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      Non-random distribution of microsatellite motifs and (TTAGGG)n repeats in the monkey frog Pithecopus rusticus (Anura, Phyllomedusidae) karyotype

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          Abstract

          The monkey frog, Pithecopus rusticus (Anura, Phyllomedusidae) is endemic to the grasslands of the Araucarias Plateau, southern Brazil. This species is known only from a small population found at the type locality. Here, we analyzed for the first time the chromosomal organization of the repetitive sequences, including seven microsatellite repeats and telomeric sequences (TTAGGG)n in the karyotype of the species by Fluorescence in situ Hybridization. The dinucleotide motifs had a pattern of distribution clearly distinct from those of the tri- and tetranucleotides. The dinucleotide motifs are abundant and widely distributed in the chromosomes, located primarily in the subterminal regions. The tri- and tetranucleotides, by contrast, tend to be clustered, with signals being observed together in the secondary constriction of the homologs of pair 9, which are associated with the nucleolus organizer region. As expected, the (TTAGGG)n probe was hybridized in all the telomeres, with hybridization signals being detected in the interstitial regions of some chromosome pairs. We demonstrated the variation in the abundance and distribution of the different microsatellite motifs and revealed their non-random distribution in the karyotype of P. rusticus. These data contribute to understand the role of repetitive sequences in the karyotype diversification and evolution of this taxon.

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          The evolutionary dynamics of repetitive DNA in eukaryotes.

          Repetitive DNA sequences form a large portion of the genomes of eukaryotes. The 'selfish DNA' hypothesis proposes that they are maintained by their ability to replicate within the genome. The behaviour of repetitive sequences can result in mutations that cause genetic diseases, and confer significant fitness losses on the organism. Features of the organization of repetitive sequences in eukaryotic genomes, and their distribution in natural populations, reflect the evolutionary forces acting on selfish DNA.
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            Origin, evolution and genome distribution of microsatellites

            Microsatellites, or simple sequence repeats (SSRs), have been the most widely applied class of molecular markers used in genetic studies, with applications in many fields of genetics including genetic conservation, population genetics, molecular breeding, and paternity testing. This range of applications is due to the fact that microsatellite markers are co-dominant and multi-allelic, are highly reproducible, have high-resolution and are based on the polymerase chain reaction (PCR). When first introduced, the development of microsatellite markers was expensive but now new and efficient methods of repetitive sequence isolation have been reported, which have led to reduced costs and microsatellite-technology has been increasingly applied to several species, including non-model organisms. The advent of microsatellite markers revolutionized the use of molecular markers but the development of biometric methods for analyzing microsatellite data has not accompanied the progress in the application of these markers, with more effort being need to obtain information on the evolution of the repetitive sequences, which constitute microsatellites in order to formulate models that fit the characteristics of such markers. Our review describes the genetic nature of microsatellites, the mechanisms and models of mutation that control their evolution and aspects related to their genesis, distribution and transferability between taxa. The implications of the use of microsatellites as a tool for estimating genetic parameters are also discussed.
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              High-throughput analysis of the satellitome illuminates satellite DNA evolution

              Satellite DNA (satDNA) is a major component yet the great unknown of eukaryote genomes and clearly underrepresented in genome sequencing projects. Here we show the high-throughput analysis of satellite DNA content in the migratory locust by means of the bioinformatic analysis of Illumina reads with the RepeatExplorer and RepeatMasker programs. This unveiled 62 satDNA families and we propose the term “satellitome” for the whole collection of different satDNA families in a genome. The finding that satDNAs were present in many contigs of the migratory locust draft genome indicates that they show many genomic locations invisible by fluorescent in situ hybridization (FISH). The cytological pattern of five satellites showing common descent (belonging to the SF3 superfamily) suggests that non-clustered satDNAs can become into clustered through local amplification at any of the many genomic loci resulting from previous dissemination of short satDNA arrays. The fact that all kinds of satDNA (micro- mini- and satellites) can show the non-clustered and clustered states suggests that all these elements are mostly similar, except for repeat length. Finally, the presence of VNTRs in bacteria, showing similar properties to non-clustered satDNAs in eukaryotes, suggests that this kind of tandem repeats show common properties in all living beings.
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                Author and article information

                Journal
                Genet Mol Biol
                Genet. Mol. Biol
                gmb
                Genetics and Molecular Biology
                Sociedade Brasileira de Genética
                1415-4757
                1678-4685
                13 January 2020
                2019
                : 42
                : 4
                : e20190151
                Affiliations
                [ 1 ]Programa de Pós-graduação em Ciências Ambientais, Área de Ciências Exatas e Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, SC, Brazil.
                [ 2 ]Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil.
                [ 3 ]Departamento de Biologia Estrutural e Funcional, Universidade Estadual de Campinas, Campinas, SP, Brazil.
                [ 4 ]Departamento de Zootecnia e Ciências Biológicas, Universidade Federal de Santa Maria, Campus de Palmeira das Missões, Palmeira das Missões, RS, Brazil.
                Author notes
                Send correspondence to Daniel Pacheco Bruschi. Programa de Pós-graduação em Genética, Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil. E-mail: danielpachecobruschi@ 123456gmail.com .
                *These authors contributed equally to this work.
                Author information
                http://orcid.org/0000-0003-2171-3088
                http://orcid.org/0000-0003-2181-1788
                Article
                00301
                10.1590/1678-4685-GMB-2019-0151
                7198017
                31968045
                ac16541c-2c92-40b3-b932-6fb0f2e1ed9d
                Copyright © 2019, Sociedade Brasileira de Genética.

                License information: This is an open-access article distributed under the terms of the Creative Commons Attribution License (type CC-BY), which permits unrestricted use, distribution and reproduction in any medium, provided the original article is properly cited.

                History
                : 16 May 2019
                : 21 October 2019
                Page count
                Figures: 2, Tables: 0, Equations: 0
                Categories
                Animal Genetics

                Molecular biology
                amphibia,fluorescence in situ hybridization,repetitive dna
                Molecular biology
                amphibia, fluorescence in situ hybridization, repetitive dna

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