Exaptação de elementos de transposição (TEs) em Drosophila mojavensis e viés de expressão de genes e TEs em gônadas de D. mojavensis e D. arizonae e seus híbridos
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Data
2021-12-17
Autores
Simão, Maryanna Cristiano [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
Elementos de transposição (TEs) são sequências repetitivas de DNA capazes de se mobilizar dentro e entre genomas que devido a essa habilidade, além de efeitos deletérios, podem trazer vantagens ao genoma hospedeiro, tais como o aumento do repertório proteico, ou influenciarem a regulação gênica. O material de estudo desta tese foi o genoma de Drosophila mojavensis, uma espécie cactofílica, nativa de regiões áridas e semiáridas, que utiliza como sítio de alimentação e reprodução um recurso menos rico que os utilizados pela maioria das espécies de Drosophila e, consequentemente, tal hábito deve estar relacionado a adaptações específicas. Como os TEs são fontes importantes de variação genética, particularmente em resposta ao estresse ambiental, como também podem fornecer matéria-prima para o surgimento de genes codificadores de proteínas (PCG) e de RNAs não codificantes (ncRNA), os quais podem assumir funções celulares importantes, um dos objetivos desta tese foi investigar a associação entre TEs e esses genes em espécies cactofílicas, como estratégia para ampliar nossa compreensão sobre a contribuição dos TEs para a evolução adaptativa. Além disso, mesmo sendo a maioria dos genes comuns aos genomas de machos e fêmeas, genes e TEs podem ser expressos diferencialmente entre testículos e ovários. A análise dos transcriptomas das gônadas torna possível investigar como ou se o viés de expressão de genes e de TEs afeta a reprodução de híbridos interespecíficos. A fim de entender melhor essas questões, foi estudado nesta tese o viés de expressão das gônadas de D. mojavensis e D. arizonae e de seus híbridos recíprocos. Neste estudo mostramos que o conteúdo de TEs representa 13,27% do genoma de D. mojavensis e que a proporção de genes que abrigam sequências de TEs dentro dos éxons é de 5,9%, e que a proporção de ordens de TEs dentro destes éxons difere daquela do genoma geral (LINEs: 78,8% > LTR: 18,5% > TIRs: 2,4% > Helitrons: 0,3%). Entre todas as inserções de TEs encontrados nos genes PCG e lncRNA, apenas 19 sequências apresentaram domínios proteicos preservados. Foram identificados vários genes candidatos à exaptação de TEs no genoma D. mojavensis e a maioria deles abrigam sítios de ligação ao DNA, particularmente domínios zinc-finger, destacando o papel dos TEs como fonte de novidades funcionais aos genomas, evidenciando que esta associação entre sítios específicos de ligação de DNA e TEs é recorrente e talvez uma das fontes principais de novidades genômicas. A maioria dos genes e TEs com viés de expressão estão presentes em ambas as espécies parentais, sendo que em testículos a expressão de genes e TEs é cerca de três vezes maior do que em ovários, destacando que a expressão entre as gônadas em Drosophila é conservada e característica do grupo. Contudo, existem diferenças específicas de genes com viés de expressão entre as espécies parentais e entre os híbridos, que podem ter um papel importante na reprodução. Além disso, as famílias de TEs superexpressas em testículos são mais diversas que os genes superexpressos, esse fato pode estar diretamente relacionado com a influência dos piRNAs na regulação, principalmente devido ao fato dos piRNAs presente nos híbridos ter um padrão diferente dos encontrados nas espécies parentais
Transposable elements (TEs) are repetitive DNA sequences able to mobilize within and between genomes that due to this ability, besides deleterious effects, can bring advantages to the host genome, such as increasing the protein repertoire or influencing gene regulation. The study material of this thesis was the genome of Drosophila mojavensis, a cactophilic species, native to arid and semi-arid regions, which uses as feeding and breeding site that is less rich in resource than those used by most Drosophila species and, consequently, such habits must be related to specific adaptations. As TEs are important sources of genetic variation, particularly in response to environmental stress, and can also provide raw material for the emergence of protein-coding genes (PCG) and non-coding RNAs (ncRNA), which can assume important cellular functions, one of the objectives of this thesis was to investigate the association between TEs and these genes in cactophilic species, as a strategy to broaden our understanding of TEs contribution to adaptive evolution. Furthermore, even though most genes are common to male and female genomes, genes and TEs may be differentially expressed between testes and ovaries. Analysis of the gonad transcriptomes makes it possible to investigate how or if the expression bias of genes and TEs affects the reproduction of interspecific hybrids. In order to better understand these questions, the expression bias of the