Molecular evolution of satellite DNA repeats and speciation of lizards of the genus Darevskia (Sauria: Lacertidae)

Genome ◽  
2006 ◽  
Vol 49 (10) ◽  
pp. 1297-1307 ◽  
Author(s):  
Vernata V. Grechko ◽  
Doina G. Ciobanu ◽  
Ilya S. Darevsky ◽  
Sergey A. Kosushkin ◽  
Dmitri A. Kramerov
Keyword(s):  
Molecular Evolution ◽  
Satellite Dna ◽  
Sequence Similarity ◽  
Distribution Patterns ◽  
Hybrid Origin ◽  
Dna Repeats ◽  
Lizard Species ◽  
Origin Of Species ◽  
Rock Lizard

Satellite DNA repeats were studied in Caucasian populations of 18 rock lizard species of the genus Darevskia. Four subfamilies (Caucasian Lacerta satellites (CLsat)I–IV) were identified, which shared 70%–75% sequence similarity. The distribution of CLsat subfamilies among the species was studied. All the species could be divided into at least 3 clades, depending on the content of CLsat subfamilies in each genome: “saxicola”, “rudis”, and “mixta” lizards. CLsatI was found in all studied species, but in very different quantities; the “saxicola” group contained this subfamily predominantly. The “rudis” group also contained CLsatIII, and the “mixta” group carried considerable amounts of CLsatII. The highest concentrations of CLsatI and CLsatII were detected in 2 ground lizards — D. derjugini and D. praticola, respectively. D. parvula predominantly carried CLsatIII. CLsatIV was found only in the Crimean species D. lindholmi. The distribution patterns of satellite subfamilies show possible postglacial speciation within the genus Darevskia. A hybrid origin of species that possess 2 or 3 CLsat subfamilies and important clarifications to the systematics of the genus are proposed.

Evolutionary dynamics of satellite DNA repeats from Phaseolus beans

PROTOPLASMA ◽  
2016 ◽  
Vol 254 (2) ◽  
pp. 791-801 ◽  
Author(s):  
Tiago Ribeiro ◽  
Karla G. B. dos Santos ◽  
Manon M. S. Richard ◽  
Mireille Sévignac ◽  
Vincent Thareau ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Evolutionary Dynamics ◽  
Dna Repeats

Satellite DNA in Plants: More than Just Rubbish

2015 ◽  
Vol 146 (2) ◽  
pp. 153-170 ◽  
Author(s):  
Manuel A. Garrido-Ramos
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Dna Repeats ◽  
Satellite Dnas ◽  
Factors Affecting ◽  
Functional Roles ◽  
Tandem Repeat Sequences ◽  
Satellite Repeats ◽  
History Of ◽  
Main Components

For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

scholarly journals Cross-species incompatibility between a DNA satellite and a chromatin protein poisons germline genome integrity

2021 ◽  
Author(s):  
Cara L Brand ◽  
Mia T Levine
Keyword(s):  
Satellite Dna ◽  
Rapid Evolution ◽  
Genome Integrity ◽  
Dna Repeats ◽  
Chromatin Protein ◽  
Genetic Rescue ◽  
Chromatin Proteins ◽  
Genomic Regions ◽  
Female Germline ◽  
Nuclear Processes

