Comparative Genomics Reveals Novel Target Genes Towards Specific Control of Plant-Parasitic Nematodes

Abstract

Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

A Meloidogyne incognita C‐type lectin effector targets plant catalases to promote parasitism

“…In the genome of M. incognita (v.2; Blanc‐Mathieu et al ., 2017; Grynberg et al ., 2020), we identified 59 proteins containing the Pfam CTLD (PF00059), consistent with the 57 CTLDs previously identified in the M. incognita genome (v.1; Abad et al ., 2008; Bauters et al ., 2017). Of these, 31 putative secreted proteins were predicted based on the presence of a predicted N‐terminal signal peptide for secretion and an absence of predicted transmembrane region.…”

“…Protein annotations, including Pfam domains, and nematode orthologues, were obtained from Grynberg et al . (2020). CTLD predictions were verified using Simple Modular Architecture Research Tool (S mart , normal mode; http://smart.embl.de/; Schultz et al ., 2000).…”

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest

“…In M . incognita , almost 23% of the genes have been described as specific to plant–parasite species, without any recognizable homology in other species (Grynberg et al, 2020 ). Interestingly, TE movements can be involved in the emergence of species or genus‐specific “orphan” genes (Jin et al, 2019 ; Ruiz‐Orera et al, 2015 ; Wu & Knudson, 2018 ).…”

TheAphelenchoidesgenomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes

“…Although numerous HGT genes have been identified and documented in different nematodes, research on the timing and subsequent maintenance of these genes, and why their copy numbers differ, has been restricted to a few PPN clades 15 .…”

“…Some of these PPN-specific genes are known to be acquired from bacteria or fungi through horizontal gene transfer (HGT) 14 , giving nematodes the ability to adapt to different environments 14 . Although numerous HGT genes have been identified and documented in different nematodes, research on the timing and subsequent maintenance of these genes, and why their copy numbers differ, has been restricted to a few PPN clades 15 .…”