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International Brachypodium Initiative Researchers Sequence Wild Grass Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a paper appearing online today in Nature, members of the International Brachypodium Initiative reported that they have sequenced the first wild grass genome.

The team used Sanger sequencing to sequence the genome of Brachypodium distachyon, a wild grass in the same Pooideae sub-family as wheat and barley that's native to the Mediterranean and Middle East. Given the plant's relationship to other plants used for everything from agriculture to biofuel research, the genome is being touted as a valuable resource for future plant studies.

"The Brachypodium genome sequence analysis reported here is … an important advance towards securing sustainable supplies of food, feed, and fuel from new generations of grass crops," the researchers wrote.

Because it's related to wheat, barley, and switchgrass, but is much simpler genetically, Brachypodium has proved to be a useful plant model for studying more complex crop plants.

"[Brachypodium] has one of the smallest known genomes among grasses, it’s easy to work with and is physically small," co-senior author Todd Mockler, a botany and plant pathology researcher at Oregon State University's Center for Genome Research and Biocomputing, said in a statement.

The team used a Sanger approach to do whole-genome shotgun sequencing of a B. distachyon line called Bd21, generating about 9.4 times coverage of the genome through paired-end sequencing of fosmid and BAC clones. They also employed Illumina sequencing to characterize Brachypodium transcriptome and small RNAs.

During their subsequent analyses of the Brachypodium genome, researchers found 25,532 protein-coding genes — a comparable protein-coding repertoire to that of rice and sorghum, plants belonging to other grass sub-families. Some 77 to 84 percent of gene families overlapped between Brachypodium, rice, and sorghum.

In contrast, though, Brachypodium's genome appears to contain fewer retrotransposon sequences than other genetically characterized grasses: these sequences made up just 21.4 percent of the B. distachyon. On the other hand, the researchers noted, retrotransposon sequences comprise 26 percent of the rice genome and 54 percent of the sorghum genome and are believed to account for more than 80 percent of the wheat's genome sequence.

By comparing B. distachyon with grass sequences from within and between grass sub-families, the team also began exploring the grass evolutionary history and relationships.

With the Brachypodium genome sequence in hand, researchers say, it should be possible to begin applying information housed within to better understand other, more complex, commercially and agriculturally valuable grass plants.

In particular, those involved say the B. distachyon genome should also serve as a jumping off point for pinpointing key functional genes in plants such as switchgrass, a potential biofuel crop, and agricultural plants, including wheat and barley.

"Our analysis of the Brachypodium genome is a key resource for securing sustainable supplies of food, feed and fuel from established crops such as wheat, barley and forage grasses and for the development of crops for bioenergy and renewable resource production," co-senior author Michael Bevan, a cell and developmental biology researcher at the John Innes Centre in the UK, said in a statement.

"It is already being widely used by crop scientists to identify genes in wheat and barley," he added, "and it is defining new approaches to large-scale genome analysis of these crops, because of the high degree of conserved gene structure and organization we identified."

Meanwhile, in an article appearing online this week in the Proceedings of the National Academy of Sciences, a pair of researchers from Yale University reported that they have completed a phylogenetic analysis of so-called "C4" grasses.

In contrast to Pooideae grasses such as Brachypodium, which are classified as "C3" plants, the C4 grasses have developed a method for concentrating carbon dioxide near an enzyme called Rubisco during photosynthesis.

Results from that study, which involved some 1,230 plant species, suggest C4 grasses evolution coincided with the plants' ability to thrive in sunny, dry habitats.

"It highlights the apparently important role that cold tolerance has played for the evolution of non-C4 grasses and especially the group Pooideae, which includes rye, barley, and wheat and many of the other grasses in the temperate and boreal habitats," senior author Stephen Smith, post-doctoral researcher at the National Evolutionary Synthesis Center in North Carolina, said in a statement.

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