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Genome of ancient fungus unlocks secrets

by Kurt Kleiner Dec 2 / 13

Researchers sequenced the genome of a fungus that is thought to have helped plants move from the ocean onto the land about 440 million years ago, and that is still crucial to plant productivity today. Among other revelations from the new work, it seems that the fungus Rhizophagus irregularis is secretly engaging in sexual reproduction.

P9-fungus
By sequencing the genome of the fungus Rhizophagus irregularis, researchers found it may be sexually reproducing in secret. (Photo courtesy of the researchers).

“These fungi are important from an ecological perspective. They’re involved in an important and ancient symbiosis with plants,” says Nicolas Corradi, a Fellow in the Integrated Microbial Biodiversity program, and an assistant professor at the University of Ottawa.

R. irregularis is a member of Glomeromycota, a phylum of fungi that are symbiotic with about two-thirds of all land plants, including important crop species such as wheat and rice. These fungi penetrate the plant’s root system and help with the uptake of nutrients like phosphorus, increasing plant productivity by as much as 20 percent. In return, the plant provides sugars the fungi need to survive.

Glomeromycota is thought to have played a key role during the development of plant life during the mid-Paleozoic, when early moss-like plants first began to colonize land and gradually developed full-fledged root systems.

The fungi’s evolutionary and agricultural importance were enough to interest researchers, but they also posed other interesting questions, says Corradi. First, they seemed to reproduce clonally, with no evidence of sexual reproduction. But with no way to reshuffle genes, it seems unlikely the fungi could have survived so long without developing fatal mutations.

Second, each cell includes numerous nuclei, and some researchers had suggested each nucleus might contain a different genome. Perhaps, they thought, the fungi were packing their genetic diversity in multiple nuclei.

But the genetic analysis suggests two things. First, the multiple nuclei do not contain highly distinct genomes, but instead are genetically similar. Second, the fungus does seem to be engaging in sexual reproduction. The analysis turned up a number of genetic markers associated with sexual reproduction in other species. “They may be cryptically sexual. They may be having sex in the dark,” Corradi says.

It may not be as fun as it sounds, though. If sexual reproduction exists it may only consist of nuclear exchange, fusion and meiosis — a process that ultimately results in daughter cells that split apart and recombine to create novel genetic combinations.

Corradi says that constructing R. irregularis’s genome was especially challenging. The fungus can’t be cultured outside of its host plant, meaning that DNA from the fungus is easily contaminated by DNA from the host, and is extremely repeated, harbouring many identical pieces of the same “genomic” puzzle.

An added difficulty was the unusually large size of the genome — about 10 times as large as was expected. One question that remains to be answered is why the genome is so large, and how it got that way.

“I have to thank CIFAR,” Corradi says. “They played a big role in helping us to complete this research.”