Fig 1.
Chromosome-scale genome assembly and repeat structure of Meloidogyne hapla strain VW9.
A. HiC contact map of M. hapla showing 16 chromosome-scale scaffolds. Green lines denote the edges of contigs, and blue lines denote the edges of scaffolds. B. Distribution of the 16-mer repeats across chromosome-scale scaffolds. Each horizontal bar represents a scaffold, with arrows indicating repeat orientation (rightward: positive strand; leftward: negative strand) and numbers showing repeat copy number per scaffold. The repeat at the end of Scaffold 10 is a variant of the others shown.
Fig 2.
DNA FISH with the 16 bp tandem repeat probe on M. hapla chromosomes in different chromosome condensation stages (A and B).
Probe is labeled with FITC (green) and chromosomes are counterstained with DAPI (blue). Arrows point to hybridization signals localized at one (white arrows) or both (yellow arrows) chromosome ends. Red arrow indicates a chromosome where tandem repeats appear to be located internally. Green arrows point to chromosomes without hybridization signals. Size bar = 5µm.
Fig 3.
Distribution of Nigon elements along the length of M. hapla scaffolds.
The X-axis represents the physical length of each scaffold, and the Y-axis represents the Nigon-defining loci per 500 Kb non-overlapping windows. The legend shows the color key for each Nigon Element from A through X.
Fig 4.
Recombination profile based on chromosome scaffolds.
Allele present in each F2 line on scaffolds 1-16. Colors represent regions with VW9 (blue) and LM (orange) alleles, whereas white areas indicate insufficient data. Panels EA, FB, and GC on the right indicate the female from which the F2 lines were derived.
Fig 5.
Recombination profile for each scaffold.
Tick marks on the x axis indicate physical position on the scaffold and those on the y axis are the corresponding genetic positions based on SNP segregation in F2 lines. High recombination zones (HRZs) are highlighted in yellow. The number of scaffolds is depicted on top of each box.
Table 1.
Alignment of Meloidogyne hapla VW9 scaffolds with genetic linkage groups.
Fig 6.
Classification of M. hapla PSPs.
A. Total PSPs were characterized by the presence or absence of orthologs in a set of 71 nematode species. The identification of orthologs was done using Orthofinder. B. Venn diagram shows the PSPs that are shared across RKNs, PPNs and other nematode species. C. The distribution of PSPs into Known and Pioneer PSPs is shown for PSPs with orthologs in other nematode species and for those unique to M. hapla. (i.e., those unique to M. hapla having single or multiple copies.
Fig 7.
Distribution of PSP genes in the High Recombination Zones (HRZs).
Each of the 16 scaffolds is divided into 100 kb bins (X-axis). Y-axis represents the number of PSPs per bin. HRZ regions are highlighted in yellow. Genome-wide enrichment analysis shows significant enrichment of PSPs in the HRZs (Hypergeometric test, p-value = 2.5*10-8).
Fig 8.
Distribution of PSPs with conserved domains along the genome of M. hapla: Ideogram of PSPs with known functional domains along the scaffolds of M. hapla genome.
Each circle represents the PSPs, and they are pinned with respect to their positions on the scaffolds. The highlighted blue regions denote the HRZs.
Fig 9.
High recombination zones and gene distribution in Scaffold 3.
A. Recombination rate (cM/Mb) of Scaffold 3 along its physical position (Mb) showing sharply defined HRZs. The dotted horizontal line indicates the average recombination rate for the whole chromosome. B. Histogram of Gene Count per 100 Kb along Scaffold 3. The highlighted regions denote HRZs. C. Stacked bar graph of PSP Count per 100 Kb along the physical positions of scaffold 3 where the highlighted regions denote HRZs. Each color represents functionally annotated PSPs, pioneer PSPs shared with other Meloidogyne species and pioneer PSPs that are unique to M. hapla. D. Highlights of the PSP genes found in HRZ of Scaffold 3. They are colored according to the ones shown in C. The arrows represent positive and negative strands. The known PSPs are labelled with their respective functional annotations.