title: Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses.
abstract: The occurrence of Stowaway MITEs and their potential footprints in the grasses was assessed within an explicit phylogenetic framework. An organismal tree was used to analyze the distribution and evolutionary dynamics of these elements and their potential excision footprints in the fourth intron of the β-amylase gene and in other introns of several nuclear genes across the Poaceae. Megablast and discontiguous megablast searches in the Entrez nucleotide database were performed for the β-amylase, blz-1, dmc1, nuc, and xly genes MITEs. These elements and their potential footprints were distributed in introns and intergenic spacers of many other nuclear genes throughout the BEP lineages; however, they were absent in the studied PACCMAD lineages. A plausible underlying dynamic of successive acquisitions and deletions of β-amylase Stowaway MITEs in the temperate grasses could be explained by three alternative hypotheses: (i) a single early acquisition of a palindrome element, similar to Tc1-Mariner, in the fourth intron of the β-amylase gene in the ancestor of the Pooideae, followed by multiple independent losses, (ii) multiple independent acquisitions of MITEs in non-related pooid lineages or (iii) different waves of acquisition of MITEs, followed by multiple losses and horizontal transfers in the temperate grasses. This last hypothesis seems to fit best with the evidence found to date.
authors.affiliation: Departmento de Ciencias Agrarias y del Medio Natural, Escuela Politécnica Superior Huesca, Universidad Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain. miguel.minay@gmail.com
authors.forename: Miguel
authors.initials: M
authors.lastname: Minaya
authors.forename: Manuel
authors.initials: M
authors.lastname: Pimentel
authors.forename: Roberta
authors.initials: R
authors.lastname: Mason-Gamer
authors.forename: Pilar
authors.initials: P
authors.lastname: Catalan
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000145:classification* / Q000235:genetics; D007438:Introns; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification* / Q000235:genetics; D006109:Poaceae / Q000145:classification* / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D001614:beta-Amylase / Q000145:classification* / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D009687:Nuclear Proteins; D010940:Plant Proteins; D001614:beta-Amylase