gonads of D. mojavensis and D. arizonae and their reciprocal hybrids was studied in this thesis. In this study, we show that TE content represents 13.27% of the D. mojavensis genome and that the proportion of genes harboring TE sequences within exons is 5.9%, and that the proportion of TE orders within these exons differs from that of the overall genome (LINEs: 78.8% > LTR: 18.5% > TIRs: 2.4% > Helitrons: 0.3%). Among all TE insertions found in PCG and lncRNA genes, only 19 sequences showed preserved protein domains. Several candidate genes for TEs exaptation were identified in the D. mojavensis genome and most of them harbor DNA-binding sites, particularly zinc-finger domains, highlighting the role of TEs as a source of functional novelties to genomes, evidencing that this association between specific DNA-binding sites and TEs is recurrent and perhaps one of the major sources of genomic novelties. Most sex-biased genes and TEs are present in both parental species, and there are three times more testis-biased genes and TEs than ovary-biased, highlighting that expression between gonads in Drosophila is conserved and characteristic of the group. However, there are specific differences in sex-bias expression between parental species and between hybrids, which may play an important role in reproduction. Furthermore, testis-biased TE families are more diverse than testes biased genes, this fact may be directly related to the influence of piRNAs on the regulation, mainly due to the fact that piRNAs from the hybrids have a different pattern than those found in the parental species.
Transposable elements (TEs) are repetitive DNA sequences able to mobilize within and between genomes that due to this ability, besides deleterious effects, can bring advantages to the host genome, such as increasing the protein repertoire or influencing gene regulation. The study material of this thesis was the genome of Drosophila mojavensis, a cactophilic species, native to arid and semi-arid regions, which uses as feeding and breeding site that is less rich in resource than those used by most Drosophila species and, consequently, such habits must be related to specific adaptations. As TEs are important sources of genetic variation, particularly in response to environmental stress, and can also provide raw material for the emergence of protein-coding genes (PCG) and non-coding RNAs (ncRNA), which can assume important cellular functions, one of the objectives of this thesis was to investigate the association between TEs and these genes in cactophilic species, as a strategy to broaden our understanding of TEs contribution to adaptive evolution. Furthermore, even though most genes are common to male and female genomes, genes and TEs may be differentially expressed between testes and ovaries. Analysis of the gonad transcriptomes makes it possible to investigate how or if the expression bias of genes and TEs affects the reproduction of interspecific hybrids. In order to better understand these questions, the expression bias of the gonads of D. mojavensis and D. arizonae and their reciprocal hybrids was studied in this thesis. In this study, we show that TE content represents 13.27% of the D. mojavensis genome and that the proportion of genes harboring TE sequences within exons is 5.9%, and that the proportion of TE orders within these exons differs from that of the overall genome (LINEs: 78.8% > LTR: 18.5% > TIRs: 2.4% > Helitrons: 0.3%). Among all TE insertions found in PCG and lncRNA genes, only 19 sequences showed preserved protein domains. Several candidate genes for TEs exaptation were identified in the D. mojavensis genome and most of them harbor DNA-binding sites, particularly zinc-finger domains, highlighting the role of TEs as a source of functional novelties to genomes, evidencing that this association between specific DNA-binding sites and TEs is recurrent and perhaps one of the major sources of genomic novelties. Most sex-biased genes and TEs are present in both parental species, and there are three times more testis-biased genes and TEs than ovary-biased, highlighting that expression between gonads in Drosophila is conserved and characteristic of the group. However, there are specific differences in sex-bias expression between parental species and between hybrids, which may play an important role in reproduction. Furthermore, testis-biased TE families are more diverse than testes biased genes, this fact may be directly related to the influence of piRNAs on the regulation, mainly due to the fact that piRNAs from the hybrids have a different pattern than those found in the parental species.
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Palavras-chave
Exaptação, Domínios zf-BED, Genes de lncRNA, Sex-biased genes, Expressão gênica gonadal, Genes diferencialmente expressos, Isolamento reprodutivo, Drosophila mojavensis, Drosophila arizonae, Exaptation, Zf-BED domains, LncRNA genes, Sex-biased genes, Gonadal gene expression, Differentially expressed genes, Reproductive isolation