title: Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts.
abstract: BACKGROUND
  CACTA elements are DNA transposons and are found in numerous organisms. Despite their low activity, several thousand copies can be identified in many genomes. CACTA elements transpose using a 'cut-and-paste' mechanism, which is facilitated by a DDE transposase. DDE transposases from CACTA elements contain, despite their conserved function, different exon numbers among various CACTA families. While earlier studies analyzed the ancestral history of the DDE transposases, no studies have examined exon loss and gain with a view of mechanisms that could drive the changes.
  
  
  RESULTS
  We analyzed 64 transposases from different CACTA families among monocotyledonous and eudicotyledonous host species. The annotation of the exon/intron boundaries showed a range from one to six exons. A robust multiple sequence alignment of the 64 transposases based on their protein sequences was created and used for phylogenetic analysis, which revealed eight different clades. We observed that the exon numbers in CACTA transposases are not specific for a host genome. We found that ancient CACTA lineages diverged before the divergence of monocotyledons and eudicotyledons. Most exon/intron boundaries were found in three distinct regions among all the transposases, grouping 63 conserved intron/exon boundaries.
  
  
  CONCLUSIONS
  We propose a model for the ancestral CACTA transposase gene, which consists of four exons, that predates the divergence of the monocotyledons and eudicotyledons. Based on this model, we propose pathways of intron loss or gain to explain the observed variation in exon numbers. While intron loss appears to have prevailed, a putative case of intron gain was nevertheless observed.
authors.affiliation: Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland ; Present address: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Center, University of Sydney, Sydney NSW 2006, Australia.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Buchmann
authors.affiliation: Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland.
authors.forename: Ari
authors.initials: A
authors.lastname: Löytynoja
authors.affiliation: Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.affiliation: Institute of Biotechnology, Viikki Biocenter, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland ; Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 1, FIN-31600 Jokioinen, Finland.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Schulman
keywords: DNA transposons; Intron loss; Molecular evolution; Plants; Transposases