Evolutionary Story of a Satellite DNA from Phodopus sungorus (Rodentia, Cricetidae)

Abstract

With the goal to contribute for the understanding of satellite DNA evolution and its genomic involvement, in this work it was isolated and characterized the first satellite DNA (PSUcentSat) from Phodopus sungorus (Cricetidae). Physical mapping of this sequence in P. sungorus showed large PSUcentSat arrays located at the heterochromatic (peri)centromeric region of five autosomal pairs and Y-chromosome. The presence of orthologous PSUcentSat sequences in the genomes of other Cricetidae and Muridae rodents was also verified, presenting however, an interspersed chromosomal distribution. This distribution pattern suggests a PSUcentSat-scattered location in an ancestor of Muridae/Cricetidae families, that assumed afterwards, in the descendant genome of P. sungorus a restricted localization to few chromosomes in the (peri)centromeric region. We believe that after the divergence of the studied species, PSUcentSat was most probably highly amplified in the (peri)centromeric region of some chromosome pairs of this hamster by recombinational mechanisms. The bouquet chromosome configuration (prophase I) possibly displays an important role in this selective amplification, providing physical proximity of centromeric regions between chromosomes with similar size and/or morphology. This seems particularly evident for the acrocentric chromosomes of P. sungorus (including the Y-chromosome), all presenting large PSUcentSat arrays at the (peri)centromeric region. The conservation of this sequence in the studied genomes and its (peri)centromeric amplification in P. sungorus strongly suggests functional significance, possibly displaying this satellite family different functions in the different genomes. The verification of PSUcentSat transcriptional activity in normal proliferative cells suggests that its transcription is not stage-limited, as described for some other satellites.

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

“…In this species the authors found short PMSsat arrays and even dispersed isolated monomers, which reinforces that the limitation of techniques to isolate and analyse the repetitive fractions of genomes (as sequencing, assembly and mapping technologies) is a determining factor for the study of repetitive sequences, as well as for its accurate classification. Other reports have also come to prove the same, showing a dispersed genomic organization of short arrays of satDNA repeat units [44,48].…”

“…However, once again, exceptions have been reported as to what is generally assumed. Indeed, satDNA can also be located at interstitial and terminal positions of chromosomes [26,47,48].…”

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

“…Isolation, cloning and sequencing of PROsat, PSUchr1sat, and PsatDNA PROsat and PsatDNA were isolated from PRO genome and PSUchr1sat from PSU genome, following a very similar strategy to the one described by Biscotti et al (2007) and Paço et al (2014). PRO genomic DNA was digested with the restriction endonucleases (REs) MboI or HinfI (for the isolation of PROsat and PsatDNA, respectively), and PSU genomic DNA was digested with the endonuclease MboI (allowing the isolation of PSUchr1sat) according to the manufacturer's instructions (Invitrogen Life Technologies).…”

A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation

“…Real-time PCR has been previously used to access the copy number of repetitive sequences, combining the use of standard primers with SYBR Green I chemistry (Navajas-Pérez et al, 2009). In the present study, we applied a more innovative methodology using specific TaqMan probe/primers, as described recently by our group in Paço et al (2014). Some drawbacks were anticipated for this method, as it is based on PCR, and for that reason some variations may remain hidden, or bias that may distort the observed representation of the satDNA variability could be introduced due to the primer specificity.…”