Secuenciamiento genómico de levadura oleaginosa Yarrowia lipolytica V53
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Date
2024
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Universidad Nacional de Trujillo
Abstract
Las levaduras oleaginosas son organismos con un gran potencial para el desarrollo de plataformas productivas de sustancias químicas a base de lípidos, como alternativa frente a la inminente escasez de combustibles y producción de aceites similares a los de origen vegetal, entre ellas Yarrowia lipolytica, con características y fisiología específicas. La presente investigación tuvo como objetivo realizar el secuenciamiento del genoma de la levadura Y. lipolytica V53, aislada y mantenida en el laboratorio de Biomoléculas de la Facultad de Ciencias Agropecuarias, quien contiene 70,2% contenido de lípidos en su biomasa. Para tal efecto se realizó la producción de su biomasa en medio YPD (30 °C/ 200 rpm/ 18 h). Se extrajo su ADN genómico. Se determinó la calidad y concentración del ADN utilizando microespectrofotometría con Nanodrop 2000c. Se evaluó la integridad del ADN con electroforesis horizontal en gel de agarosa. Verificada su calidad básica, se secuenció utilizando la tecnología Illumina con el secuenciador Miseq, con pair-end reads de 2x150 pb. Asimismo, se realizó el preprocesamiento de datos, analizándose la calidad de las secuencias obtenidas usando el software FastQC, planteándose un recorte de secuencias con Fastp, obteniéndose un total de 9’343,733 de secuencias totales de Y. lipolytica V53, con cero secuencias de mala calidad, una longitud de secuencia máxima de 149 bases y porcentaje de Guanina y Citosina de 63 %, tanto en R1 como en R2. Los resultados obtenidos permitirían la realización del ensamble de secuencias, para obtener posiblemente el genoma completo de la cepa trabajada, su caracterización y análisis.
ABSTRACT Oily yeasts are organisms with great potential for the development of lipid-based chemical substances production platforms as an alternative for the imminent lack of fuels and oil production similar to those of plant origin including Yarrowia lipolytica, with specific characteristics and physiology. The aim of the present research was to sequence the genome of the yeast Y. lipolytica V53, isolated and maintained in the Biomolecules laboratory of the Faculty of Agricultural Sciences, which contains 70.2% lipid content in its biomass. For this aim, biomass production was executed in YPD medium (30 °C/ 200 rpm/ 18 h). The genomic DNA was extracted. The DNA quality and concentration were determined using microspectrophotometry with Nanodrop 2000c. The DNA integrity was assessed with horizontal agarose gel electrophoresis. Once its basic quality was confirmed, it was sequenced using Illumina technology with the Miseq sequencer, with pair-end reads of 2x150 bp. Furthermore, data preprocessing was performed, analyzing the quality of the sequences obtained using FastQC software, with a sequence trimming with Fastp, obtaining a total of 9'343,733 total sequences of Y. lipolytica V53, with zero sequences of poor quality, a maximum sequence length of 149 bases and Guanine and Cytosine percentage of 63 %, both in R1 and R2. The results obtained would allow the assembly of sequences, to possibly obtain the complete genome of the strain worked, its characterization and analysis.
ABSTRACT Oily yeasts are organisms with great potential for the development of lipid-based chemical substances production platforms as an alternative for the imminent lack of fuels and oil production similar to those of plant origin including Yarrowia lipolytica, with specific characteristics and physiology. The aim of the present research was to sequence the genome of the yeast Y. lipolytica V53, isolated and maintained in the Biomolecules laboratory of the Faculty of Agricultural Sciences, which contains 70.2% lipid content in its biomass. For this aim, biomass production was executed in YPD medium (30 °C/ 200 rpm/ 18 h). The genomic DNA was extracted. The DNA quality and concentration were determined using microspectrophotometry with Nanodrop 2000c. The DNA integrity was assessed with horizontal agarose gel electrophoresis. Once its basic quality was confirmed, it was sequenced using Illumina technology with the Miseq sequencer, with pair-end reads of 2x150 bp. Furthermore, data preprocessing was performed, analyzing the quality of the sequences obtained using FastQC software, with a sequence trimming with Fastp, obtaining a total of 9'343,733 total sequences of Y. lipolytica V53, with zero sequences of poor quality, a maximum sequence length of 149 bases and Guanine and Cytosine percentage of 63 %, both in R1 and R2. The results obtained would allow the assembly of sequences, to possibly obtain the complete genome of the strain worked, its characterization and analysis.
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Keywords
Yarrowia lipolytica, Extracción de ADN, Calidad de secuencias, Secuenciamiento genómico