title: Polypteridae (Actinopterygii: Cladistia) and DANA-SINEs insertions.
abstract: SINE sequences are interspersed throughout virtually all eukaryotic genomes and greatly outnumber the other repetitive elements. These sequences are of increasing interest for phylogenetic studies because of their diagnostic power for establishing common ancestry among taxa, once properly characterized. We identified and characterized a peculiar family of composite tRNA-derived short interspersed SINEs, DANA-SINEs, associated with mutational activities in Danio rerio, in a group of species belonging to one of the most basal bony fish families, the Polypteridae, in order to investigate their own inner specific phylogenetic relationships. DANA sequences were identified, sequenced and then localized, by means of fluorescent in situ hybridization (FISH), in six Polypteridae species (Polypterus delhezi, P. ornatipinnis, P. palmas, P. buettikoferi P. senegalus and Erpetoichthys calabaricus) After cloning, the sequences obtained were aligned for phylogenetic analysis, comparing them with three Dipnoan lungfish species (Protopterus annectens, P. aethiopicus, Lepidosiren paradoxa), and Lethenteron reissneri (Petromyzontidae)was used as outgroup. The obtained overlapping MP, ML and NJ tree clustered together the species belonging to the two taxonomically different Osteichthyans groups: the Polypteridae, by one side, and the Protopteridae by the other, with the monotypic genus Erpetoichthys more distantly related to the Polypterus genus comprising three distinct groups: P. palmas and P. buettikoferi, P. delhezi and P. ornatipinnis and P. senegalus. In situ hybridization with DANA probes marked along the whole chromosome arms in the metaphases of all the Polypteridae species examined.
authors.affiliation: Dipartimento di Scienze della Vita, Seconda Università degli Studi di Napoli, via Vivaldi 43, 81100, Caserta, Italy. ria.morescalchi@unina2.it
authors.forename: Maria Alessandra
authors.initials: MA
authors.lastname: Morescalchi
authors.forename: Marco
authors.initials: M
authors.lastname: Barucca
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Stingo
authors.forename: Teresa
authors.initials: T
authors.lastname: Capriglione
mesh_terms: D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D005399:Fishes / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D059785:Karyotype; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*; D013045:Species Specificity
chemical_list: D017931:DNA Primers; D004251:DNA Transposable Elements; D018626:Retroelements