Construction and Characterization of a Repetitive DNA Library in Parodontidae (Actinopterygii: Characiformes): A Genomic and Evolutionary Approach to the Degeneration of the W Sex Chromosome

Abstract

Repetitive DNA sequences, including tandem and dispersed repeats, comprise a large portion of eukaryotic genomes and are important for gene regulation, sex chromosome differentiation, and karyotype evolution. In Parodontidae, only the repetitive DNAs WAp and pPh2004 and rDNAs were previously studied using fluorescence in situ hybridization. This study aimed to build a library of repetitive DNA in Parodontidae. We isolated 40 clones using C o t-1; 17 of these clones exhibited similarity to repetitive DNA sequences, including satellites, minisatellites, microsatellites, and class I and class II transposable elements (TEs), from Danio rerio and other organisms. The physical mapping of the clones to chromosomes revealed the presence of a satellite DNA, a Helitron element, and degenerate short interspersed element (SINE), long interspersed element (LINE), and tc1-mariner elements on the sex chromosomes. Some clones exhibited dispersed signals; other sequences were not detected. The 5S rDNA was detected on an autosomal pair. These elements likely function in the molecular degeneration of the W chromosome in Parodontidae. Thus, the location of these elements on the chromosomes is important for understanding the function of these repetitive DNAs and for integrative studies with genome sequencing. The presented data demonstrate that an intensive invasion of TEs occurred during W sex chromosome differentiation in the Parodontidae.

In situ Localization of (GATA)n and (TTAGGG)n Repeated DNAs and W Sex Chromosome Differentiation in Parodontidae (Actinopterygii: Characiformes)

“…The family Parodontidae has been used in studies of sex chromosome differentiation, investigating the invasion of repetitive sequences and the increase in W chromosome size [Centofante et al, 2002;Rosa et al, 2006;Vicari et al, 2006;Bellafronte et al, 2009Bellafronte et al, , 2011Bellafronte et al, , 2012Schemberger et al, , 2014. In this study, in situ localization of the (GATA)n sequence revealed the accumulation of this microsatellite in proto-sex and sex chromosomes of 7 species: A. hasemani , A. ibitiensis , Apareiodon sp., P. hilarii , A. affinis , P. cf.…”

“…The proximal region of FSR is composed of a DNA satellite (sat1WP). In the terminal region, an extensive amount of TE Helitron was verified and, in its whole extension, the FSR is invaded by degenerated TEs of different classes [Schemberger et al, 2014]. Thus, molecular differentiation and erosion of genetic activity of the W chromosome in Parodontidae occurred by accumulation of repetitive sequences of different kinds and classes, which may form domains in the chromatin and have a relation to the expression control of genes present in sex chromosomes and sexual determination.…”

“…Molecular differentiation and gene erosion in the evolution of sex chromosomes involve the accumulation of repetitive DNAs and transposable elements (TEs) [Steinemann and Steinemann, 2005;Schemberger et al, 2014].…”

“…On the other hand, Schemberger et al [2014] isolated a C o t-1 library for repetitive DNA in Parodontidae and verified a great amount of satellite and TE repetitive sequences, including those related to molecular degeneration of the W chromosome. These data show that the pseudo-autosomal region of the W chromosome is composed of the long arm of the Z chromosome and the short arm of the W chromosome, which harbors the DNA satellite p Ph 2004 in the genus Parodon .…”

“…Within this family, some species are homomorphic in relation to the presence of sex chromosomes, whereas other species present ZZ/ZW systems at different stages of accumulation of repetitive DNA [Schemberger et al, , 2014. Here, we report our analysis of the distribution patterns of (GATA)n and (TTAGGG)n repeats in different Parodontidae genomes to verify chromosome rearrangements focusing on the W chromosomes.…”