Abstract
The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions – thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841) and Semaprochilodus taeniurus (Valenciennes, 1817) and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (Semaprochilodus insignis, Semaprochilodus taeniurus, and Prochilodus lineatus (Valenciennes, 1836) by cross-FISH using Cot-1 DNA (renaturation kinetics) probes. We found that the repetitive fractions of the genomes of Semaprochilodus insignis and Semaprochilodus taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of Prochilodus lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of Semaprochilodus insignis and Semaprochilodus taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the Semaprochilodus insignis and Semaprochilodus taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the Prochilodus lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of the genomes in this group of fish.
Highlights
Multiple copies of DNA sequences, known as “repetitive DNA”, compose large portions of eukaryotic genomes
Repetitive DNA is generally divided into two groups: (1) tandem repeats, which include DNA satellites, minisatellites, and microsatellites; and (2) dispersed interspersed repeats composed of transposable elements (TEs) (Timberlake 1978, Charlesworth 1994, Jurka 2005), but there are other gene families with sequence repetitions known as repetitive DNA, such as the genes encoding for ribosomal RNA (Long 1980)
While the structure and organization of this genome fraction is still poorly understood in fish, most of these non-coding repetitive sequences appear to be located in heterochromatic regions (Fishcher et al 2004, Martins et al 2011)
Summary
Multiple copies of DNA sequences, known as “repetitive DNA”, compose large portions of eukaryotic genomes. The repetitive sequences were largely considered to be “junk”, “selfish”, or “parasitic” DNA (Doolittle and Sapienza 1980, Orgel and Crick 1980, Nowak 1994) due to the lack of any known functions in the genome for these sequences. With everincreasing volumes of genomic information, these repetitive sequences are known to play larger roles in the structural and functional evolution of the genome (Shapiro and Vonsternberg 2005, Biémont and Vieira 2006). Repetitive sequences are known to be involved in chromosomal rearrangements and responsible for significant proportions of the karyotypic variations observed in many groups (Kidwell 2002, Schneider et al 2013)
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