The puzzling character of repetitive DNA in Phodopus genomes (Cricetidae, Rodentia)

Abstract

Three novel repetitive DNA sequences are described, presenting a similar heterochromatic chromosomal location in two hamster species: Phodopus roborovskii and Phodopus sungorus (Cricetidae, Rodentia). Namely, two species-specific repetitive sequences (PROsat from P. roborovskii and PSUchr1sat from P. sungorus) surrounding a third one (PsatDNA), that is shared by both hamster genomes. Fiber-FISH analyses revealed that PROsat intermingles with PsatDNA in P. roborovskii and PSUchr1sat intermingles with PsatDNA in P. sungorus. A model explaining the evolution of this intricate chromosomal distribution is proposed, which can explain better the evolution of these very derivative genomes (in comparison to the ancestral Muroidea). The most plausible evolutionary scenario seems to be the expansion of a number of repeats into other's domain, most probably resulting in its intermingling, followed by the subsequent spread of these complex repeats from a single chromosomal location to other chromosomes. Evidences of an association between repetitive sequences and the chromosome evolution process were observed, namely for PROsat. Most probably, the evolutionary breakpoints that shaped PRO and PSU chromosomes (pericentric inversions and fusions) occurred within the boundaries of PROsat blocks in the ancestor. The repeats high diversity at the heterochromatic regions of Phodopus chromosomes, together with its complex organization, suggests that these species are important models for evolutionary studies, namely in the investigation of a possible relationship between repetitive sequences and the occurrence of chromosomal rearrangements and consequently, in genome evolution.

High-throughput analysis of the satellitome revealed enormous diversity of satellite DNAs in the neo-Y chromosome of the cricket Eneoptera surinamensis

“…However, overlapping distribution of non-homologous satDNAs as observed here for E . surinamensis was reported only in a few cases, e.g., the DBC-150 and pBuM satDNAs family in several Drosophila species 54 the pSc200 and pSC250 families in the rye chromosomes 55 and the PROsat, PSUchr1sat and PsatDNA satDNAs in two species of hamsters 56 .…”

Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene

“…In fact, a considerable part of micro and minisatellites in eukaryotic genomes are embedded within mobile elements [115,117], which points to an important role of TEs in its genomic distribution, explaining its common dispersed chromosomal location. Moreover, TEs are present in pericentromeric regions of a wide range of species [27,70,74], being these regions also mainly built by satDNAs, which certainly facilitate the dispersion of these highly tandem repeats by retrotransposition. The first duplications of a tandem repeat were originated from a part of a TE.…”

“…Regarding LINE-1 retrotransposons, several reports suggest a location of these elements in pericentromeric regions of different mammalian species chromosomes [27,66,70,[118][119][120], pointing to an intermingling of these retrotransposons with satDNAs [66,118]. This complex organization pattern of repetitive sequences in the pericentromeric regions eventually favours the dispersion of satDNAs to other genomic locations by LINE-1 retrotransposition, since these elements frequently allow for the transduction of flanking non-LINE-1 DNA to new genomic locations ( Figure 4B).…”

“…In summary, this fraction seems to be involved in DNA packaging, the evolutionary events of the genome (through promoting DNA instability), gene expression, and epigenetic mechanisms [14][15][16][17][18][19][20][21][22][23][24][25]. The analysis of the DNA sequences located in chromosomal breakpoint regions strongly suggests that repetitive sequences work as a driving force in the occurrence of chromosomal rearrangements, since these regions are extremely rich in these sequences [26,27]. The repetitive nature, per se, of the different classes of repeats located in these breakpoint regions favours recombinational events between homologous sequences in non-homologous regions, which may culminate in chromosomal restructurings [21].…”

Selection Constrains High Rates of Tandem Repetitive DNA Mutation inDaphnia pulex

“…Since many tandem repeats are contained in satellite DNA near centromeric regions, there is evidence that selection acts on the sequence motifs themselves, as they serve to bind centromere and histone proteins for centromere maintenance and chromosome separation (Henikoff et al 2001;Malik 2009). These functions have implications for genome stability, and changes in satellite DNA sequences have been shown in some cases to be drivers of speciation by inducing chromosome rearrangements leading to karyotype divergence (Paço et al 2015). Moreover, some satellite sequences are transcribed and may be involved in the regulation of heterochromatin formation (Palomeque and Lorite 2008;Plohl et al 2008).…”