DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements

Abstract

Background: Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history.

Results: Our analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes.

Conclusions: Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes.

Keywords: Comparative genomics; DNA methylation; GC content; MULEs; Molecular evolution; New genes; Oryza; Recombination rate.

Fig. 1

Number of non-autonomous MULEs across the 11-genome dataset. Non-autonomous MULEs were divided into two categories, genic-MULEs and nongenic-MULEs. The proportion of genic-MULEs among non-autonomous MULEs is shown in blue and the proportion of nongenic-MULEs is shown in red

Fig. 2

Number of non-autonomous MULEs across the 11-genome dataset. Based on the presence and absence of non-autonomous MULEs in the phylogenetic tree of ten Oryza and one Leersia species and the evolutionary parsimony principle, we inferred the number of non-autonomous MULEs for each external species and internal branch across the ten Oryza and one Leersia phylogenetic tree

Fig. 3

GC-content distributions of non-TE genes, MULE-derived putative genes, MULE internal sequences of MULE-derived putative genes, and the parental sequences of MULE-derived putative genes. Density distribution of GC content of non-TE genes (in purple), MULE-derived putative genes (in red), MULE internal sequences of MULE-derived putative genes (in blue), and the parental sequences of MULE-derived putative genes (in green). MULE-derived putative genes, especially the parts derived from MULEs, have a much higher GC content than non-TE genes across the 11 genome dataset (Wilcoxon rank sum test, P value < 2.2e-16). The GC content of MULE-derived putative genes is less than that of the MULE internal sequences of MULE-derived putative genes which is less than that of the parental sequences of MULE-derived putative genes (Wilcoxon rank sum test, P < 0.05, except for the comparison of MULE-derived putative genes and MULE internal sequences in L. perrieri and O. brachyantha)

Fig. 4

Methylation level distribution of parental sequences of MULE-derived putative genes and randomly selected non-TE genic regions across the O. sativa ssp. japonica genome. A density distribution of the methylation levels of parental sequences of MULE-derived putative genes (green) and that of randomly selected non-TE genic regions across the O. sativa ssp. japonica genome (red) in three cytosine contexts. The figure shows that the parental sequences of MULE-derived putative genes have lower methylation levels compared with non-TE genic regions

Fig. 5

Methylation levels of genic-MULEs identified in the O. sativa ssp. japonica genome change over evolutionary time. a The methylation levels of MULE internal sequences with three evolutionary ages (Asian genic-MULEs, AA genic-MULEs, and AB genic-MULEs) in three cytosine contexts (CG context in red, CHG context in blue, and CHH context in green). Methylation levels of MULE internal sequences increase over time in three cytosine contexts (Wilcoxon rank sum test, P < 0.05, except the comparison of AA genic-MULEs and AB genic-MULEs in the CHH context, P = 0.07087). b A sliding window analysis of the average methylation level in 500-bp upstream flanking sequences (yellow), left TIR (green), internal sequence (red), right TIR (purple), and 500-bp downstream flanking sequences (blue) of genic-MULEs with three evolutionary ages in three cytosine contexts. Methylation levels vary across the different regions of MULEs. Methylation levels of the TIR regions in the CHH context decrease over evolutionary time (Wilcoxon rank sum test, P < 0.0501)

Fig. 6

Validation of dynamic methylation patterns of genic-MULEs. a Distributions of TE content inside the genic-MULE internal sequences with three evolutionary ages. This analysis shows that older genic-MULEs have significantly lower or similar TE content compared with younger elements (Wilcoxon rank sum test, P = 3.006e-5 for Asian & AA, and P = 0.004681 for Asian & AB). b Density distribution of TIR similarity of genic-MULEs with three evolutionary ages in each domesticated Oryza species (O. sativa ssp. japonica, O. sativa ssp. indica, and O. glaberrima) and their wild progenitors (O. nivara, O. rufipogon, and O. barthii, respectively). TIR similarity decreases over time (Wilcoxon rank sum test, P < 0.003). **: P < 0.01, ***: P < 0.001

Fig. 7

Mean number of 24-nucleotide small RNAs uniquely mapping to genic-MULE internal sequences and TIRs in the O. sativa ssp. japonica genome. a Mean number of 24-nucleotide small RNAs uniquely mapping to genic-MULE internal sequences in nine tissues and one wild-type (wt) and two RNA interference lines. The number of 24-nucleotide small RNAs increases over time (t-test, P < 0.002), which is consistent with the change in methylation levels in genic-MULE internal sequences over time. b Mean number of 24-nucleotide small RNAs uniquely mapping to genic-MULE TIRs. The number of 24-nucleotide small RNAs decreases over time (t-test, P < 0.004), which is consistent with the dynamics of methylation levels in genic-MULE TIR regions over time

Fig. 8

Expression profile of MULE-derived putative genes in O. sativa ssp. japonica. a Proportion of MULE-derived putative genes expressed across seven tissues with different evolutionary ages (Asian genic-MULEs, AA genic-MULEs, AB genic-MULEs, and all genic-MULEs). A higher proportion of the MULE-derived putative genes are expressed in mature pollen compared with all annotated Oryza genes (Fisher exact test, *P = 0.0183 for Asian MULE-derived putative genes, ***P = 0.0006463 for AA MULE-derived putative genes, **P = 0.001295 for all MULE-derived putative genes). b Heatmap of relative gene expression levels for MULE-derived putative genes versus all annotated Oryza genes. These data suggest that MULE-derived putative genes, especially those associated with younger genic-MULEs, are highly expressed in mature pollen compared with all annotated Oryza genes (note that the data size of expressed MULE-derived putative genes from AB genic-MULEs is very small, with only 17 genes detected, which might not, therefore, represent a statistically significant pattern)