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

Louzada, Sandra; Vieira-da-Silva, A.; Mendes-da-Silva, Ana; Kubı́čková, Svatava; Rubeš, Jiřı́; Adega, Filomena; Chaves, Raquel

doi:10.1016/j.ympev.2015.06.008

Cited by 10 publications

(21 citation statements)

References 51 publications

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“…However, more precise genomic and bioinformatic analyses have now shown that these sequences do not have such a tight genomic organization. Some satDNAs may present dispersed isolated monomers in a genome [47] while TEs may have a kind of tandem organization of their copies [69]. Moreover, it became evident that a repetitive element can often be remodelled into a different sequence, a repetitive non-coding sequence or even a coding sequence.…”

Section: Discussionmentioning

confidence: 99%

“…However, satDNAs with a different organization have already been reported. Louzada and colleagues (2015) [47], identify a satDNA (PMsat) with high sequence conservation in the genomes of five rodents. However, the PMSat is not always organized into long array repeat units, even in species where it is highly abundant, as is the case of Peromyscus maniculatus bairdii.…”

Section: Tandem Repeats Organizationmentioning

confidence: 99%

“…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].…”

Section: Tandem Repeats Organizationmentioning

confidence: 99%

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

Paço

Freitas

Vieira-da-Silva

2019

Genes

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Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.

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Section: Discussionmentioning

confidence: 99%

Section: Tandem Repeats Organizationmentioning

confidence: 99%

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

Paço

Freitas

Vieira-da-Silva

2019

Genes

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“…The satDNAs within the library may differ in monomer sequence, size, abundance, distribution and location (reviewed in [12]). Expansions and contractions of satDNA arrays can dramatically change the landscape of repetitive sequences, leading to significant differences of satDNA copy number among related species [49,50]. That is the case of the Drosophila genus, which contains very dissimilar satDNAs, varying from 0.5% in some species genomes to as high as 50% in others [51,52].…”

Section: Satdna Features and Organization In The Genome And Chromosommentioning

confidence: 99%

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

Louzada

Lopes

Ferreira

et al. 2020

Genes

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Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.

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“…However, the copy number of centromeric repeats on the bi-armed VVU chromosomes is not sufficient for the production of a detectable signal with the canine satellite DNA probe. The reduction of centromeric heterochromatin on biarmed chromosomes, compared to acrocentrics, was previously reported, e.g., among Artiodactyla and Rodentia [Modi et al, 1996;Kopecna et al, 2014;Louzada et al, 2015]. (2) Assuming a low chromosome number in the ancestral carnivore karyotype (2n = 38), the domestic dog (2n = 78) seems to represent one of the most derived karyotypes among Canidae [Graphodatsky et al, 2001;Nash et al, 2008].…”

Section: Discussionmentioning

confidence: 72%

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox

Vozdová¹,

Kubı́čková²,

Černohorská³

et al. 2016

Cytogenet Genome Res

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Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox.

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

Cited by 10 publications

References 51 publications

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

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

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox

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