High-Resolution Genome Assembly and Linkage Mapping of Northen Root-Knot Nematode, Meloidogyne hapla

Root-knot Nematodes (RKNs) are devastating agricultural pests that cause billions of dollars in crop losses every year. Meloidogyne hapla is a valuable model for studying these parasites because of its compact genome and flexible reproduction strategies that enable genetic research. In this work:

• We generated a contiguous, chromosome-scale genome assembly of M. hapla using a combination of long and short read sequencing technologies.
• We validated our assembly with genetic maps and discovered significant structural variations between different strains of M. hapla such as chromosome fusions and breakages.
• We identified zones of extraordinarily high recombination on most chromosomes which were enriched in genes encoding secreted peptides most likely involved in parasitism. This suggests that recombination may be a key mechanism driving the evolution of new strategies to overcome plant defenses.
• We found an unusual 16-nucleotide repeat at chromosome-ends instead of typical telomere repeats hinting at an alternative mechanism for telomere maintenance in this species.

Our study provides important genetic and genomic resources for M. hapla and sheds light on the role of genome architecture and recombination in shaping the evolution of parasitism in root-knot nematodes.

Paper Highlights

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Apollo Genome Browser

Along with the Phoenix IT team at UC Davis, I maintain Apollo genome browser for nematodes sequenced in the Siddique Lab. This provides our collaborators with an easy-to-use web interface to visualize the genomes, review evidence tracks and manually annotate the gene models.

Apollo genome browser showing gene annotations and multiple data tracks for Meloidogyne hapla

Identification and Characterization of Effector Genes in Meloidogyne hapla

What makes one strain of M hapla avirulent and another virulent on a specific host plant?
To answer this, I combine comparative genomics, QTL and variant analysis to identify candidate effector genes. Then, I characterize these genes using RNAi knockdown and over-expression assays to understand their role in parasitism and host interaction.

Infection of two strains of Meloidogyne hapla VW9 and LM on different bean varieties Nemasnap and BlackValentine. The pictures shown are roots infested with M hapla females and stained with Acid Fuchsin Dye.