are consider ed to retain the characteristics of more primitive angiosperms Availability of the pl astidial genomes from several members of both these classes of plants provides an opportunity to identify and understand larg escale genomic patterns in organelles of early angiosperms In this work, chloroplast genomes from nine ATrich basal angiosperm and magnoliid species were analyzed to unearth pa tterns, 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 ge nomes examined, while gene expression, hydrophobicity and aromaticity, were found to have a limited but important effect on pattern determination 1 INTRODUCTION Chloroplasts, initially originated by the process of endosymbiosis from cyanobacteria about 115 billion years ago, are the most important cellular organelles of autotrophs On account of their small size, high copy number, conservation and extensive characterization at the molecular level, a large number of completely sequenced plastid genomes are now publicly available The angiosperms, or flowering plants, are one of the major groups of extant seed plants and arguably the most diverse major extant plant group on the planet, with at least 260,000 living species classified in 453 families Basal angiosperms represent the first flowering plants that branched off from ancestral angiosperms at su ccessive occasions before the appearance of the "tru e" dicots Eudicots, and comprise of distinct evolutionary groups, of which the first three to diverge were Amborellales, Nymphaeales and Austrobaileyales (Soltis & Soltis 2004) Magnoliids, on the other hand, are the oldest known angiosperms, represented by a heterogenous group that are neither eudicotyledons nor monocotyledons, and are considered to retain the characteristics of more primitive angiosperms Economically important products derived from magnoliids include edible fruits, spices such as black and white pepper Piper nigrum, cinnamon Cinnamomum verum , and camphor Cinnamomum camphora (Soltis et al, 2005) The magnoliid clade contains most of those lineages that were typically referred to as "primitive angiosperms" in earlier classification schemes (Cronquist, 1988) This work was undertaken with the aim of conducting a genomewide survey of codon usage patterns across the available chloroplast genomes of Basal Angiosperms and Magnoliids The term ‘codon usage bias’ describes the unbalanced usage of synonymous codons during translation of a given genome Codon usage can vary between species and also between different genomic regions of the same species, so there is much fluctuation observed in genes and genomes Several factors support this phenomenon, such as genome composition bias (Bernardi and Berbardi, 1986), natural translation selection (Ikemura, 1985), hydrophobhicity and aromaticity Previous codon usage studies demonstrate that codon usage bias is a complex phenomenon, which involves various biological factors such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation 144 Yadav M, Babu S and Yadav G Patterns of Codon Usage in Plastidial Genomes of Ancient Plants Provide

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