title: OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies.
abstract: BACKGROUND
  In eukaryotic genomes, most genes are members of gene families. When comparing genes from two species, therefore, most genes in one species will be homologous to multiple genes in the second. This often makes it difficult to distinguish orthologs (separated through speciation) from paralogs (separated by other types of gene duplication). Combining phylogenetic relationships and genomic position in both genomes helps to distinguish between these scenarios. This kind of comparison can also help to describe how gene families have evolved within a single genome that has undergone polyploidy or other large-scale duplications, as in the case of Arabidopsis thaliana - and probably most plant genomes.
  
  
  RESULTS
  We describe a suite of programs called OrthoParaMap (OPM) that makes genomic comparisons, identifies syntenic regions, determines whether sets of genes in a gene family are related through speciation or internal chromosomal duplications, maps this information onto phylogenetic trees, and infers internal nodes within the phylogenetic tree that may represent local - as opposed to speciation or segmental - duplication. We describe the application of the software using three examples: the melanoma-associated antigen (MAGE) gene family on the X chromosomes of mouse and human; the 20S proteasome subunit gene family in Arabidopsis, and the major latex protein gene family in Arabidopsis.
  
  
  CONCLUSIONS
  OPM combines comparative genomic positional information and phylogenetic reconstructions to identify which gene duplications are likely to have arisen through internal genomic duplications (such as polyploidy), through speciation, or through local duplications (such as unequal crossing-over). The software is freely available at http://www.tc.umn.edu/~cann0010/.
authors.affiliation: Plant Biology Department, University of Minnesota, St, Paul, MN 55108, USA. cann0010@umn.edu
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.forename: Nevin D
authors.initials: ND
authors.lastname: Young
mesh_terms: D000818:Animals; D000951:Antigens, Neoplasm / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D003546:Cysteine Endopeptidases / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D020440:Gene Duplication; D017343:Genes, Plant; D018745:Genome, Plant; D006801:Humans; D008545:Melanoma / Q000235:genetics; D051379:Mice; D009097:Multienzyme Complexes / Q000235:genetics; D010802:Phylogeny; D046988:Proteasome Endopeptidase Complex; D021122:Protein Subunits / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014960:X Chromosome / Q000235:genetics
chemical_list: D000951:Antigens, Neoplasm; D018744:DNA, Plant; D009097:Multienzyme Complexes; D021122:Protein Subunits; D003546:Cysteine Endopeptidases; D046988:Proteasome Endopeptidase Complex