Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

Abstract

The root-knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four "host races" had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4-gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro-economic challenges.

Keywords: Meloidogyne incognita; agricultural pest; clonal evolution; host races; parallel adaptation; population genomics.

Figure 1

World map showing geographical origins for all samples used in the study. Expanded map of Brazil showing the states where the 11 isolates sequenced in this study were collected. Each state is highlighted with a different colour. The countries listed in the literature for other sequenced genomes are completely coloured. The crops from which the samples were isolated are illustrated by photographs, which are pointed by arrows coming from the name of the respective isolate. The names of the Brazilian isolates are in 4 different colour sources for each race (race 1 in green, 2 in red, 3 in black and 4 in blue). The names of the isolates of the literature are written in white or black

Figure 2

Linkage Disequilibrium and 4‐gametes test of M. incognita (a) and G. rostochiensis (b) isolates. The r ² correlation between markers, indicating linkage disequilibrium (LD), is given as a function of the physical distance between the SNV markers (red line). The proportion of pairs of two‐state markers that pass the 4‐gamete test is given as a function of the distance between the markers (blue line). (a): on M. incognita scaffolds and (b): on G. rostochiensis phased haplotypes

Figure 3

Distribution of the number of variants per race and isolate. Number of variants per isolate (dark blue) and isolate‐specific variants (light blue) for the 11 Brazilian isolates

Figure 4

PCA of the Brazilian M. incognita isolates groups them into three clusters (A, B, and C). The geographical origins are associated with coloured shapes: black circle: Paraná, orange diamond: Santa Catarina, green square: São Paulo, red triangle: Mato Grosso, blue star: pool. Host plant representative pictures are displayed next to the isolates: soybean pod (R1‐2 and R3‐2); cotton flower (R3‐1, R3‐4, R4‐4, and R4‐1); coffee grain (R2‐6); cucumber vegetable (R1‐3); tobacco leaves (R1‐6 and R2‐1); and watermelon fruit slice (R4‐3)

Figure 5

Phylogenetic network for M. incognita isolates based on SNV present in coding sequences. The phylogenetic network based only on changes in coding sequences produced a bifurcating tree and shows the same grouping than the PCA analysis, into 3 distinct clusters

Figure 6

PCA of all publicly available genomes for M. incognita isolates, worldwide. The isolates were regrouped based on SNV patterns confirming the same three clusters. Origin countries are indicated by flags (Brazil for R1‐2, R1‐3, R1‐6, R2‐1, R2‐6, R3‐1, R3‐2, R3‐4, R4‐1, R4‐3, R4‐4; United States for L27, 557R, HarC, W1, VW6; Mexico for Morelos; Libya for A14; Ivory Coast for L9; Guadeloupe Island in the French Antilles for L19)