López Varas, Leticia

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https://academica-e.unavarra.es/handle/2454/49460

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López Varas

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Leticia

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Producción Agraria

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751471

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810984

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2014 - 20153
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Author: López Varas, Leticia × Subject: Pleurotus ostreatus ×

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Now showing 1 - 3 of 3
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    PublicationOpen Access
    Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi
    (BioMed Central, 2014) Castanera Andrés, Raúl; Pérez Garrido, María Gumersinda; López Varas, Leticia; Sancho, Rubén; Santoyo Santos, Francisco; Alfaro Sánchez, Manuel; Gabaldón Estevan, Juan Antonio; Pisabarro de Lucas, Gerardo; Oguiza Tomé, José Antonio; Ramírez Nasto, Lucía; Producción Agraria; Nekazaritza Ekoizpena; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
    Background: Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species. Results: Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron’s boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons. Conclusion: P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.
  • Thumbnail Image
    PublicationOpen Access
    Análisis genómico y transcriptómico de genes capturados por helitrones en "Pleurotus ostreatus"
    (2014) López Varas, Leticia; Ramírez Nasto, Lucía; Escuela Técnica Superior de Ingenieros Agrónomos; Nekazaritza Ingeniarien Goi Mailako Eskola Teknikoa
    El creciente número de organismos eucariotas secuenciados permite estudiar la aparición de elementos de transposición en gran cantidad de genomas. Dentro de los transposones de clase II se encuentran los transposones de círculo rodante (también conocidos como helitrones), que han sido descritos recientemente en plantas, animales y hongos utilizando herramientas bioinformáticas. Los helitrones se caracterizan fundamentalmente por codificar una proteína con un origen de replicación REP y un dominio helicasa PIF1 y por la capacidad de capturar genes enteros o fragmentos de genes, incrementando su número y dispersándolos por el genoma del huésped. En el genoma de P. ostreatus se han descrito dos familias de helitrones denominadas HELPO1 y HELPO2, que contienen elementos potencialmente autónomos que codifican helicasas RepHel, además de genes capturados de función desconocida. En este trabajo hemos analizado el efecto de la dosis génica (número de copias) y el perfil transcriptómico de estos helitrones portadores de genes utilizando PCR en tiempo real. Como resultados presentamos un protocolo basado en la PCR a tiempo real para cuantificar el número de copias de estos elementos en otras cepas monocarióticas de P. ostreatus de las que no se dispone de secuencia genómica y que existe expresión de algunos genes capturados cuya función aún no se conoce
  • Thumbnail Image
    PublicationOpen Access
    Validation of reference genes for transcriptional analyses in Pleurotus ostreatus by using reverse transcription-quantitative PCR
    (American Society for Microbiology, 2015) Castanera Andrés, Raúl; López Varas, Leticia; Pisabarro de Lucas, Gerardo; Ramírez Nasto, Lucía; Producción Agraria; Nekazaritza Ekoizpena; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
    Recently, the lignin-degrading basidiomycete Pleurotus ostreatus has become a widely used model organism for fungal genomic and transcriptomic analyses. The increasing interest in this species has led to an increasing number of studies analyzing the transcriptional regulation of multigene families that encode extracellular enzymes. Reverse transcription (RT) followed by real-time PCR is the most suitable technique for analyzing the expression of gene sets under multiple culture conditions. In this work, we tested the suitability of 13 candidate genes for their use as reference genes in P. ostreatus time course cultures for enzyme production. We applied three different statistical algorithms and obtained a combination of stable reference genes for optimal normalization of RT-quantitative PCR assays. This reference index can be used for future transcriptomic analyses and validation of transcriptome sequencing or microarray data. Moreover, we analyzed the expression patterns of a laccase and a manganese peroxidase (lacc10 and mnp3, respectively) in lignocellulose and glucose-based media using submerged, semisolid, and solid-state fermentation. By testing different normalization strategies, we demonstrate that the use of nonvalidated reference genes as internal controls leads to biased results and misinterpretations of the biological responses underlying expression changes.