title: Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula).
abstract: Acipenseriformes is a basal lineage of ray-finned fishes and comprise 27 extant species of sturgeons and paddlefishes. They are characterized by several specific genomic features as broad ploidy variation, high chromosome numbers, presence of numerous microchromosomes and propensity to interspecific hybridization. The presumed palaeotetraploidy of the American paddlefish was recently validated by molecular phylogeny and Hox genes analyses. A whole genome duplication in the paddlefish lineage was estimated at approximately 42 Mya and was found to be independent from several genome duplications evidenced in its sister lineage, i.e. sturgeons. We tested the ploidy status of available chromosomal markers after the expected rediploidization. Further we tested, whether paralogs of Hox gene clusters originated from this paddlefish specific genome duplication are cytogenetically distinguishable.
  
  
  
  We found that both paralogs HoxA alpha and beta were distinguishable without any overlapping of the hybridization signal - each on one pair of large metacentric chromosomes. Of the HoxD, only the beta paralog was unequivocally identified, whereas the alpha paralog did not work and yielded only an inconclusive diffuse signal. Chromosomal markers on three diverse ploidy levels reflecting different stages of rediploidization were identified: quadruplets retaining their ancestral tetraploid condition, semi-quadruplets still reflecting the ancestral tetraploidy with clear signs of advanced rediploidization, doublets were diploidized with ancestral tetraploidy already blurred. Also some of the available microsatellite data exhibited diploid allelic band patterns at their loci whereas another locus showed more than two alleles.
  
  
  
  Our exhaustive staining of paddlefish chromosomes combined with cytogenetic mapping of ribosomal genes and Hox paralogs and with microsatellite data, brings a closer look at results of the process of rediploidization in the course of paddlefish genome evolution. We show a partial rediploidization represented by a complex mosaic structure comparable with segmental paleotetraploidy revealed in sturgeons (Acipenseridae). Sturgeons and paddlefishes with their high propensity for whole genome duplication thus offer suitable animal model systems to further explore evolutionary processes that were shaping the early evolution of all vertebrates.
authors.affiliation: Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 277 21, Liběchov, Czech Republic. radka.symonova@uibk.ac.at.|Research Institute for Limnology, University of Innsbruck, Mondseestr. 9, Mondsee, Austria. radka.symonova@uibk.ac.at.
authors.forename: Radka
authors.initials: R
authors.lastname: Symonová
authors.affiliation: University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, 389 25, Vodňany, Czech Republic.
authors.forename: Miloš
authors.initials: M
authors.lastname: Havelka
authors.affiliation: Benaroya Research Institute & University of Washington, Seattle, WA, 98101, USA.
authors.forename: Chris T
authors.initials: CT
authors.lastname: Amemiya
authors.affiliation: Department of Biological and Environmental Sciences, Samford University, 800 Lakeshore Drive, Birmingham, AL, 35229, USA.
authors.forename: William Mike
authors.initials: WM
authors.lastname: Howell
authors.affiliation: Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 277 21, Liběchov, Czech Republic.
authors.forename: Tereza
authors.initials: T
authors.lastname: Kořínková
authors.affiliation: University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, 389 25, Vodňany, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Flajšhans
authors.affiliation: University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, 389 25, Vodňany, Czech Republic.
authors.forename: David
authors.initials: D
authors.lastname: Gela
authors.affiliation: Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 277 21, Liběchov, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Ráb
mesh_terms: D000818:Animals; D004171:Diploidy; D029941:Fish Proteins / Q000235:genetics*; D005399:Fishes / Q000235:genetics*; D020440:Gene Duplication; D023281:Genomics; D060005:Genotyping Techniques; D017404:In Situ Hybridization, Fluorescence; D018895:Microsatellite Repeats / Q000235:genetics; D012270:Ribosomes / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D029941:Fish Proteins
keywords: Ancient fish genome; HoxA/D paralogs mapping; Rediploidization; Sturgeon whole genome duplication