Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue-specific Homologous Genes of Rice and Arabidopsis

Overview

Journal DNA Res

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2008 Oct 2

PMID 18827062

Citations 13

Authors

Pamela Mukhopadhyay

Surajit Basak

Tapash Chandra Ghosh

Affiliations

Soon will be listed here.

Abstract

Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome expression data for both rice and Arabidopsis has made it possible to examine the evolutionary forces in shaping codon usage pattern in both housekeeping and tissue-specific genes in plants. In the present work, we have taken 4065 rice-Arabidopsis homologous gene pairs to study evolutionary forces responsible for codon usage divergence between housekeeping and tissue-specific genes. In both rice and Arabidopsis, it is mutational bias that regulates error minimization in highly expressed genes of both housekeeping and tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes are under strong selective constraint in plants. However, in tissue-specific genes, lowly expressed genes are under stronger selective constraint compared with highly expressed genes. We demonstrated that constraint acting on mRNA secondary structure is responsible for modulating codon usage variations in rice tissue-specific genes. Thus, different evolutionary forces must underline the evolution of synonymous codon usage of highly expressed genes of housekeeping and tissue-specific genes in rice and Arabidopsis.

Citing Articles

Codon usage bias.

Parvathy S, Udayasuriyan V, Bhadana V Mol Biol Rep. 2021; 49(1):539-565.

PMID: 34822069 PMC: 8613526. DOI: 10.1007/s11033-021-06749-4.

Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus.

Wang P, Mao Y, Su Y, Wang J BMC Genomics. 2021; 22(1):781.

PMID: 34717552 PMC: 8557549. DOI: 10.1186/s12864-021-08106-y.

Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations.

Chu D, Wei L BMC Genomics. 2020; 21(1):333.

PMID: 32349669 PMC: 7190201. DOI: 10.1186/s12864-020-6745-3.

Codon usage and codon pair patterns in non-grass monocot genomes.

Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Harikrishna J Ann Bot. 2017; 120(6):893-909.

PMID: 29155926 PMC: 5710610. DOI: 10.1093/aob/mcx112.

The Evolutionary Basis of Translational Accuracy in Plants.

Camiolo S, Sablok G, Porceddu A G3 (Bethesda). 2017; 7(7):2363-2373.

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