Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant‐parasitic nematode Meloidogyne incognita

• Published in: Molecular ecology Vol. 28; no. 10; pp. 2559 - 2572
• Main Authors: Castagnone‐Sereno, Philippe, Mulet, Karine, Danchin, Etienne G. J., Koutsovoulos, Georgios D., Karaulic, Mégane, Da Rocha, Martine, Bailly‐Bechet, Marc, Pratx, Loris, Perfus‐Barbeoch, Laetitia, Abad, Pierre
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01-05-2019; Wiley
• Subjects: Adaptation; adaptive evolution; Animals; array comparative genomic hybridization; Asexual reproduction; Biological Evolution; Copy number; DNA Copy Number Variations - genetics; Environmental changes; Environmental conditions; Environmental Sciences; Evolution & development; Evolution, Molecular; experimental evolution; gene copy number variations; Genetic diversity; Genomes; Genomics; Genotypes; Herbivores; Host plants; Hybridization; Life Sciences; Meloidogyne incognita; Nematodes; parthenogenesis; Pest resistance; Plant Diseases; Plant Physiological Phenomena - genetics; Plant Roots - genetics; Plants - genetics; Plants - parasitology; Reproduction (biology); Reproduction, Asexual - genetics; root‐knot nematodes; Species; Tylenchoidea - genetics; Tylenchoidea - pathogenicity; Tylenchoidea - physiology; gene copy number variations; parthenogenesis; experimental evolution; adaptive evolution; array comparative genomic hybridization; root-knot nematodes
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.15095

Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms, and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root‐knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant‐parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environmental constraints, for example, resistant hosts. Here, we used a genomewide comparative hybridization strategy to evaluate variations in gene copy numbers between genotypes of M. incognita resulting from two parallel experimental evolution assays on a susceptible vs. resistant host plant. We detected gene copy number variations (CNVs) associated with the ability of the nematodes to overcome resistance of the host plant, and this genetic variation may reflect an adaptive response to host resistance in this parthenogenetic species. The CNV distribution throughout the nematode genome is not random and suggests the occurrence of genomic regions more prone to undergo duplications and losses in response to the selection pressure of the host resistance. Furthermore, our analysis revealed an outstanding level of gene loss events in nematode genotypes that have overcome the resistance. Overall, our results support the view that gene loss could be a common class of adaptive genetic mechanism in response to a challenging new biotic environment in clonal animals.