Resumo
Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology. Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. [...](AU)
Assuntos
Filogenia , Virologia/métodos , Evolução Molecular , Modelos Moleculares , Epidemiologia Molecular/métodos , Fenômenos GenéticosResumo
Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology. Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. [...]
Assuntos
Evolução Molecular , Filogenia , Modelos Moleculares , Virologia/métodos , Epidemiologia Molecular/métodos , Fenômenos GenéticosResumo
Background: Short interspersed nuclear elements (SINEs) are transposable elements which are transcribed by RNA polymerase III and widespread in mammalian genomes. Can-SINE is a family of SINE sequences specific to carnivores, predominant in their genomes and present in high copy numbers. The aim of this study was to characterize sequences of Can-SINEs integrated into sequences of endogenous retroviruses (ERVs) from Brazilian wild cats Puma concolor and Leopardus geoffroyi. Additionally, these sequences are considered from some perspectives of their evolution. Material, Methods and Results: By using PCR and sequencing to screen for ERVs within the genomes of L. geoffroyi and P. concolor, two new ERV sequences were amplified with an insertion around 220 nucleotides long, similar to published carnivore SINEs. The sequences were further identified and characterized using a combination of BLAST, BLAT searches and phylogenetic analyses. The results showed that SINE sequences integrated into the ERV from P. concolor (SINE_Pco) and L. geoffroyi (SINE_Lg) are lysine-tRNA derived. These sequences presented a typical RNA polymerase III-specific internal promoter sequence followed by a microsatellite region (TC)n and by an A/T-rich tail with the polyadenylation signal AATAAA. BLAST searches using the whole sequence of L. geoffroyi clone as query (ERV plus SINE) detected two sequences which were highly similar to the cougar (P. concolor) and the domestic cat. However, the SINE from Leopardus geoffroyi is not present in these related sequences. On the other hand, during searches using the whole sequence of the P. concolor clone as query, we found the same SINE insertion in a very similar ERV from domestic cat. All insertions occurred in the RT domain, but SINE_Lg was integrated in a distinct site when compared to SINE_Pco. Another interesting difference between these SINE sequences was that the statistics reported in BLAST searches recovered a much higher number of hits from the domestic cat genome using SINE_Lg as seed than in searches for sequences related to SINE_Pco. The phylogenetic tree based on the SINE fragment grouped these new SINE sequences with Can-SINEs from felids. Within this major clade SINE_Lg and SINE_Pco are related to different lineages of felids Can-SINEs. Discussion: In this study we showed that two different sequences from felid endogenous retrovirus harbor Can-SINE sequences. These insertions are not surprising taking account that ~11% of domestic cat genome is composed of SINE sequences and they are ubiquitous in felid genomes. Furthermore, the insertions of SINEs into the ERV sequences reported here are not unique events. However, they are curious insertions representing genomic fossils and a little piece of felid history. Based on the results of the phylogenetic analyses and position of the integration sites, we suggest that SINE_Lg and SINE_Pco represent independent integration events originated by derived copies from different progenitors. We hypothesized that SINE_Lg is a "young" integration due to the absence of highly similar ERVs from Puma concolor and Felis catus. This lineage may be recently active in felid genomes given that we found very similar MegaBLAST hits at EST database from domestic cat. Instead, SINE_Pco seems to be "old", sharing an identical insertion site to ERVs from domestic cat and its lineage could be inactive in felids considering that any MegaBLAST hits resulted from EST database searches. The latter suggests an integration event in an ancestor species at least 6.7 million years ago, which represents the split between puma and domestic cat lineages.
Assuntos
Animais , Retrovirus Endógenos , Elementos Nucleotídeos Curtos e Dispersos/genética , Felis/genética , Puma/genéticaResumo
Background: Short interspersed nuclear elements (SINEs) are transposable elements which are transcribed by RNA polymerase III and widespread in mammalian genomes. Can-SINE is a family of SINE sequences specific to carnivores, predominant in their genomes and present in high copy numbers. The aim of this study was to characterize sequences of Can-SINEs integrated into sequences of endogenous retroviruses (ERVs) from Brazilian wild cats Puma concolor and Leopardus geoffroyi. Additionally, these sequences are considered from some perspectives of their evolution. Material, Methods and Results: By using PCR and sequencing to screen for ERVs within the genomes of L. geoffroyi and P. concolor, two new ERV sequences were amplified with an insertion around 220 nucleotides long, similar to published carnivore SINEs. The sequences were further identified and characterized using a combination of BLAST, BLAT searches and phylogenetic analyses. The results showed that SINE sequences integrated into the ERV from P. concolor (SINE_Pco) and L. geoffroyi (SINE_Lg) are lysine-tRNA derived. These sequences presented a typical RNA polymerase III-specific internal promoter sequence followed by a microsatellite region (TC)n and by an A/T-rich tail with the polyadenylation signal AATAAA. BLAST searches using the whole sequence of L. geoffroyi clone as query (ERV plus SINE) detected two sequences which
