Conserved patterns in the evolution of Tribolium satellite DNAs

Mravinac, Brankica; Plohl, Miroslav; Ugarković, Đurđica

doi:10.1016/j.gene.2004.02.055

Cited by 31 publications

(12 citation statements)

References 31 publications

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“…In addition to preferential monomer length in the nine TR families structural analyses further revealed a periodic distribution of A or T tracts (4–10 nucleotides), in the same manner as observed in TCAST and other centromeric satDNAs found in several other Tribolium species. 22 The periodic appearance of AA/TT dimers along eukaryotic DNA sequences, including those in centromeric regions, promote this nucleotide sequence pattern as a feature that may facilitate nucleosome formation. 45 , 46 In this regard, periodically distributed tracts of As and/or Ts, present in many centromeric satDNAs of tenebrionid beetles were shown to define the sequence-induced curvature of the DNA helix axis and could facilitate the tight packing of DNA in centromeric heterochromatin.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of tandem repeats inTribolium castaneumgenome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

Pavlek

Gelfand

Plohl

et al. 2015

DNA Res

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Although satellite DNAs are well-explored components of heterochromatin and centromeres, little is known about emergence, dispersal and possible impact of comparably structured tandem repeats (TRs) on the genome-wide scale. Our bioinformatics analysis of assembled Tribolium castaneum genome disclosed significant contribution of TRs in euchromatic chromosomal arms and clear predominance of satellite DNA-typical 170 bp monomers in arrays of ≥5 repeats. By applying different experimental approaches, we revealed that the nine most prominent TR families Cast1–Cast9 extracted from the assembly comprise ∼4.3% of the entire genome and reside almost exclusively in euchromatic regions. Among them, seven families that build ∼3.9% of the genome are based on ∼170 and ∼340 bp long monomers. Results of phylogenetic analyses of 2500 monomers originating from these families show high-sequence dynamics, evident by extensive exchanges between arrays on non-homologous chromosomes. In addition, our analysis shows that concerted evolution acts more efficiently on longer than on shorter arrays. Efficient genome-wide distribution of nine TR families implies the role of transposition only in expansion of the most dispersed family, and involvement of other mechanisms is anticipated. Despite similarities in sequence features, FISH experiments indicate high-level compartmentalization of centromeric and euchromatic tandem repeats.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of tandem repeats inTribolium castaneumgenome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

Pavlek

Gelfand

Plohl

et al. 2015

DNA Res

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“…The conserved and variable segments in satellite DNA sequences were defined according to Mravinac et al (2004) by sliding window analysis using window size of 10 bp and step size of 1 bp. Windows that exhibited more than 2 standard deviations from the average variability were considered.…”

Section: Rna Extraction and Rt-pcrmentioning

confidence: 99%

CpSAT-1, a transcribed satellite sequence from the codling moth, Cydia pomonella

et al. 2016

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Satellite DNA (satDNA) is a non-coding component of eukaryotic genomes, located mainly in heterochromatic regions. Relevance of satDNA began to emerge with accumulating evidence of its potential yet hardly comprehensible role that it can play in the genome of many organisms. We isolated the first satDNA of the codling moth (Cydia pomonella, Tortricidae, Lepidoptera), a species with holokinetic chromosomes and a single large heterochromatic element, the W chromosome in females. The satDNA, called CpSAT-1, is located on all chromosomes of the complement, although in different amounts. Surprisingly, the satellite is almost missing in the heterochromatic W chromosome. Additionally, we isolated mRNA from all developmental stages (1st-5th instar larva, pupa, adult), both sexes (adult male and female) and several tissues (Malpighian tubules, gut, heart, testes, and ovaries) of the codling moth and showed the CpSAT-1 sequence was transcribed in all tested samples. Using CpSAT-1 specific primers we amplified, cloned and sequenced 40 monomers from cDNA and gDNA, respectively. The sequence analysis revealed a high mutation rate and the presence of potentially functional motifs, mainly in non-conserved regions of the monomers. Both the chromosomal distribution and the sequence analysis suggest that CPSAT-1 has no function in the C. pomonella genome.

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“…1). satDNAs from different organisms, as primates, cattle, rodents, nematodes, and insects, also present internal short repeats (e.g., Miklos and Gill 1982; Singer 1982; Modi 1992, 1993; Castagnone-Sereno et al 2000; Modi et al 2003; Lorite et al 2004; Mravinac et al 2004). The functional significance of these internal repeats is unclear but it has been assumed that it is associated with the conformation of chromatin (Modi 1993; Plohl 2010), as DNA secondary and tertiary structures can be induced by particular distributions of nucleotides (reviewed by Plohl 2010).…”

Section: Discussionmentioning

confidence: 99%

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

Paço

Adega

Meštrović

et al. 2014

Genome Biology and Evolution

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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.

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Conserved patterns in the evolution of Tribolium satellite DNAs

Cited by 31 publications

References 31 publications

Genome-wide analysis of tandem repeats inTribolium castaneumgenome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

Genome-wide analysis of tandem repeats inTribolium castaneumgenome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms

CpSAT-1, a transcribed satellite sequence from the codling moth, Cydia pomonella

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

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