Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change

Szitenberg, Amir; Salazar-Jaramillo, Laura; Blok, Vivian C.; Laetsch, Dominik R.; Joseph, Soumi; Williamson, Valerie M.; Blaxter, Mark L.; Lunt, David H.

Abstract

The Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation. Here we sequence 19 genomes, representing five species of key RKN collected from different geographic origins. We show that a hybrid origin that predated speciation within the MIG has resulted in each species possessing two divergent genomic copies. Additionally, the apomictic MIG species are hypotriploids, with a proportion of one genome present in a second copy. The hypotriploid proportion varies among species. The evolutionary history of the MIG genomes is revealed to be very dynamic, with non-crossover recombination both homogenising the genomic copies, and acting as a mechanism for generating divergence between species. Interestingly, the automictic MIG species M. floridensis differs from the apomict species in that it has become homozygous throughout much of its genome.

Citation

Szitenberg, A., Salazar-Jaramillo, L., Blok, V. C., Laetsch, D. R., Joseph, S., Williamson, V. M., …Lunt, D. H. (2017). Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change. Genome Biology and Evolution, 9(10), 2844-2861. https://doi.org/10.1093/gbe/evx201

• Journal Article Type: Article
• Acceptance Date: Sep 22, 2017
• Online Publication Date: Sep 25, 2017
• Publication Date: Oct 1, 2017
• Deposit Date: Oct 15, 2017
• Publicly Available Date: Oct 15, 2017
• Journal: Genome biology and evolution
• Print ISSN: 1759-6653
• Electronic ISSN: 1759-6653
• Publisher: Oxford University Press
• Peer Reviewed: Peer Reviewed
• Volume: 9
• Issue: 10
• Pages: 2844-2861
• DOI: https://doi.org/10.1093/gbe/evx201
• Keywords: Meloidogyne; coverage ratio; genome evolution; phylogenomics; recombination
• Public URL: https://hull-repository.worktribe.com/output/472433
• Publisher URL: https://academic.oup.com/gbe/article/doi/10.1093/gbe/evx201/4237402/Comparative-genomics-of-apomictic-rootknot
• Additional Information: This is a copy of an open access article published in Genome biology and evolution, 2017.