Moss genome sequenced: shows how aquatic plants adapted to dry land - key to development of drought-tolerant energy crops, cellulosic biofuels

An international team of 70 scientists from over 40 institutions, led by the U.S. Department of Energy's Joint Genome Institute, announces it has sequenced the genome of a dainty yet ephemeral moss, providing scientists with keys to the genetic changes that allowed aquatic plants to venture onto land. The newly discovered, ancient genes for tolerance to desiccation may aid researchers seeking to develop drought-tolerant bioenergy crops that can be grown in arid zones, the scientists say. The sequencing of the moss genome - the first nonvascular land plant to be sequenced - is the highlight of Science magazine's latest rapid online publication Science Express and will be printed in Science in January 2008.

The JGI is an international collaboration uniting some of the world's leading scientists who are working to sequence the genomes of energy crops, microorganisms, algae, and other plants that will contribute to a science-driven bioenergy future that helps solve the planet's unfolding climate and energy crisis.

The new genome library of the moss offers a wealth of opportunities for new insights into plant genes and their functions and the molecular mechanisms involved in plant cell wall synthesis and assembly. This is so because the moss in question - Physcomitrella patens - is a model organism for the study of plant biology. New insights into the plant cell wall - the main component of terrestrial biomass - could unlock the key to cellulosic biofuels, which are based on breaking the cell wall down, the scientists say.

Some 400 million years ago, on a lifeless lakeshore lapped by waves, floating algae learned to survive in the open air and launched an invasion that transformed the Earth into a green paradise. The secrets of these first steps onto land are now being revealed thanks to the sequencing of a modern descendent of these first land dwellers, the dainty Physcomitrella patens that sprouts on recently exposed shorelines, quickly fruits, and then dies.

Land plants may have evolved in this transition zone where, as the water rises and falls, aquatic plants found themselves repeatedly but not continuously exposed to the air and had to come up with ways of protecting their seeds or spores from desiccation, says Jeffrey Boore, Joint Genome Institute project leader, adjunct associate professor of integrative biology at the University of California, Berkeley.

Because of the key position of mosses in the evolution of green plants, the Physcomitrella genome may hold the key to the origin of such traits as desiccation tolerance, said Brent Mishler, a UC Berkeley professor of integrative biology who, with Ralph Quatrano of Washington University in St. Louis, originally proposed the moss genome project.

One of the claims to fame of mosses is the ability to dry up completely and come back to life again, said Mishler, who is director of the University and Jepson Herbaria, two collections of pressed plants housed together along with research labs, libraries and archives at UC Berkeley.

The scientists have been looking for years at all levels, from the organism down to the molecular level, at how mosses do this, and the genome sequence will help speed that work.

Bioenergy applications
From the Department of Energy's perspective, Boore said, discovering the genes involved in desiccation tolerance may help plant biologists incorporate the trait into other plants to improve their growth in arid conditions, allowing, for example, biofuel feedstocks to be grown on marginal land. And many other bioenergy applications are opening up:
energy :: sustainability :: biomass :: bioenergy :: cellulosic biofuels :: energy crops :: drought-tolerance :: bioconversion :: genomics :: genome :: plant biology ::biotechnology ::

Physcomitrella is also a model organism that is easily manipulated for study of how many plant genes function. It is to flowering plants what the fruit fly is to humans; that is, in the same way that the fly and mouse have informed animal biology, the genome of this moss will advance exploration of plant genes and their functions and utility, said Joint Genome Institute director Eddy Rubin.

Unlike vascular plant systems, the scientists can target and delete specific moss genes to study their function in important crop processes, and replace them with genes from crop plants to allow the study of the evolution of gene function. In addition to the genome, extensive genomic tools are now available in Physcomitrella to study comparative gene function and evolution as related to bioenergy and other processes of importance to crops.

The availability of the Physcomitrella genome is expected to create important new opportunities for understanding the molecular mechanisms involved in plant cell wall synthesis and assembly, according to Chris Somerville, UC Berkeley professor of plant and microbial biology and Director of the Energy Biosciences Institute (EBI), a partnership between UC Berkeley, Lawrence Berkeley National Laboratory, the University of Illinois at Urbana-Champaign and the global energy company BP.

Cellulosic biofuels
The ease with which genes can be experimentally modified in Physcomitrella will facilitate a wide range of studies of the cell wall, the principal component of terrestrial biomass, he said. Additionally, the moss has fewer cell types than higher plants and has a much more rapid lifecycle, which also greatly facilitates experimental studies of cell walls. Thus, the completion of the genome is an important step forward in facilitating basic research concerning the development of cellulosic biofuels.

In the Science paper, researchers from more than 40 institutions report that the Physcomitrella genome contains just under 500 million nucleotides and possesses nearly 36,000 genes, which is about 50 percent more than are thought to be in the human genome. Physcomitrella is the first nonvascular land plant to be sequenced. Vascular plants lack specialized tissues (phloem or xylem) for circulating fluids, instead possessing specialized tissues for internal transport. They neither flower nor produce seeds, but reproduce via spores.

Mishler says that Physcomitrella is well-placed phylogenetically to fill in the large gap between the unicellular green alga Chlamydomonas, also sequenced by the Joint Genome Institute, and the flowering plants.

Having the full Physcomitrella genome available to the public greatly advances bioinformatic comparisons and functional genomics in plants, Mishler adds, who is part of a major effort within the Berkeley Natural History Museums - a consortium of six museums at UC Berkeley - to link the two. This is a great example of how phylogenetics can integrate with functional and applied studies.

Mishler further noted that the draft genome sequence is only the beginning. Plant scientists plan to meet regularly to assign specific functions to the newly identified genes based on experiments in the moss or by analogy with related genes in other organisms. This experimentation process is called 'annotation'. The first so-called annotation jamboree was hosted in June 2006 by UC Berkeley and the Joint Genome Institute, and another is planned in Finland next year.

The genome sequencing was enabled through the Joint Genome Institute's Community Sequencing Program. The work involved Boore, David Cove and Andrew Cuming of the University of Leeds (United Kingdom); Mitsuyasu Hasebe and Tomoaki Nishiyama of Japan's National Institute for Basic Biology; Ralf Reski and Stefan Rensing of the University of Freiburg in Germany. In total 70 researchers from Belgium, Germany, the UK, Japan and the US collaborated on this breakthrough project.

International teams of leading scientists are working under the umbrella of the JGI to sequence the genomes of energy crops, algae, microorganisms and other plants that will contribute to a science-driven bioenergy future for the planet. Teams under the JGI were the first to sequence an entire tree's genome, namely that of the poplar, a model biomass crop. Other recent achievements include the sequencing of microbes found in termite guts, which could unlock the conversion of lignocellulosic biomass into biofuels. Crops currently being sequenced are, amongst others, eucalyptus, foxtail millet, cassava and sorghum.

Picture: Scanning electron micrograph of Physcomitrella patens gametophores (moss shoots). Credit: John Doonan, The John Innes Centre, Norwich, UK.

References:
Stefan A. Rensing, "The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants", Published Online December 13, 2007, Science, DOI: 10.1126/science.1150646

Joint Genome Institute: DOE JGI Community Sequencing Program Delivers First Moss Genome - December 13, 2007.

Biopact: Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production - November 22, 2007

Biopact: Joint Genome Institute announces 2008 genome sequencing targets with focus on bioenergy and carbon cycle - June 12, 2007

Biopact: The first tree genome is published: Poplar holds promise as renewable bioenergy resource - September 14, 2006