Cuing environmental responses in fungi

Genomes assembled and finished at HudsonAlpha provide clues to the evolution of sensory perception

Two fungal genomes assembled and finished at the HudsonAlpha Institute for Biotechnology are helping researchers understand the evolution of sensory perception. Fungi can sense environmental signals and react accordingly, changing their development, direction of growth and metabolism. Sensory perception lies at the heart of adaptation to changing conditions and helps fungi to improve growth and recycle organic waste and to know when and how to infect a plant or animal host. New results based on characterizing and then conducting a comparative analysis of two genome sequences published online May 26, 2016, in the journal Current Biology shed new light on the evolution of sensory perception in fungi.

For the study, researchers at the HudsonAlpha Genome Sequencing Center (GSC) worked in collaboration with colleagues at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility. Together, the project team sequenced and annotated two Mucoromycotina genomes, specifically those of Phycomyces blakesleeanus and its relative Mucor circinelloides. The work at HudsonAlpha was led by Jane Grimwood, PhD, a co-director for the GSC.

“Since P. blakesleeanus is an important model fungal system for sensory perception, we were excited to see what we could learn from its sequenced genome,” Grimwood said. “It’s certainly interesting to see the molecular mechanisms underlying the fungi’s unique sensory responses.”

The larger fungal research project was led by DOE JGI in collaboration with scientists at 31 research centers and universities from 13 countries and coordinated by scientists from the University of Seville in Spain. Capturing the genomic variation of fungi allows researchers to build a foundation for translating their genomic potential into practical applications. For example, understanding the mechanisms by which these environmental cues are sensed could provide insights on how some fungi can change their growth patterns to act as pathogens rather than benign organisms.

“Very little is known about basal fungi such as Mucoromycotina, and genomics may be the most efficient way to understand their metabolism,” said DOE JGI Fungal Genomes program head Igor Grigoriev of this project, which was done as part of a 2006 Community Science Program project. “Many members of this phyla show very high sensitivity to environmental signals, which when understood could be used for natural control of some of these metabolic processes. The high capacity for accumulating lipids in Mucor circinelloides, for example, may have biofuels applications.”

The team found that both species had undergone whole genome duplication, a rare occurrence in fungi. The genome duplication led to an expansion of gene families and the development of specialized genes, providing new proteins that have enabled these fungi to refine the way they perceive signals from the environment to regulate their growth and development.

Biologists have been fascinated for well over a century by the finely-tuned sensory responses of the sporangiophores of P. blakesleeanus. The sporangiophore is a long, rapidly growing giant cell with many nuclei that responds to light, gravity, touch, and even the mere presence of nearby objects. These “spore carriers” are special aerial hyphae that grow into the air for several centimeters and disperse the spores formed at their tip.

The fruiting bodies (sporangiophores) of Phycomyces blakesleeanus grow out of the mycelium and reach several cm in length. The speed and direction of growth is controlled by signals from the environment including light, gravity, touch, wind, and the presence of nearby
objects. The ball at the top of each fruiting body is the sporangium with spores. (Photo by Maria del Mar Gil Sanchez)

“Phycomyces blakesleeanus is best known because it was studied by Nobel laureate Max Delbrück, who recognized its potential as a model organism for the study of sensory perception,” noted University of Seville researcher Luis Corrochano, the study’s first author. “Delbrück was attracted by the elegant simplicity of the behavior of the fruiting body from P. blakesleeanus that can react to light and other signals from the environment, including gravity, wind and adjacent objects by changing its direction of growth.” Fittingly, the researchers dedicated this study to Delbrücks memory.

Mucor circinelloides, a related fungus, has similar environmental responses, and sometimes also acts  as a human pathogen. The genome sequences of Phycomyces and Mucor provide evidence that an ancient genome duplication yielded new genes to expand signal transduction pathways and improve the mechanisms for sensing light and other signals in this group of fungi. Responses to light cues in particular have led to the development of specialized fungal genes. For example, the team found that the fungi approximate the sensitivity of the human eye to both dim light of stars at night, and the luster of mid-day in bright sunlight. These results advance understanding the role of genome dynamics in the evolution of sensory perception which, in turn, could provide leads to genes and pathways useful for understanding fungal adaptation and for accelerating the breakdown of biomass for bioenergy.

About HudsonAlpha: HudsonAlpha Institute for Biotechnology is a nonprofit institute dedicated to innovating in the field of genomic technology and sciences across a spectrum of biological challenges. Founded in 2008, its mission is four-fold: sparking scientific discoveries that can impact human health and well-being; bringing genomic medicine into clinical care; fostering life sciences entrepreneurship and business growth; and encouraging the creation of a genomics-literate workforce and society. The HudsonAlpha biotechnology campus consists of 152 acres nestled within Cummings Research Park, the nation’s second largest research park. Designed to be a hothouse of biotech economic development, HudsonAlpha’s state-of-the-art facilities co-locate nonprofit scientific researchers with entrepreneurs and educators. The relationships formed on the HudsonAlpha campus encourage collaborations that produce advances in medicine and agriculture. Under the leadership of Dr. Richard M. Myers, a key collaborator on the Human Genome Project, HudsonAlpha has become a national and international leader in genetics and genomics research and biotech education, and includes more than 30 diverse biotech companies on campus. To learn more about HudsonAlpha, visit:

About DOE JGI: The U.S. Department of Energy Joint Genome Institute, User Facility of Lawrence Berkeley National Laboratory supported by the DOE Office of Science, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter. DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit

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