Background: Short interspersed nuclear elements (SINEs) are transposable elements which are transcribed by RNA polymerase III and widespread in mammalian genomes. Can-SINE is a family of SINE sequences specific to carnivores, predominant in their genomes and present in high copy numbers. The aim of this study was to characterize sequences of Can-SINEs integrated into sequences of endogenous retroviruses (ERVs) from Brazilian wild cats Puma concolor and Leopardus geoffroyi. Additionally, these sequences are considered from some perspectives of their evolution. Material, Methods and Results: By using PCR and sequencing to screen for ERVs within the genomes of L. geoffroyi and P. concolor, two new ERV sequences were amplified with an insertion around 220 nucleotides long, similar to published carnivore SINEs. The sequences were further identified and characterized using a combination of BLAST, BLAT searches and phylogenetic analyses. The results showed that SINE sequences integrated into the ERV from P. concolor (SINE_Pco) and L. geoffroyi (SINE_Lg) are lysine-tRNA derived. These sequences presented a typical RNA polymerase III-specific internal promoter sequence followed by a microsatellite region (TC)n and by an A/T-rich tail with the polyadenylation signal AATAAA. BLAST searches using the whole sequence of L. geoffroyi clone as query (ERV plus SINE) detected two sequences which
Resumo
Background: Short interspersed nuclear elements (SINEs) are transposable elements which are transcribed by RNA polymerase III and widespread in mammalian genomes. Can-SINE is a family of SINE sequences specific to carnivores, predominant in their genomes and present in high copy numbers. The aim of this study was to characterize sequences of Can-SINEs integrated into sequences of endogenous retroviruses (ERVs) from Brazilian wild cats Puma concolor and Leopardus geoffroyi. Additionally, these sequences are considered from some perspectives of their evolution. Material, Methods and Results: By using PCR and sequencing to screen for ERVs within the genomes of L. geoffroyi and P. concolor, two new ERV sequences were amplified with an insertion around 220 nucleotides long, similar to published carnivore SINEs. The sequences were further identified and characterized using a combination of BLAST, BLAT searches and phylogenetic analyses. The results showed that SINE sequences integrated into the ERV from P. concolor (SINE_Pco) and L. geoffroyi (SINE_Lg) are lysine-tRNA derived. These sequences presented a typical RNA polymerase III-specific internal promoter sequence followed by a microsatellite region (TC)n and by an A/T-rich tail with the polyadenylation signal AATAAA. BLAST searches using the whole sequence of L. geoffroyi clone as query (ERV plus SINE) detected two sequences which
Background: Short interspersed nuclear elements (SINEs) are transposable elements which are transcribed by RNA polymerase III and widespread in mammalian genomes. Can-SINE is a family of SINE sequences specific to carnivores, predominant in their genomes and present in high copy numbers. The aim of this study was to characterize sequences of Can-SINEs integrated into sequences of endogenous retroviruses (ERVs) from Brazilian wild cats Puma concolor and Leopardus geoffroyi. Additionally, these sequences are considered from some perspectives of their evolution. Material, Methods and Results: By using PCR and sequencing to screen for ERVs within the genomes of L. geoffroyi and P. concolor, two new ERV sequences were amplified with an insertion around 220 nucleotides long, similar to published carnivore SINEs. The sequences were further identified and characterized using a combination of BLAST, BLAT searches and phylogenetic analyses. The results showed that SINE sequences integrated into the ERV from P. concolor (SINE_Pco) and L. geoffroyi (SINE_Lg) are lysine-tRNA derived. These sequences presented a typical RNA polymerase III-specific internal promoter sequence followed by a microsatellite region (TC)n and by an A/T-rich tail with the polyadenylation signal AATAAA. BLAST searches using the whole sequence of L. geoffroyi clone as query (ERV plus SINE) detected two sequences which
Resumo
Retrovírus endógenos (ERVs) são vírus altamente difundidos no genoma de vertebrados. ERVs surgem quando retrovírus exógenos infectam células germinativas e se disseminam no genoma de seus hospedeiros, transmitindo seu material genético através das gerações por meio de herança mendeliana. ERVs são fundamentais na evolução dos genomas, sendo eles responsáveis por uma parte da diversidade genética de seus hospedeiros. O conhecimento sobre ERVs na família Felidae (Mammalia, Carnivora) estava praticamente restrito ao gato doméstico, e não se conhecia diversidade e padrões de evolução desses retroelementos em outras espécies. Este estudo teve como objetivo investigar diversidade, distribuição e padrões evolutivos de ERVs em espécies de gatos silvestres. Utilizando ferramentas de biologia molecular e bioinformática, foram identificadas e caracterizadas 85 sequências similares a retrovírus endógenos nos representantes das oito espécies brasileiras: Leopardus pardalis, L. wiedii, L. colocolo, L. geoffroyi, L. tigrinus, Puma concolor, P. yagouaroundi e Panthera onca. Encontrou-se uma predominância de ERVs similares a Gammaretrovirus, um padrão característico em muitas espécies de mamíferos. As análises filogenéticas evidenciaram três grupos principais de Gammaretrovirus, cada um evoluindo de maneira peculiar. Em uma visão geral, os ERVs provenientes de diferentes hospedeiros apresentaram-se distribuídos de forma heterogênea nas filogenias, dificultando a constatação de um padrão coevolutivo. No entanto, análises mais detalhadas de algumas sequências demonstraram peculiaridades, como no caso de um grupo de sequências similares a de um ERV oriundo do morcego Myotis lucifugus. Através de análises filogenéticas em comparação com dados obtidos na literatura, sugere-se que a infecção desse retrovírus ocorreu em uma espécie ancestral de felídeo, na segunda metade do Mioceno. Os resultados obtidos permitiram demonstrar que os felídeos neotropicais apresentam ERVs que seguem padrões semelhantes aos descritos a respeito de outros mamíferos, sugerindo também alguns casos de infecções de retrovírus muito similares entre diferentes ordens de mamíferos