title: Dynamics of Rex3 in the genomes of endangered Iberian Leuciscinae (Teleostei, Cyprinidae) and their natural hybrids.
abstract: BACKGROUND
  Iberian Leuciscinae are greatly diverse comprising taxa of hybrid origin. With highly conservative karyotypes, Iberian Chondrostoma s.l. have recently demonstrated sub-chromosomal differentiation and rapid genome restructuring in natural hybrids, which was confirmed by ribosomal DNA (rDNA) transposition and/or multiplication. To understand the role of repetitive DNAs in the differentiation of their genomes, a genetic and molecular cytogenetic survey was conducted in Achondrostoma oligolepis, Anaecypris hispanica, Iberochondrostoma lemmingii, I. lusitanicum, Pseudochondrostoma duriense, P. polylepis, Squalius pyrenaicus and hybrids between A. oligolepis x (P. duriense/P. polylepis), representing 'alburnine', chondrostomine and Squalius lineages.
  
  
  RESULTS
  Partial Rex3 sequences evidenced high sequence homology among Leuciscinae (≥98 %) and different fish families (80-95 %) proposing a relatively recent activity of these elements in the species inspected. Low nucleotide substitution rates (<20 %) and intact ORFs suggests that Rex3 may in fact be active in these genomes. The chromosomal distribution of Rex3 retroelement was found highly concentrated at pericentromeric and moderately at subtelomeric blocks, co-localizing with 5S rDNA loci, and correlating with blocks of heterochromatin and C0t-1 DNA. This accumulation was evident in at least 10 chromosome pairs, a pattern that seemed to be shared among the different species, likely pre-dating their divergence. Nevertheless, species-specific clusters were detected in I. lusitanicum, P. duriense, P. polylepis and S. pyrenaicus demonstrating rapid and independent differentiation. Natural hybrids followed the same patterns of accumulation and association with repetitive sequences. An increased number of Rex3 clusters now associating also with translocated 45S rDNA clusters vouched for other genomic rearrangements in hybrids. Rex3 sequence phylogeny did not agree with its hosts' phylogeny but the observed distribution pattern is congruent with an evolutionary tendency to protect its activity, a robust regulatory system and/or events of horizontal transfer.
  
  
  CONCLUSIONS
  This is the first report directed at retroelement physical mapping in Cyprinidae. It helped outlining conceivable ancestral homologies and recognizing retrotransposon activation in hybrids, being possibly associated with genome diversification within the subfamily. The extensive diversity of Iberian Leuciscinae makes them excellent candidates to explore the processes and mechanisms behind the great plasticity distinguishing vertebrate genomes.
authors.affiliation: Faculty of Sciences, Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal.
authors.forename: Carla Sofia A
authors.identifier: 0000-0002-7133-0600
authors.initials: CS
authors.lastname: Pereira
authors.affiliation: Faculty of Sciences, Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal.
authors.forename: Marlon F
authors.initials: MF
authors.lastname: Pazian
authors.affiliation: Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, Liběchov, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Ráb
authors.affiliation: Faculty of Sciences, Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal.
authors.forename: Maria João
authors.initials: MJ
authors.lastname: Collares-Pereira
keywords: Anaecypris hispanica; C0t-1 DNA; Chondrostoma s.l. sp; Fish hybrids; Karyotype differentiation; Squalius pyrenaicus; Transposable elements