Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Comparison Of Orthologous Loci From Small Grass Genomes Brachypodium And Rice: Implications For Wheat Genomics And Grass Genome Annotation

Beat Keller , Philip Knobel , Eligio Bossolini , Thomas Wicker

  Institute of Plant Biology, University of Zurich, 8008 Zurich, Switzerland

Brachypodium sylvaticum and distachyon were recently proposed as new model plants because of their small genomes and their phylogenetic position between rice and Triticeae crops. We sequenced a 371 kb region in B. sylvaticum, the largest genomic sequence available from this species so far, providing quantitative data on gene conservation, colinearity and phylogeny. We compared it with orthologous regions from rice and wheat. Brachypodium and wheat show perfect macro-colinearity of genetic markers, whereas rice contains a ~220 kb inversion. Rice contains almost twice as many genes as Brachypodium in the region studied whereas wheat has about 40% more. Through comparative annotation we identified alternative transcripts and improved the annotation for several rice genes, indicating that ~15% of rice genes might require re-annotation. Surprisingly, our data suggest that 10-15% of functional sequences in small grass genomes may not encode any proteins. From available genomic and EST sequences we estimated Brachypodium to have diverged from wheat about 35-40 MYA, significantly less than the divergence of rice and wheat. However, our data also indicate that orthologous regions from Brachypodium and wheat differ considerably in gene content and, thus, the Brachypodium genome sequence can probably not replace genomic studies in the large Triticeae genomes.