RESUMO
BACKGROUND: The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in > 90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. RESULTS: In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. CONCLUSIONS: Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves' polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.
Assuntos
Genoma de Planta , Ilex paraguariensis/genética , Especificidade de Órgãos/genética , Análise de Sequência de RNA/métodos , Transcriptoma/genética , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Genes de Plantas , Anotação de Sequência Molecular , Folhas de Planta/genética , Raízes de Plantas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Metabolismo Secundário/genéticaRESUMO
ABSTRACT Men who have sex with men (MSM) can reduce their risk of acquiring human immunodeficiency virus (HIV) by using various prevention strategies and by understanding the effectiveness of each option over the short- and long-term. Strategies examined were: circumcision; insertive anal sex only; consistent, 100% self-reported condom use; and pre-exposure prophylaxis (PrEP). PrEP efficacy was based on three levels of adherence. The cumulative HIV acquisition risk among MSM over periods of 1 year and 10 years were estimated with and without single and combinations of prevention strategies. A Bernoulli process model was used to estimate risk. In the base case with no prevention strategies, the 1-year risk of HIV acquisition among MSM was 8.8%. In contrast, the 1-year risk associated with circumcision alone was 6.9%; with insertive sex only, 5.5%; with 100% self-reported condom use, 2.7%; and with average, high, and very high PrEP adherence, 5.1%, 2.5%, and 0.7%, respectively. The 10-year risk of HIV acquisition among MSM with no prevention strategy was 60.3%. In contrast, that associated with circumcision alone was 51.1%; with insertive sex only, 43.1%; with 100% self-reported condom use, 24.0%; and with average, high, and very high PrEP adherence, 40.5%, 22.2%, and 7.2%, respectively. While MSM face substantial risk of HIV, there are now a number of prevention strategies that reduce risk. Very high adherence to PrEP alone or with other strategies appears to be the most powerful tool for HIV prevention.(AU)
RESUMEN Los hombres que tienen relaciones sexuales con otros hombres (HSH) pueden reducir su riesgo de contraer el virus de la inmunodeficiencia humana (VIH) si utilizan diversas estrategias de prevención y comprenden la eficacia de cada opción a corto y largo plazo. Las estrategias examinadas fueron: la circuncisión; las relaciones anales insertivas solamente; el 100% de uso sostenido y autonotificado de condones; y la profilaxis preexposición (PrEP). La eficacia de la PrEP se basó en tres niveles de adherencia. Se calculó el riesgo acumulativo de la transmisión del VIH entre los HSH en períodos de 1 y 10 años con a) una única estrategia de prevención, b) sin estrategia de prevención y c) con combinaciones de estrategias de prevención. Se usó un modelo del proceso de Bernoulli para calcular el riesgo. En el caso base sin estrategias de prevención, el riesgo de transmisión del VIH a 1 año entre HSH fue 8,8%. En contraste, el riesgo de 1 año asociado a la circuncisión solamente fue de 6,9%; a las relaciones insertivas solamente fue de 5,5%; al 100% de uso autonotificado de condón, 2,7%; y a la adherencia media, alta y muy alta a la PrEP, 5,1%, 2,5% y 0,7%, respectivamente. El riesgo de transmisión del VIH a los 10 años entre HSH sin estrategia de prevención fue de 60,3%. En contraste, la transmisión asociada a la circuncisión solamente fue de 51,1%; a las relaciones insertivas solamente, 43,1%; al 100% de uso autonotificado de condón, 24,0%; y a la adherencia media, alta y muy alta a la PrEP, 40,5%, 22,2% y 7,2%, respectivamente. Si bien los HSH enfrentan un riesgo sustancial de contraer el VIH, existen ahora varias estrategias de prevención que reducen dicho riesgo. Una adherencia muy alta a la PrEP sola o en combinación con otras estrategias parece ser la herramienta más potente para la prevención de la infección por el VIH.(AU)
Assuntos
Humanos , Masculino , Infecções por HIV/prevenção & controle , Preservativos , Comportamento de Redução do Risco , Sexo sem Proteção , Profilaxia Pré-Exposição , Estados Unidos/epidemiologiaRESUMO
Men who have sex with men (MSM) can reduce their risk of acquiring human immunodeficiency virus (HIV) by using various prevention strategies and by understanding the effectiveness of each option over the short- and long-term. Strategies examined were: circumcision; insertive anal sex only; consistent, 100% self-reported condom use; and pre-exposure prophylaxis (PrEP). PrEP efficacy was based on three levels of adherence. The cumulative HIV acquisition risk among MSM over periods of 1 year and 10 years were estimated with and without single and combinations of prevention strategies. A Bernoulli process model was used to estimate risk. In the base case with no prevention strategies, the 1-year risk of HIV acquisition among MSM was 8.8%. In contrast, the 1-year risk associated with circumcision alone was 6.9%; with insertive sex only, 5.5%; with 100% self-reported condom use, 2.7%; and with average, high, and very high PrEP adherence, 5.1%, 2.5%, and 0.7%, respectively. The 10-year risk of HIV acquisition among MSM with no prevention strategy was 60.3%. In contrast, that associated with circumcision alone was 51.1%; with insertive sex only, 43.1%; with 100% self-reported condom use, 24.0%; and with average, high, and very high PrEP adherence, 40.5%, 22.2%, and 7.2%, respectively. While MSM face substantial risk of HIV, there are now a number of prevention strategies that reduce risk. Very high adherence to PrEP alone or with other strategies appears to be the most powerful tool for HIV prevention.
Los hombres que tienen relaciones sexuales con otros hombres (HSH) pueden reducir su riesgo de contraer el virus de la inmunodeficiencia humana (VIH) si utilizan diversas estrategias de prevención y comprenden la eficacia de cada opción a corto y largo plazo. Las estrategias examinadas fueron: la circuncisión; las relaciones anales insertivas solamente; el 100% de uso sostenido y autonotificado de condones; y la profilaxis preexposición (PrEP). La eficacia de la PrEP se basó en tres niveles de adherencia. Se calculó el riesgo acumulativo de la transmisión del VIH entre los HSH en períodos de 1 y 10 años con a) una única estrategia de prevención, b) sin estrategia de prevención y c) con combinaciones de estrategias de prevención. Se usó un modelo del proceso de Bernoulli para calcular el riesgo. En el caso base sin estrategias de prevención, el riesgo de transmisión del VIH a 1 año entre HSH fue 8,8%. En contraste, el riesgo de 1 año asociado a la circuncisión solamente fue de 6,9%; a las relaciones insertivas solamente fue de 5,5%; al 100% de uso autonotificado de condón, 2,7%; y a la adherencia media, alta y muy alta a la PrEP, 5,1%, 2,5% y 0,7%, respectivamente. El riesgo de transmisión del VIH a los 10 años entre HSH sin estrategia de prevención fue de 60,3%. En contraste, la transmisión asociada a la circuncisión solamente fue de 51,1%; a las relaciones insertivas solamente, 43,1%; al 100% de uso autonotificado de condón, 24,0%; y a la adherencia media, alta y muy alta a la PrEP, 40,5%, 22,2% y 7,2%, respectivamente. Si bien los HSH enfrentan un riesgo sustancial de contraer el VIH, existen ahora varias estrategias de prevención que reducen dicho riesgo. Una adherencia muy alta a la PrEP sola o en combinación con otras estrategias parece ser la herramienta más potente para la prevención de la infección por el VIH.