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Uy24-18874.Pdf UNIVERSIDAD DE LA REPÚBLICA - FACULTAD DE CIENCIAS PROGRAMANamaste DE POSGRADO EN BIOTECNOLOGÍA UTILIZACIÓN DE SECUENCIAS BARCODE PARA CLASIFICAR MUESTRAS DE ESPECIES VEGETALES DE INTERÉS INDUSTRIAL Tesis para optar por el título de Magister en Biotecnología Lic. Bioq. Fabiana Rey Bentos Montevideo, 2017 UNIVERSIDAD DE LA REPÚBLICA - FACULTAD DE CIENCIAS PROGRAMA DE POSGRADO EN BIOTECNOLOGÍA TESIS DE MAESTRÍA EN BIOTECNOLOGÍA "UTILIZACIÓN DE SECUENCIAS BARCODE PARA CLASIFICAR MUESTRAS DE ESPECIES VEGETALES DE INTERÉS INDUSTRIAL" Lic.Bioq. Fabiana Rey Bentos ORIENTADORES: TRIBUNAL: Dr. Fabián Capdevielle Dr. Claudio Martínez Dra. Mary Lopretti Dra. Alexandra Castro Dr. Fernando Alvarez Montevideo, 2017 2 AGRADECIMIENTOS Al Laboratorio Tecnológico del Uruguay (LATU) por permitirme llevar a cabo esta tesis y financiarla. A los miembros del Tribunal por acceder a corregirla, por sus opiniones, aportes y enseñanzas. A mis tutores por la paciencia y comprensión, y por no abandonar hasta el final. A mi familia por el apoyo y el sostén en los momentos mas difíciles, por el tiempo y los consejos. A mis amigos que tantas veces me oyeron hablar de "la tesis" y me dieron ánimo para seguir adelante. A mi jefe, Gustavo Domínguez, por su paciencia y palabras de aliento. A mis compañeros de trabajo por su apoyo y no dejarme flaquear hasta el final de este largo camino. A todos muchas gracias por estar de una forma u otra! 3 TABLA DE CONTENIDO AGRADECIMIENTOS ................................................................................................................ 3 TABLA DE CONTENIDO ............................................................................................................ 4 GLOSARIO Y ABREVIATURAS .................................................................................................... 6 LISTA DE FIGURAS Y TABLAS ..................................................................................................... 8 RESUMEN ........................................................................................................................... 11 1. INTRODUCCIÓN ................................................................................................................ 12 1.1. TRAZABILIDAD Y AUTENTICIDAD DE ALIMENTOS ............................................................. 12 1.2. PLANTAS AROMÁTICAS Y MEDICINALES ........................................................................ 14 1.2.1. Definiciones .................................................................................................... 14 1.2.2. Comercio internacional y antecedentes nacionales ........................................ 15 1.2.3. Características de las especies vegetales evaluadas. ....................................... 17 1.3. METODOLOGÍAS PARA EL RECONOCIMIENTO DE ESPECIES VEGETALES DE INTERÉS INDUSTRIAL ............................20 1.4. DNA BARCODING ..................................................................................................... 23 1.4.1. Generalidades ................................................................................................ 23 1.4.2. DNA barcoding en plantas .............................................................................. 26 1.4.3. Barcode of Life ................................................................................................ 29 1.4.4. Aplicaciones del DNA barcoding .................................................................... 31 1.5. PROCEDIMIENTOS PARA CLASIFICACIÓN DE MUESTRAS ................................................... 33 2. OBJETIVOS ...................................................................................................................... 35 2.1. OBJETIVO GENERAL ................................................................................................... 35 2.2. OBJETIVOS ESPECÍFICOS ............................................................................................. 35 3. METODOLOGÍA ................................................................................................................ 36 3.1. MATERIAL VEGETAL .................................................................................................. 36 3.2. EXTRACCIÓN DE ADN ............................................................................................... 37 3.3. OBTENCIÓN DE SECUENCIAS BARCODE .......................................................................... 39 3.3.1. Amplificación del locus rbcL ............................................................................ 39 3.3.2. Locus matK ..................................................................................................... 40 4 3.3.3. Secuenciación ................................................................................................. 