Agaricus Bisporus Mushroom Genome Sequencing.
The sequencing of the Agaricus bisporus genome (using the H97 strain, one of the parents of U1) is underway at the U.S. Department of Energy's Joint Genome Institute (JGI) facility in Walnut Greek, CA. The sequencing project began in February 2008 under the direction of the JGI sequencing team.
Agaricus and related genera most often are adapted to exploit leaf litter and related humic components of soils as substrates. This is considered by the U.S. Department of Energy to be of strategic importance in understanding and managing the earth's carbon cycling processes.
A major milestone was achieved in November 2008. Work was completed on the 4X scaffold, defining an estimated 99.8 percent of the mushroom genome. 4X refers to the fact that enough DNA has been decoded about 120,000,000 individual characters to equal four times the length of the entire nuclear genome. However, the DNA sequencing process is semi-random, meaning that one segment might be sequenced 10 times, and another one missed entirely. For that reason there will be gaps in the sequence at this stage, and so more sequencing, to reach the 8X level and close many gaps, is underway.
The term scaffold refers to the fact that even though there are gaps in the sequence at this stage, we know where most of those gaps are, and what is on either side. That framework makes it relatively easier to fill those gaps. For the 13 nuclear chromosomes that make up the A. bisporus genome, only 15 gaps remain outside of the 4X scaffold.
The size of the genome is now estimated by the JGI to be 30 million characters (= nucleotides), slightly smaller than the 34 million predicted from kinetics experiments over 20 years ago by the University of Toronto, Erindale. Of that 30, 29.5 million characters have been sequenced and fitted together into blocks; the rest are either in the gaps or else make up shorter segments not yet fitted together into the whole.
Right now, during the development and quality checking stages, the 4X sequence is available for review by the many investigators on the project. As soon as possible the entire sequence will be made available to the public. Meanwhile, I have compared some of Sylvan's own sequence database with sequence obtained by JGI, and the matches are either perfect (for H97) or excellent (when different strains are compared).
Over the next 3-4 years the project intends to do several things, including completing and correcting the sequence of Agaricus bisporus strain H97, and augmenting it with most or all of the sequence of a tetrasporic strain, JB137-s8. It will also be necessary to find and identify each of the estimated 10,000 to 12,000 functioning genes, a process called annotation, and to begin to assess their functions and properties. As that work progresses, we will begin to see experiments aimed at improved control over properties of the mushroom crop and of the mushroom product. In coming years this will provide strategies and tools for strain and crop improvement to both spawn and mushroom producers. Then the art of mushroom growing will have a lot more science on its side.
For more information, visit http://www.jgi.doe.gov/seguencing/why/99189.html
Richard W. Kerrigan, Ph.D.
Director of Research Sylvan Research
198 Nolte Drive Kittanning, PA 16201
Agoricus bisporus, conifer forest soil, Moss Beach, CA.
Photo R.W. Kerrigan