Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs

Scientific Reports
Hui SongZhibiao Nan

Abstract

The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth. Additionally, expression breadth was positively correlated with polypeptide length, but there was no correlation between gene expression and polypeptide length. Inferred selective pressure was also negatively correlated with both gene expression and expression breadth in all one-to-one orthologs, while positively but non-significantly correlated with gene expression in sequences with signatures of positive selection. Gene expression levels and expression breadth were significantly higher for single-copy genes than for multiple-copy genes. Similarly, the gene expression and expression breadth in sequences with signatures of purifying selection were higher than t...Continue Reading

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Citations

Jun 4, 2019·Plant Cell Reports·Raju NainiVudem Dashavantha Reddy
May 12, 2019·Molecular Genetics and Genomics : MGG·Hui SongGuofeng Yang
Apr 5, 2019·BMC Plant Biology·Nobuyuki Mizuno, Yasuo Yasui
Oct 20, 2018·BMC Plant Biology·Hui SongJuan Sun
Jan 19, 2021·Mitochondrial DNA. Part B, Resources·Zhiwen ChenCorrinne E Grover
Mar 13, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Shuwei DongHui Song
Nov 26, 2021·Molecular Biology Reports·Sujatha Thankeswaran ParvathyVijaipal Bhadana

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Methods Mentioned

BETA
RNA-seq

Software Mentioned

JMP
CodonW
PAML
OrthoMCL
Bowtie
gplots
CRAN
R
Trinity
SAM

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