title: Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris).
abstract: Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602.
authors.forename: Dongying
authors.initials: D
authors.lastname: Gao
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Dongyan
authors.initials: D
authors.lastname: Zhao
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602.
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602.
authors.forename: Aiko
authors.initials: A
authors.lastname: Iwata-Otsubo
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Mexico 36821.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Herrera-Estrella
authors.affiliation: Department of Horticulture, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Ning
authors.initials: N
authors.lastname: Jiang
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 sjackson@uga.edu.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D049810:Genetic Speciation; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D027805:Phaseolus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements; D010940:Plant Proteins
keywords: CACTA; DNA transposon; Phaseolus; common bean; genome evolution