Um novo conjunto de DNAs satélites compartilhado por todos os Characoidei (Characiformes, Teleostei)
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Data
2022-07-01
Autores
Giglio, Leonardo Moura
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Universidade Estadual Paulista (Unesp)
Resumo
O genoma dos organismos eucariotos apresenta uma porção repetitiva bastante expressiva, com a classe dos DNAs satélites podendo representar grande parte do DNA nuclear e, também, contribuir para a diferença do tamanho dos genomas entre diferentes espécies. Considera-se que os DNAs satélites surgem a partir de duplicações de novo de sequências preexistentes no genoma das espécies, se disseminam, e posteriormente expandem seus arranjos, a forma em que se organizam. Esses arranjos passam por processos de homogeneização e posterior fixação de sua composição, sob o regime da evolução em concerto. Esses mecanismos evolutivos podem agir independentemente nas diferentes espécies, inclusive, agir independentemente nos diferentes arranjos dentro de um mesmo genoma, o que normalmente resulta em DNAs satélites gênero ou espécie específicos. Porém, hoje temos conhecimento de alguns casos de satélites que se mantiveram conservados em diferentes espécies distribuídas por táxons maiores, como toda uma ordem, apresentando inclusive transcrição, o que vai contra as predições da evolução em concerto em um contexto de ausência de função. Outro modelo de evolução de DNAs satélites é o da hipótese library , que prediz que grupos proximamente relacionados compartilham uma porção do conteúdo ancestral de DNAs satélites, apresentando normalmente diferenças quantitativas relativas a sua abundância no genoma. No presente estudo utilizamos a subordem dos peixes Characoidei, da ordem dos Characiformes, altamente diversa e com origem antiga, e portanto considerada ideal para verificar a existência de satélites compartilhados pelo grupo, testar a hipótese library, e analisar a ação da evolução em concerto nos satélites destas espécies. Para isto, utilizamos bibliotecas genômicas de 15 espécies de diferentes famílias da ordem dos Characiformes e realizamos análises bioinformáticas com a aplicação do TAREAN, uma ferramenta que utiliza um algoritmo de agrupamento de reads para realizar o isolamento dos DNAs satélites das espécies, além de ferramentas de montagem de novo, alinhamento e mapeamento de cópias para realizar a comparação destes satélites entre as espécies. Encontramos sete DNAs satélites presentes nas quatro superfamílias de peixes Characoidei analisadas, demonstrando o compartilhamento de satélites super conservados por toda uma subordem, o que contraria as predições da evolução em concerto, e também corroboram com a hipótese library de evolução dos DNAs satélties.
The eukaryotic genomes present a very expressive repetitive portion, with the satellite DNAs class representing a great part of the nuclear DNA and, also, contributing to the differences observed in the species genome sizes. Its assumed that the satellite DNAs originate by de novo duplications in preexistent sequences in the genome, are scattered to different locations and, subsequently, expand their arrays, the way they are organized. These arrays goes through composition homogenization and fixation steps, under the concerted evolution regime. These evolutive mechanisms can act independently in each species, or even act differently in arrays of different genomic locations, and that usually results in genus- or species-specific sallite DNAs. However, today we know of some cases of satellites that have remained conserved in different species distributed over larger taxa, such as an entire order, even presenting transcription, which goes against the predictions of concerted evolution in a context of absent function. Another model of satellite DNA evolution is the library hypothesis, which predicts that closely related groups share a portion of the ancestral content of satellite DNAs, typically showing quantitative differences relative to their abundance in the genome. In the present study, we used the suborder of Characoidei fishes, from the order Characiformes, highly diverse and with ancient origin, and therefore considered ideal to verify the existence of satellites shared by the group, test the library hypothesis, and analyze the action of the concerted evolution in the satellites of these species. For this, we used genomic libraries of 15 species from different families of the Characiformes order and performed bioinformatic analyses with the application of TAREAN, a tool that uses a read clustering algorithm to isolate the species satellite DNAs, as well as de novo assembly, alignment, and copy mapping tools to compare these satellites between species. We found seven satellite DNAs present in the four analyzed Characoidei fish superfamilies, demonstrating the sharing of super conserved satellites across an entire suborder, which contradicts the predictions of concerted evolution, and also corroborates with the library hypothesis of satellite DNA evolution.
The eukaryotic genomes present a very expressive repetitive portion, with the satellite DNAs class representing a great part of the nuclear DNA and, also, contributing to the differences observed in the species genome sizes. Its assumed that the satellite DNAs originate by de novo duplications in preexistent sequences in the genome, are scattered to different locations and, subsequently, expand their arrays, the way they are organized. These arrays goes through composition homogenization and fixation steps, under the concerted evolution regime. These evolutive mechanisms can act independently in each species, or even act differently in arrays of different genomic locations, and that usually results in genus- or species-specific sallite DNAs. However, today we know of some cases of satellites that have remained conserved in different species distributed over larger taxa, such as an entire order, even presenting transcription, which goes against the predictions of concerted evolution in a context of absent function. Another model of satellite DNA evolution is the library hypothesis, which predicts that closely related groups share a portion of the ancestral content of satellite DNAs, typically showing quantitative differences relative to their abundance in the genome. In the present study, we used the suborder of Characoidei fishes, from the order Characiformes, highly diverse and with ancient origin, and therefore considered ideal to verify the existence of satellites shared by the group, test the library hypothesis, and analyze the action of the concerted evolution in the satellites of these species. For this, we used genomic libraries of 15 species from different families of the Characiformes order and performed bioinformatic analyses with the application of TAREAN, a tool that uses a read clustering algorithm to isolate the species satellite DNAs, as well as de novo assembly, alignment, and copy mapping tools to compare these satellites between species. We found seven satellite DNAs present in the four analyzed Characoidei fish superfamilies, demonstrating the sharing of super conserved satellites across an entire suborder, which contradicts the predictions of concerted evolution, and also corroborates with the library hypothesis of satellite DNA evolution.
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Palavras-chave
Genética animal, Genômica, DNA repetitivo, Ostariophysi, Bioinformática, Genomics, Bioinformatics, Repetitive DNA