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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.

Authors

Amir Szitenberg

Laura Salazar-Jaramillo

Vivian C. Blok

Dominik R. Laetsch

Soumi Joseph

Valerie M. Williamson

Mark L. Blaxter



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.

Journal Article Type Article
Publication Date Oct 1, 2017
Journal Genome biology and evolution
Print ISSN 1759-6653
Electronic ISSN 1759-6653
Publisher Oxford University Press (OUP)
Peer Reviewed Peer Reviewed
Volume 9
Issue 10
Pages 2844-2861
APA6 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
DOI https://doi.org/10.1093/gbe/evx201
Keywords Meloidogyne; coverage ratio; genome evolution; phylogenomics; recombination
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.

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Copyright Statement
© The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.







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