Satellite DNA spans megabases of eukaryotic genome sequence. These vast stretches of tandem DNA repeats undergo high rates of sequence turnover, resulting in radically different satellite DNA landscapes between closely related species. Such extreme evolutionary plasticity suggests that satellite DNA accumulates mutations with no functional consequence. Paradoxically, satellite-rich genomic regions support essential, conserved nuclear processes, including chromosome segregation, dosage compensation, and nuclear structure. A leading resolution to this paradox is that deleterious alterations to satellite DNA trigger adaptive evolution of chromatin proteins to preserve these essential functions. Here we experimentally test this model of coevolution between chromatin proteins and DNA satellites by conducting an evolution-guided manipulation of both protein and satellite. We focused on an adaptively evolving, ovary-enriched chromatin protein, called Maternal Haploid (MH) from Drosophila. MH co-localizes with an 11 Mb 359-bp satellite array present in Drosophila melanogaster but absent in its sister species, D. simulans. Using CRISPR/Cas9-mediated transgenesis, we swapped the D. simulans version of MH into D. melanogaster. We discovered that D. melanogaster females encoding only the D. simulans mh (mh[sim]) do not phenocopy the mh null mutation. Instead, MH[sim] is toxic to D. melanogaster ovaries: we observed elevated ovarian cell death, reduced ovary size, and subfertility in mh[sim] females. Using both cell biological and genetic approaches, we demonstrate that MH[sim] poisons oogenesis through a DNA damage pathway. Remarkably, deleting the D. melanogaster-specific 359 satellite array from mh[sim] females completely restores female germline genome integrity and fertility. This genetic rescue offers experimental evidence that rapid evolution resulted in a cross-species incompatibility between the 359 satellite and MH. These data suggest that coevolution between ostensibly inert repetitive DNA and essential chromatin proteins preserves germline genome integrity.

scholarly journals Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis

2018 ◽  
Author(s):  
Jaclyn M Fingerhut ◽  
Jessica V Moran ◽  
Yukiko Yamashita
Keyword(s):  
Gene Expression ◽  
Satellite Dna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Gene Expression Program ◽  
Dna Repeats ◽  
Regulate Gene Expression ◽  
Unique Gene ◽  
Expression Of Genes ◽  
Expression Program

Intron gigantism, where genes contain megabase-sized introns, is observed across species, yet little is known about its purpose or regulation. Here we identify a unique gene expression program utilized for the proper expression of genes with intron gigantism. We find that two Drosophila genes with intron gigantism, kl-3 and kl-5, are transcribed in a spatiotemporal manner over the course of spermatocyte differentiation, which spans ~90 hours. The introns of these genes contain megabases of simple satellite DNA repeats that comprise over 99% of the gene loci, and these satellite-DNA containing introns are transcribed. We identify two RNA-binding proteins that specifically localize to kl-3 and kl-5 transcripts and are needed for the successful transcription or processing of these genes. We propose that genes with intron gigantism require a unique gene expression program, which may serve as a platform to regulate gene expression during cellular differentiation.

scholarly journals A Preliminary Investigation of Marine Yeast Biodiversity in New Zealand Waters

2021 ◽  
Author(s):  
◽  
Melissa Francis
Keyword(s):  
Sequence Data ◽  
Sequence Similarity ◽  
Preliminary Investigation ◽  
Distribution Patterns ◽  
Marine Yeasts ◽  
Marine Yeast ◽  
Yeast Biomass ◽  
Ecological Implications ◽  
Terrestrial Environments ◽  
Biocontrol Potential

<p>This is the first known investigation of marine yeast biodiversity from waters surrounding New Zealand’s main Islands. Marine yeasts were cultured onto agar plates from algae sampled at three locations in the Wellington Region. DNA extractions and PCR amplifications of the internal transcribed spacer (ITS) regions were conducted, and resultant sequence data were used for isolate identification and phylogenetic analysis. Yeasts isolated during this investigation were not unique; seventy-four isolates were identified from a range of genera that are frequently detected in marine and terrestrial environments worldwide. Furthermore, high ITS sequence similarity was observed between yeasts isolated during this investigation and those from geographically distant locations. These findings may indicate that marine yeasts are ubiquitous at a global level, although evidence is insufficient as to whether yeasts also demonstrate biogeographic distribution patterns. Yeasts isolated during this investigation may have ecological implications in New Zealand’s marine environment; marine yeasts are likely to play a general saprophytic role and certain genera are pathogenic. Isolates were also identified from genera that have previously demonstrated beneficial properties and applications, including the production of useful compounds and highly nutritious yeast biomass, biocontrol potential against the postharvest decay of produce, and degradation abilities that may enable bioremediation of polluted marine environments.</p>

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