41 3.4. ANÁLISIS DE DATOS MEDIANTE BARCODE OF LIFE DATA SYSTEMS (BOLD) ....................... 42 3.4.1. Ingreso de datos ............................................................................................. 42 3.4.2. Clasificación .................................................................................................... 43 3.4.3. Clasificación usando base de datos GenBank .................................................. 44 3.5. ANÁLISIS DE DATOS MEDIANTE UN PROCEDIMIENTO ESTADÍSTICO DE CLASIFICACIÓN (IMPLEMENTADO MEDIANTE PLATAFORMA WEKA)................................. .......................... 45 4. RESULTADOS Y DISCUSIÓN .................................................................................................. 46 4.1 EXTRACCIÓN DE ADN ................................................................................................ 46 4.2. OBTENCIÓN DE SECUENCIAS BARCODE .......................................................................... 50 4.2.1. Locus rbcL ...................................................................................................... 50 4.2.2. Locus matK ..................................................................................................... 57 4.3. ANÁLISIS DE DATOS MEDIANTE BARCODE OF LIFE DATA SYSTEMS (BOLD) .................. 60 4.3.1. Clasificación .................................................................................................... 60 4.3.2. Clasificación usando base de datos Genbank .................................................. 69 4.4. ANÁLISIS DE DATOS MEDIANTE UN PROCEDIMENTO ESTADÍSTICO DE CLASIFICACIÓN (IMPLEMENTADO MEDIANTE PLATAFORMA WEKA)........................... ................................ 76 5. CONCLUSIONES Y PERSPECTIVAS ........................................................................................... 90 6. REFERENCIAS BIBLIOGRÁFICAS ............................................................................................. 92 7. ANEXOS ........................................................................................................................ 101 5 GLOSARIO Y ABREVIATURAS ADN: ácido desoxirribonucleico ARFF: Attribute-Relation File Format Barcode: código de barras BID: Banco Interamericano de Desarrollo BOLD: Barcode of Life Data Systems BSA: seroalbúmina bovina CBI: Centre for the Promotion of Imports from Developing Countries CBOL: Consortium for the Barcode of Life CTAB: bromuro de cetiltrimetilamonio DBGW: Database Working Group DDBJ: DNA Database of Japan DMSO: dimetilsulfóxido DNA barcoding: metodología basada en el uso de una secuencia barcode para la identificación de la especie a la que pertenece un especimen dNTPs: desoxinucleótidos trifosfato EDTA: ácido etilendiaminotetraacético EMBL: European Molecular Biology Laboratory UE: Union Europea FAO: Organización de las Naciones Unidas para la Alimentación y la Agricultura FIDA: Fondo Internacional para el Desarrollo Agrícola FPTA: Fondo de Promoción de Tecnología Agropecuaria FUNDASOL: Fundación Uruguaya de Cooperación y Desarrollo Solidarios IAEA: Agencia Internacional de Energía Atómica 6 INIA: Instituto Nacional de Investigaciones Agropecuarias LATU: Laboratorio Tecnológico del Uruguay k-NN: algoritmo del vecino mas cercano (Nearest Neighbour algorithm) Locus: posición de un gen o secuencia en un cromosoma NCBI: National Center for Biotechnology Information MERCOSUR: Mercado Común del Sur OMS: Organización Mundial de la Salud PACPYMES: Programa de Apoyo a la Competitividad y Promoción de Exportaciones PCR: reacción en cadena de la polimerasa PVP: polivinilpirrolidona Secuencia barcode: secuencia de ADN proveniente de una región definida del genoma, utilizada para identificar especies TAE: solución tampón Tris - Acetato - EDTA USDA: United States Department of Agriculture USP: United States Pharmacopeia Voucher: muestra representativa de un organismo identificado taxonómicamente por un experto que se encuentra depositada en un herbario. 7 LISTA DE FIGURAS Y TABLAS Figura 1. Componentes principales del proyecto Barcode of Life (BOL) y su contribución a la taxonomía, reconstrucción de filogenias moleculares e investigaciones en genética de poblaciones. .................................................................................................................... 25 Figura 2. Poder de discriminación entre especies de los 7 loci por separado, y en combinaciones de 2 y 3. .................................................................................................. 28 Figura 3. Diagrama de las etapas y componentes del proceso de DNA barcoding ............. 30 Tabla 1. Descripción de los materiales vegetales de referencia utilizados. ....................... 36 Tabla 2.
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