title: Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation.
abstract: BACKGROUND
  The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium-Festuca complex show very diverse phenotypes, and many of them are related to agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity.
  
  
  RESULTS
  We have generated de novo transcriptome assemblies for four species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some of the differences between the more stress tolerant Festuca, and the less stress tolerant Lolium species.
  
  
  CONCLUSIONS
  Our data presents a comprehensive transcriptome sequence comparison between species from the Lolium-Festuca complex, with the identification of potential candidate genes underlying some important phenotypical differences within the complex (such as VRN2). The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them. It is likely that the knowledge of the genomes will be largely transferable between species within the complex.
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark. Adrian.Czaban@mbg.au.dk.
authors.forename: Adrian
authors.initials: A
authors.lastname: Czaban
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany. sapna.sharma@helmholtz-muenchen.de.
authors.forename: Sapna
authors.initials: S
authors.lastname: Sharma
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark. Stephen.Byrne@mbg.au.dk.
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Byrne
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany. manuel.spannagl@helmholtz-muenchen.de.
authors.forename: Manuel
authors.initials: M
authors.lastname: Spannagl
authors.affiliation: Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany. k.mayer@helmholtz-muenchen.de.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark. Torben.Asp@mbg.au.dk.
authors.forename: Torben
authors.initials: T
authors.lastname: Asp
mesh_terms: D019295:Computational Biology; D031751:Festuca / Q000235:genetics* / Q000378:metabolism; D008129:Lolium / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA; D017385:Sequence Homology; D013312:Stress, Physiological; D059467:Transcriptome