Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Abstract

Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges of compatible hosts. Hence, other mechanisms than the accumulation of point mutations are probably involved in the genomic dynamics and plasticity necessary for adaptability. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE content, and used population genomics approach to estimate the mobility of these TEs across 12 geographical isolates, presenting phenotypic variations. The TE content is more abundant in DNA transposons and the distribution of TE copies identity to their consensuses sequence suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed variations across the different isolates. Compared to the M. incognita reference genome, we detected the insertion of some TEs either within genic regions or in the upstream regulatory regions. These predicted TEs insertions might thus have a functional impact. We validated by PCR the insertion of some of these TEs, confirming TE movements probably play a role in the genome plasticity with possible functional impacts.