title: Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops.
abstract: BACKGROUND
  Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms.
  
  
  RESULTS
  We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions.
  
  
  CONCLUSIONS
  AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).
authors.affiliation: Department of Biological Sciences, Youngstown State University, Youngstown, OH, 44555, USA. xmin@ysu.edu.|Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH, 44555, USA. xmin@ysu.edu.
authors.forename: Xiang Jia
authors.initials: XJ
authors.lastname: Min
authors.affiliation: Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Powell
authors.affiliation: Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Braessler
authors.affiliation: Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH, 44555, USA.|Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA.|Present address: Center for Health Informatics, University of Cincinnati, Cincinnati, OH, 45267-0840, USA.
authors.forename: John
authors.initials: J
authors.lastname: Meinken
authors.affiliation: Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Yu
authors.affiliation: Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
mesh_terms: D017398:Alternative Splicing; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D066264:Datasets as Topic; D002523:Edible Grain / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D007438:Introns; D058977:Molecular Sequence Annotation; D059368:RNA Isoforms
chemical_list: D059368:RNA Isoforms