Chloroplast gene expression level is negatively correlated with evolutionary rates and selective pressure while positively with codon usage bias in Ophioglossum vulgatum L

Abstract

Background Characterization of the key factors determining gene expression level has been of significant interest. Previous studies on the relationship among evolutionary rates, codon usage bias, and expression level mostly focused on either nuclear genes or unicellular/multicellular organisms but few in chloroplast (cp) genes. Ophioglossum vulgatum is a unique fern and has important scientific and medicinal values. In this study, we sequenced its cp genome and transcriptome to estimate the evolutionary rates (dN and dS), selective pressure (dN/dS), gene expression level, codon usage bias, and their correlations. Results The correlation coefficients between dN, dS, and dN/dS, and Transcripts Per Million (TPM) average values were -0.278 (P = 0.027 < 0.05), -0.331 (P = 0.008 < 0.05), and -0.311 (P = 0.013 < 0.05), respectively. The codon adaptation index (CAI) and tRNA adaptation index (tAI) were significantly positively correlated with TPM average values (P < 0.05). Conclusions Our results indicated that when the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was stronger. We provided evidence from cp gene data which supported the E-R (E stands for gene expression level and R stands for evolutionary rate) anti-correlation.

Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes

“…The CAI, with values ranging from 0 to 1, is another effective measure of codon usage bias. The higher the CAI value, the better the adaptability of the sequence [ 6 ]. CAI value approaching 1 indicates a strong codon bias [ 3 ].…”

“…Recent studies have revealed that specific synonymous codon usage biases affect protein folding [ 4 , 5 ]. When the gene expression level was higher, the evolutionary rates and selective pressure were lower, but the codon usage bias was strong [ 6 ]. Except for tryptophan (Trp) and methionine (Met), all amino acids are encoded by at least two synonymous codons [ 7 ].…”

Organellar phylogenomics of Ophioglossaceae fern genera

“…A tentative hypothesis is also provided here to explain these interesting patterns in Ophioglossoideae by considering its mixotrophic lifestyle and huge nuclear genomes. In addition, evolutionary rate heterogeneity and AT-biased codon usages in this fern lineage are likely associated with gene expression levels ( Hao et al., 2022a ). Therefore, future investigation of rate statics and transcriptomic profiles is also critical to study comparative genomics in Ophioglossoideae.…”

Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression

“…[ 49 ] The correlation between AAG or GCG repeats and mRNA levels may be due to codon usage bias, which has verified a positive correlation with expression levels. [ 50 ] The dominant amino acids coded by AAG and GCG repeats and their proportion ebb and flow as TPM max increases in the P. malipoense transcriptome but not for TPM CV (Figure 4d,e ) implying that the expression regulation effect of triplet repeats within CDS was not tissue‐specific and may be linked with codon usage or features of homopolypeptides. The alternative polyadenylation (APA), a universal mechanism of posttranscriptional regulation, [ 51 ] could explain the correlation between A repeats in the 3’‐UTR and high expression potential and tissue‐specificity.…”