Identification and characterization of a new family of long satellite DNA, specific of true toads (Anura, Amphibia, Bufonidae)

Abstract

Amphibians have some of the most variable genome sizes among vertebrates. Genome size variation has been attributed to repetitive and noncoding DNA, including satellite repeats, transposable elements, introns, and nuclear insertions of viral and organelle DNA. In vertebrates, satellite DNAs have been widely described in mammals, but few molecular studies have been carried out in amphibians. Here, we provide a detailed characterization of a new family of satellite DNA, present in all 15 examined species of the family Bufonidae. Southern-blot analysis and PCR reveal that this satellite is formed by monomers of 807 bp, is organized in tandem arrays, and has an AT-content of 57.4%. Phylogenetic analyses show that most clades exhibit species-specific variances, indicating that this satellite DNA has evolved by concerted evolution. The homogenization/fixation process is heterogeneous in Bufonidae, where the genera Bufo and Bufotes do not show species-specific differences, while populations from Rhinella marina exhibit population-specific changes. Additionally, variants of this satellite DNA have been identified in Duttaphrynus melanostictus and R. marina, supporting the ‘library hypothesis’ (a set, ‘library’, of satellite DNAs is shared by a species group). Physical mapping in Bufo bufo, Bufo spinosus, Epidalea calamita and Bufotes viridis provides evidence that this repetitive DNA is not dispersed in the karyotype, but accumulated in pericentromeric regions of some chromosomal pairs. This location, together with its presence in the transcriptomes of bufonids, could indicate a role in centromere function or heterochromatin formation and maintenance.

Cytogenetic Analysis in the Toad Species Bufo spinosus, Bufotes viridis and Epidalea calamita (Anura, Bufonidae) from the Mediterranean Area

“…The hybridization pattern shows that B. bufo , B. spinosus and B. viridis have a large accumulation of repetitive DNA in the centromeres of all chromosomes, while in E. calamita the signal spreads along chromosome arms, with accumulation at the centromeres and at the tip of the chromosomes. Of note is the presence in E. calamita of intense signals in 1p and 3p in pericentromeric position (see Figure S2 ), probably due to the presence of satellite DNA BamHI-800 in this position [ 25 ].…”

“…Similar hybridization pattern, although less evident, is observed when B. viridis genomic DNA is used as probe with the chromosomes of the previous species ( Figure 5 C,G). Finally, the ends of E. calamita chromosomes show intense hybridization signals with B. spinosus probe ( Figure 5 N), while the probe from B. viridis reveals less intense signals in telomeric and in some centromeric regions that could be due to BamHI-800 satellite DNA [ 25 ] ( Figure 5 O).…”

“…Capture permits for B. spinosus and E. calamita were provided by the Junta de Andalucía, Dirección General de Gestión del Medio Natural (2010, 2012). B. viridis clutches were sampled for a previous work [ 25 ]. B. bufo samples (DNA and mitotic chromosomes) were a generous gift from Francesco Zaccanti’s laboratory.…”

“…B. bufo samples (DNA and mitotic chromosomes) were a generous gift from Francesco Zaccanti’s laboratory. Mitotic chromosomes from an adult E. calamita were available from a previous work [ 25 ]. All animal protocols were approved by the Ethics Committee for Research on Animals of the University of Jaén (2009).…”

Consequences of polyploidy and divergence as revealed by cytogenetic mapping of repetitive elements in African clawed frogs (Xenopus, Pipidae)

“…In Amphibia, cytogenetic mapping of repetitive sequences is a subject of study of inter-and intraspeci c rearrangements, karyotype evolution, and/or cytotaxonomy [da Phimphan et al, 2021;Guzmán et al, 2022]. African clawed frogs of the genus Xenopus involve almost 30 species and include two subgenera (Xenopus and Silurana).…”