Genome Expression Dynamics Reveal the Parasitism Regulatory Landscape of the Root-Knot Nematode Meloidogyne incognita and a Promoter Motif Associated with Effector Genes

Abstract

Root-knot nematodes (genus Meloidogyne) are the major contributor to crop losses caused by nematodes. These nematodes secrete effector proteins into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effector genes. The details of how root-knot nematodes regulate transcription remain sparse. Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands, providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus, and we name it Mel-DOG. Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode and identify a new set of candidate effector genes that will guide future functional analyses.

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

“…This is a considerable enrichment over the genome as a whole (~14%, p value = 1.05e-26). The more copies of the motif in the promoter the more likely the corresponding gene encodes a signal peptide, analogous to other unrelated sequences but conceptually similar effector promoter motifs identified in other plant-parasitic nematode species [ 40 , 48 , 49 ]. Of those genes with two copies of the motif in their promoter, 60% encode a signal peptide.…”

“…Promoter motif enrichment analyses were carried out as previously described for cyst and root knot nematodes [ 48 , 49 ]. In brief, the 1500 bp promoter regions of 83 putative homologues of genes with validated expression in either gland cell of plant-parasitic nematodes [including 27 validated in R .…”

“…Promoter motif enrichment analyses were carried out as previously described for cyst and root knot nematodes [48,49]. In brief, the 1500 bp promoter regions of 83 putative homologues of genes with validated expression in either gland cell of plant-parasitic nematodes [including 27 validated in R. similis herein, and 56 validated in other species with sequence similarity to genes in R. similis (BLAST, e-value < e -5 ) and encode a signal peptide] were compared to the promoter regions of genes unlikely to be expressed in the gland cells (including 7 validated in R. similis to be expressed in other tissues herein, and 100 other genes randomly selected from the genome).…”

Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

“…[] indicates no histone modification has been identified. Full table of known subventral glands (SvG) effector genes can be found as Supplementary Table S5 (Da Rocha et al, 2021), 34 non-redundant M. incognita effectors have been identified in DG (i.e., columns: effector-gene number, gene name and accession number on M. incognita genome). For this study, DG effector genes were classified according to both their expression level and flanking histone modifications during eggs-to-J2s transition.…”

“…Protein-coding genes were considered to be associated with a histone modification if at least 1 bp of the protein-coding gene annotation overlapped with the identified histone modification. to the successful interaction leading to feeding sites and the production of the next generation of eggs (Nguyen et al, 2018;Da Rocha et al, 2021). In M. incognita, subventral glands (SvG) are mostly active during the earliest steps, whereas dorsal gland (DG) is active in the latest steps of the infection.…”