title: Chompy: an infestation of MITE-like repetitive elements in the crocodilian genome.
abstract: Interspersed repeats are a major component of most eukaryotic genomes and have an impact on genome size and stability, but the repetitive element landscape of crocodilian genomes has not yet been fully investigated. In this report, we provide the first detailed characterization of an interspersed repeat element in any crocodilian genome. Chompy is a putative miniature inverted-repeat transposable element (MITE) family initially recovered from the genome of Alligator mississippiensis (American alligator) but also present in the genomes of Crocodylus moreletii (Morelet's crocodile) and Gavialis gangeticus (Indian gharial). The element has all of the hallmarks of MITEs including terminal inverted repeats, possible target site duplications, and a tendency to form secondary structures. We estimate the copy number in the alligator genome to be approximately 46,000 copies. As a result of their size and unique properties, Chompy elements may provide a useful source of genomic variation for crocodilian comparative genomics.
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multiscale Systems, Louisiana State University, 202 Life Sciences Bldg., Baton Rouge, LA 70803, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Hedges
authors.forename: Scott W
authors.initials: SW
authors.lastname: Herke
authors.forename: Justin D
authors.initials: JD
authors.lastname: Fowlkes
authors.forename: Erin W
authors.initials: EW
authors.lastname: Barnes
authors.forename: Daniel K
authors.initials: DK
authors.lastname: LaVie
authors.forename: Lindsey M
authors.initials: LM
authors.lastname: Goodwin
authors.forename: Llewellyn D
authors.initials: LD
authors.lastname: Densmore
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D000489:Alligators and Crocodiles / Q000235:genetics*; D000818:Animals; D004251:DNA Transposable Elements; D018628:Gene Dosage; D020071:Interspersed Repetitive Sequences; D005810:Multigene Family
chemical_list: D004251:DNA Transposable Elements