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# Intron/exon architecture is required to understand patterns of variation in nucleotide, codon or amino acid compositions of plant protein-coding genes

Adrienne Ressayre, Pierre P. Montalent, S. Glemin, Laurana Serres Giardi, C Dillmann, Johann Joets

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Adrienne Ressayre, Pierre P. Montalent, S. Glemin, Laurana Serres Giardi, C Dillmann, et al.. Intron/exon architecture is required to understand patterns of variation in nucleotide, codon or amino acid compositions of plant protein-coding genes. SMBE 2015 Annual Conference, Aug 2015, Vienna (AUSTRIA), Austria. http://hal-05267351

HAL Id: hal-05267351

https://hal.inrae.fr/hal-05267351v1

Submitted on 18 Sep 2025

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# Intron/exon architecture is required to understand patterns of variation in nucleotide, codon or amino acid compositions of plant protein-coding genes

A. Ressayre*, P. Montalent*, S. Glémin**, L. Serres-Giardi**,
C. Dillmann*, J. Joets*

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*UMR GQE-Le Moulon, INRA, Université Paris-Sud. France.

**Institut des Sciences de l'Evolution, UMR 5554 CNRS, Université Montpellier II. France.

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## 1. Do introns change nucleotide composition of neighboring coding regions ?

Flowering plant genomes are intron-rich and present large differences in nucleotide composition. The causes of these differences are still debated. Introns are non-coding sequences transcribed but removed during the maturation of the mRNAs. While variation in gene intron number are often associated with variation in coding sequence nucleotide composition, the implication of introns remains to be established. Taking advantage of the large number of plant genes and introns, we sought for variation in nucleotide composition associated with intron presence.

## 2.1. *Arabidopsis* versus rice genomes: large differences for GC content and small differences in intron number

<figure><img src="image_8.png" /><figcaption>Distribution of GC content (proportion of G + C within a sequence) in gene coding regions (CDS) of *Arabidopsis thaliana* (blue) and Rice, *Oryza sativa* (red)</figcaption></figure>

## 3.1. CDS GC content decreases with intron number in both genomes

GC content distributions within intron number classes are outlined using colors varying with intron number from cold (low intron number) to warm (high intron number, legends in each panel). Variations are large in the heterogeneous rice genome, small in the homogeneous genome of *Arabidopsis*.

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## 3.2. Exons present step-gradients in GC content modulated by intron number

Codon GC content according to distance from the starting codon in Rice genes with 3 introns.

At the codon level, the exon rank makes more differences than the distance from starting codon.

<figure><img src="image_10.png" /><figcaption>GC-gradient is better explained by the exon rank</figcaption></figure>

## 2.2. Taking into account gene architecture

In both genomes, we worked on the subset of gene models supported by expression data (full-length cDNA), having both UTRs described and less than 15 introns inserted in coding regions. Genes were sorted according to the number of introns interrupting the coding regions (CDS), hereafter called intron number classes.

We performed comparisons

* between genes within a genome differing by intron numbers (3.1)
* between exons for genes having a given intron number differing by their rank along the gene (3.2)
* between genes having the same number of introns within CDS but differing by the presence/absence of an intron in their 5' or 3' UTRs (3.3)

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## 3.3. Gradients are modified when an intron is present in UTR

In both species, around one quarter of the genes have an intron inserted in their 5' UTR or their 3' UTR. In these subsets of genes, gradients are modified in the extremities hosting the UTR introns.

<caption>Exon gradients in genes with an intron in the 5' UTR</caption>

Intron presence is associated with a marked decrease in first exon GC content. The GC content of the other exons is less affected.

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## 3.4. Exon rank and gene intron number change nucleotide composition

Correlations in GC content between synonymous and non-synonymous sites within coding regions vary between the two genomes and within genomes depending on the scale of observations.

<figure><img src="image_13.png" /><figcaption>GC content standard deviation of as a function of Pearson correlation coefficient.</figcaption></figure>

Correlations between GC content at synonymous and non synonymous sites can be computed on all CDS within the genome, on CDS within intron number classes, and per exon rank along the genes within intron number classes.

<figure><img src="image_14.png" /><figcaption>Whole genome scale (black diamond), intron number classes (solid squares), gene intron number (colors), exon rank (numbers)</figcaption></figure>

Correlations shift from null to negative in *Arabidopsis* and from positive to negative in Rice in internal introns as intron number increases. Negative correlations are at least partially responsible for the decrease in GC content dispersion observed as gene intron number increases in both species.

## 4. Conclusion

In the two studied genomes, patterns of variation in CDS GC content are intricately associated with intron presence.

Patterns found at different scales are consistent among intron number classes within a genome and between the two genomes. They vary with exon rank position along the genes.

Our observations suggest that introns might play a role in GC content patterns of variation in plant genes.