A mossy renaissance
The world’s top moss researchers—all eight of them—were gathered in a college lecture hall in Freiburg, Germany when they found out they had been granted funding to sequence a common moss (Physcomitrella patens) genome. It was September 2004, just a year after the group had made a joint decision to increase the moss field’s visibility. The moss field wasn’t getting enough respect, the researchers believed, and they wanted to do something about it.
“Our group had decided we needed to accomplish two things to get our science into people’s living rooms: publish more high-profile papers and create concrete applications for our research,” says Ralph Quatrano, a plant biologist at Washington University in St. Louis. “To us, sequencing the genome was the best way to accomplish those goals.”
The coalition’s strategy to sequence and disseminate the genome, set up that day in a University of Freiburg lecture hall, has thrust the field into the spotlight, attracting new scientists, racking up citations, and establishing moss as an integral component of evolutionary studies. Now, scientists are racing to release a second version in an effort to maintain the field’s momentum.
Physcomitrella holds a unique phylogenetic position; it evolved when aquatic plants transitioned to terrestrial living approximately 400–500 million years ago. Sequencing the genome could help scientists better understand plant evolution, specifically how aquatic plants adapted to deal with the stressful heat and dehydration that come with living on land.
The moss community invited roughly a hundred plant biologists from both aquatic and terrestrial fields to study and annotate the Physcomitrella genome, and published their collective evolutionary interpretation in Science in January 2008 (319:64–69, 2008). The 70-author paper has been cited more than 125 times, according to ISI Web of Knowledge, and attendance at the annual meetings of the International Physcomitrella Genome Consortium has increased from less than a dozen in 2004 to approximately 80 in 2009.
The excitement surrounding the first edition of the Physcomitrella genome prompted the researchers and US Department of Energy’s Joint Genome Institute to start work on a second version in late 2009. “We wanted to provide a more detailed, accurate genetic map,” says Stefan Rensing, a plant biologist at the University of Freiburg in Germany who is leading the bioinformatics and comparative genomics components of the most recent sequencing effort.
The moss community expects to release the second, “more user friendly” version of the Physcomitrella genome later this year, says Rensing. It will be published as a paper, similar to the 2008 Science article, but also made available on cosmoss.org, Genbank, and JGI’s phytozome.org.
The new version of the genome will have better structural and functional annotation, says Rensing, and a more accurate representation of chromosomes. Rensing and his colleagues are also comparing Physcomitrella’s genomic structure with similar organisms, such as the lycophyte Selaginella moellendorffii and the forthcoming genomes for the liverwort Marchantia polymorpha and the moss Ceratodon purpureus. The comparisons will allow the scientists to locate the moss’s promoter regions, which typically lie upstream of genes in eukaryotes and are binding sites for transcription factors.
Promoter regions are thought to be where organisms incorporate environmental signals into changes in gene expression, which could help scientists further deduce how aquatic plants transitioned to land.
“I think we can learn a lot about our favorite pathways and processes by including Physcomitrella in our experimental repertoire,” says Sabeeha Merchant, who studies green algae at the University of California, Los Angeles. Merchant used the genome to help identify 200 algal proteins as key factors in chloroplast metabolism.
“It has been quite a stunning experience to coordinate the efforts of an entire field of researchers toward a common goal,” says Quatrano.