# Dynamics of intron insertion/deletion in plant genes

Adrienne Ressayre, Raouf-Marrounanne Nacer

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Adrienne Ressayre, Raouf-Marrounanne Nacer. Dynamics of intron insertion/deletion in plant genes. Petit Pois Déridé, Jun 2019, Gif-sur-Yvette, France. hal-05298740

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Submitted on 6 Oct 2025

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ET ÉVOLUTION

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# 1. Background and questions: introns in eukaryotes, born to be removed

Introns are non-coding sequences interrupting coding sequences of eukaryote genes

<figure><img src="image_7.png" /><figcaption>**Fig. 1:** Eukaryote gene structure and formation of mRNA. A typical eukaryote protein-coding gene is composed of coding sequence (CDS, red) interrupted by introns (blue) flanked by two UnTranslated Regions (UTRs, brown). Introns are removed during the maturation of mRNAs by the spliceosome, the largest cellular machinery of the cell (300 interacting proteins !). The exons are formed by CDS and/or UTRs.</figcaption></figure>

The evolutionary significance of introns is still unclear. Intron origin and maintenance are thought to be due to semi-neutral processes allowed by the low effective population size of most eukaryote species [1].

<figure><img src="image_8.png" /><figcaption>**Fig. 2:** Reconstruction of intron gains and losses and intron density in eukaryotes. Intron density (intron count per kb) is shown next to terminal taxa and branch width are proportional to intron density. Edges are colored by the relative amount of intron gain and loss (inset, each point corresponds to an edge in the tree). Gain% is the percentage of introns gained, loss% of introns lost within the same lineage. From [2].</figcaption></figure>

To date, introns were observed in all eukaryote species, yet in very different quantities (fig. 2). In Angiosperms, an evolutionary stasis for intron number is described.

Flowering plant genomes are intron-rich. We decided to take advantage of the large number of both plant genes and their associated introns to investigate intron dynamics from an intra-genomic perspective and study the evolutionary time scale at which the intron/exon structure varies.

We have undertaken a survey in Angiosperm species for which genome sequence and annotation are available.

# 2. Within genome intron dynamics: model and data

## BIRTH AND DEATH model WITH CLASSES

We extended Lynch model [1] to describe the dynamics of introns at the genome level :

$$N_0 \Leftrightarrow N_1 \Leftrightarrow \dots \Leftrightarrow N_{c-1} \Leftrightarrow N_c \Leftrightarrow N_{c+1} \Leftrightarrow \dots$$
$$b \qquad b \qquad b \qquad b \qquad b \qquad b$$
$$d \qquad d \qquad d \qquad d \qquad d \qquad d$$

A gene having *c* introns belongs to the *c*th class and can either lose an intron (probability *d*) and moves to the *c* − 1th class, gain an intron (probability *b*) and moves to the *c* + 1th class or remain the same (probability 1 − *b* − *d*).

Let *N*<sub>*c*</sub> be the number of genes having *c* introns, at steady-state :

$$N_{c+1} = \frac{b}{d}N_c = \left(\frac{b}{d}\right)^{c+1}\left(1 - \frac{b}{d}\right)N$$

with *N* the total number of introns of the genome. The expected distribution of gene intron numbers is geometric of parameter *b/d*. As a result, we expect that the logs of the gene counts per intron number classes form a straight line.

## INTRON DISTRIBUTION IN *Arabidopsis* GENES

### A. *thaliana* genome [3]:

- 27 201 protein coding genes,

- 117 237 introns.

For each of the genes, we collected the number of introns in the coding sequences (CDS) and their lengths.

A line can be fitted on intermediate intron number classes. However, the simple model fails to give account for the whole distribution, especially for the heavy tail but also for genes with low intron number.

Simulations were made with (1) birth and death rates depending on CDS lengths but a constant death rate at the gene level and (ii) interference between intron positions (new introns cannot insert too close from existing ones). Taking into account these two features is sufficient to give account for the heavy tail.

<figure><img src="image_9.png" /></figure>

# 3. A preliminary survey in plants: birth-death ratio, intron density and exon proportion

## SAMPLED GENOMES

28 genomes from the Phytozome genomic database [4] were sampled (red points in the phylogeny). All protein coding genes were used.

For each of them, we estimated :

* the birth-death ratio on classes 3 to 15,
* the median intron density at plateau (see below): median of $\frac{nb_i}{L_{CDS}}$ per intron number class for genes having between 15 to 25 introns,
* the genome-wide intron density: $\frac{\sum nb_i}{\sum L_{CDS}}$ over all the locus in the genome,
* the median exon proportion ($\frac{L_{CDS}}{L_{intron}+L_{CDS}}$) at plateau (see below) per intron number classes for genes having between 15 to 25 introns,
* the genome-wide mean exon proportion.

With $L_{CDS}$ for CDS length and $nb_i$ for intron number.

We started our survey recently. The results are preliminary and need further work to be confirmed. Caution is required...

## INTRON DENSITY

<figure><img src="image_10.png" /></figure>

<figure><img src="image_11.png" /></figure>

In all plants, a clear plateau slightly above 7 introns per kb is reached (left). Larger variation for whole genome intron densities (right) are observed.

## BIRTH-DEATH RATIO

### Plant phylogenetic tree

<figure><img src="image_12.png" /></figure>

<figure><img src="image_13.png" /></figure>

In all plants, dots for intermediate intron number classes were found close to the fitted line. In contrast, gene classes with few introns, are often located away from the line, either above as in rice or *Arabidopsis*, or below like in *Vitis vinifera*. Among the causes, annotation problems (genes without introns are less well predicted) might be involved. For example in rice, taking the subsample of gene models supported by expression evidence cancel out the problem. However, changes in birth-death ratio might also be involved.

## CODING SEQUENCE PROPORTION

<figure><img src="image_14.png" /></figure>

The plateau for exon proportion is not well defined in most species. In contrast to intron density, CDS proportion is remarkably variable with a five-fold variation among species. Most of the variation is due to changes in intron lengths between species.

# 4. Conclusion

Intron number distribution in plant genome are roughly geometric, supporting the hypothesis that the intron insertion/deletion process is mainly stochastic and at steady-state, with a balanced birth-death ratio of 0.82 insertion for one deletion in most species.

Variation in intron density are also moderate especially in genes with a high number of introns.

In contrast, variation in intron length is huge, suggesting that a large part of the variation in gene exon/intron structure occurring in plants is variation in intron length rather than in gene intron number.

# 5. References

[1] M. Lynch (2002) Intron evolution as a population-genetic process. PNAS 99: 6119-6123.

[2] M. Csuros and col. (2011) A detailed history of intron dynamics inferred from a global survey of 100 complete genomes. PLoS Comput Biol 7(9): e1002150.

[3] The Arabidopsis Information Resource site. http://www.arabidopsis.org/

[4] https://phytozome.jgi.doe.gov/pz/portal.html