Abstract
Transposable element activity can be harmful to the host’s genome integrity, but it can also provide selective advantages. One strategy to cope with transposons is epigenetic control through DNA base modifications. We report the non-canonic DNA modification dynamics of fig (Ficus carica L.) by exploiting high-quality genome reference and related N4-methylcytosine (4mC) and N6-methyladenine (6mA) data. Overall, 1.49% of transposon nucleotides showed either 4mC or 6mA modifications: the 4mC/6mA ratio was similar in Class I and Class II transposons, with a prevalence of 4mC, which is comparable to coding genes. Different percentages of 4mC or 6mA were observed among LTR-retrotransposon lineages and sub-lineages. Furthermore, both the Copia and Gypsy retroelements showed higher modification rates in the LTR and coding regions compared with their neighbour regions. Finally, the unconventional methylation of retrotransposons is unrelated to the number of close genes, suggesting that the 4mC and 6mA frequency in LTR-retrotransposons should not be related to transcriptional repression in the adjacency of the element. In conclusion, this study highlighted unconventional DNA modification patterns in fig transposable elements. Further investigations will focus on functional implications, in regards to how modified retroelements affect the expression of neighbouring genes, and whether these epigenetic markers can spread from repeats to genes, shaping the plant phenotype.
Highlights
Transposable elements (TEs) are mobile sequences generally accounting for the largest fraction of the genome’s repetitive component, i.e., the amount of DNA with no obvious functional–regulatory or protein-coding relevance for the organism
The most abundant RE order in plant genomes are long terminal repeats REs (LTR-REs), which are made of the sequences encoding the transposition machinery, including a GAG domain, which is committed to the production of virus-like particles, and a polyprotein involved in the retrotranscription and insertion of the DNA into the genome, flanked by two long terminal sequences, which are identical at the time of insertion
Among the structural analyses we conducted, we explored the abundance of the different unconventional modifications that were found to be associated with the fig transposable elements, revealing that, in general, 4mC seems to be more frequent than 6mA
Summary
Transposable elements (TEs) are mobile sequences generally accounting for the largest fraction of the genome’s repetitive component, i.e., the amount of DNA with no obvious functional–regulatory or protein-coding relevance for the organism. Class I TEs (retrotransposons, REs) use a ‘copy-and-paste’ strategy to transpose, which implies the generation of an RNA intermediate to be retrotranscribed and inserted in the genome; Class II TEs (DNA transposons) move through DNA excision with a ‘cut-and-paste’ mechanism [1] Both types are sub-divided into orders and lineages, based on sequence homology and on whether or not the TEs encode their own transposition machinery. The most abundant RE order in plant genomes are long terminal repeats REs (LTR-REs), which are made of the sequences encoding the transposition machinery, including a GAG domain, which is committed to the production of virus-like particles, and a polyprotein involved in the retrotranscription and insertion of the DNA into the genome, flanked by two long terminal sequences, which are identical at the time of insertion These kinds of REs make up the main portion of many genomes [2,3], and are subdivided into two major superfamilies, called Gypsy and Copia, that differ in the position of the protein domains within their encoded polyprotein [1]. Genomes have evolved several layers of defense to contain TE activity
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