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International Team Sequences Fungal Species Known for Plant Root Symbiosis

NEW YORK (GenomeWeb News) – A mycorrhizal fungus species known for forming mutually beneficial interactions with plant roots has lost fewer metabolic genes than might be expected in an obligate symbiont, a genome sequencing study online this week in the Proceedings of the National Academy of Sciences suggests.

An international team led by investigators in France sequenced the haploid genome of Rhizophagus irregularis, a so-called arbuscular mycorrhizal fungus that forms symbiotic relationships with plant roots and contributes to phosphorus cycling. The genome offered a look at the nature of the R. irregularis lineage's long-standing relationship with land plants, revealing apparent players in plant communication and phosphorus use.

But while the newly sequenced genome contained few of the plant wall degradation enzyme-coding genes found in other fungi, researchers noted, it did harbor a relatively robust repertoire of primary metabolic genes.

"Through analysis of this and other mycorrhizal genomes, we can help to better understand interactions and conditions critical for a sustainable growth of bioenergy plants, but also staple crops, a prerequisite to help feeding the world," senior author Francis Martin, with the French National Institute for Agricultural Research, or INRA, said in a statement.

R. irregularis belongs to an early diverging fungal phylum marked by mutually symbiotic relationships with plants, Martin and his colleagues noted, explaining that such interactions are suspected of helping to spur land plant evolution by contributing to conditions that made early roots possible.

Along with these plant interactions, the arbuscular mycorrhizal fungi are known for their ability to pack hundreds of nuclei into shared cytoplasmic spaces, eventually reproducing asexually with the help of multinucleated spores.

In an effort to understand the stability and diversity of the genomes in those numerous nuclei — as well as the features involved in successful relationships with plant roots — researchers used a combination of Sanger, short-read Illumina, and long-read Pacific Biosciences sequencing to tackle the 155 million base haploid genome of an R.irregularis strain grown in a carrot root.

The resulting genome assembly spanned 101 million bases of the fungus' haploid genome, including around 98 percent of the coding sequences, they reported, and contained an estimated 28,232 protein-coding genes.

Together with transcriptome sequence data for the fungus, the polymorphism patterns in the genome pointed to related stable and similar sets of nuclei within R.irregularis, the team noted.

A closer look at the fungal genome indicated that it is missing some genes typically found in fungi, researchers noted. For instance, they saw a decreased set of genes coding for proteins that can degrade plant cell walls and genes involved in producing toxic secondary metabolites.

Nevertheless, the R.irregularis genome contained a fairly robust collection of nutrient uptake genes and genes involved in primary metabolic processes.

"Obligate parasites often have broken metabolism, missing some genes in critical metabolic pathway which make them dependent on their host," co-author Igor Grigoriev, with the US Department of Energy's Joint Genome Institute, said in a statement. "We did not find such genes here."

The team even saw signs of expansion to certain gene families, including an enhanced repertoire of genes involved in capturing and metabolizing phosphorus and a jump in genes coding for signaling and secreted proteins that are suspected of helping the fungus communicate with its plant host.

All told, study authors said, findings from the genome analysis suggest that the plant-friendly fungus "has the dual ability to interact with the soil environment with respect to mineral nutrient uptake and to integrate the complex cues imposed by its in planta life."