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Genomics of Trypanosoma cruzi and Brucella abortus

Objetivos. Secuenciar el genoma completo del organismo en estudioIdentificar y caracterizar genesClasificar genes conocidos / desconocidosPredecir funci

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Genomics of Trypanosoma cruzi and Brucella abortus

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    1. Genomics of Trypanosoma cruzi and Brucella abortus Curso de Actualización en Enfermedades Parasitarias Octubre, 2002 Fernán Agüero IIB - UNSAM

    2. Objetivos Secuenciar el genoma completo del organismo en estudio Identificar y caracterizar genes Clasificar genes conocidos / desconocidos Predecir función Estudiar expresión cualitativa y cuantitativamente.

    3. Secuenciación del genoma Shotgun (secuenciación de fragmentos escogidos al azar) Cromosoma por cromosoma Todo el genoma (Whole Genome Shotgun)

    4. Secuenciación genómica

    5. Secuenciación genómica

    6. Secuenciación genómica

    7. Secuenciación genómica

    8. Secuenciación genómica

    9. GSS sequencing (Trypanosoma cruzi) ˜ 12,000 random genomic sequences Average length: 374 bp 4.3 Mbp (total) 50.9 % GC

    10. Distribution of fractional GC content

    11. Blastx analysis

    12. Gene discovery ˜ 947 putative new genes (from blastx analysis)

    13. Clustering of GSS sequences

    14. Gene families

    15. Repetitive DNA families TRBSEQA A highly repeated interspersed DNA element Mol. Biochem. Parasitol. 51, 271-280 (1992) HCR6 interspersed DNA element. (entry from RepBase) TRBSEQA A highly repeated interspersed DNA element Mol. Biochem. Parasitol. 51, 271-280 (1992) HCR6 interspersed DNA element. (entry from RepBase)

    16. Unknown families

    17. Frequency of dinucleotides in the survey

    18. Frequency of trinucleotides in the survey

    19. Di- and tri-nucleotide repeats TpA is suppressed - reason ? AAA (TTT) more abundant than ACA (CAC, TGT, GTG)

    20. Simple repeats

    21. Simple repeats (1-6 bp) 1,556 GSS (13.5%) had 62 different simple repeats 46,965 bp (0.74%) (T)n was the most abundant simple repeat found followed by (CA)n

    22. Low complexity regions

    23. Low complexity regions 1,001 low complexity regions detected 56,455 bp (0.89%) A-rich, T-rich and AT-rich regions, comprise more than 80% of the low complexity regions found

    24. Producing ESTs

    25. EST sequencing Gene discovery Annotation of finished sequence

    26. The Value of Cluster Data Microarray Studies Clusters represent unique forms associated with a specific state Gene Discovery Unique transcripts revealed in association with expression libraries Functional Annotation Virtual genes can be searched against the database to provide functional annotation of the products of a genome Expressed Gene Structure Exons boundaries are revealed by transcript confirmation

    27. Secuenciación de ESTs

    28. Un cluster de ESTs

    29. IIB-UNSAM: Lab. Genómica y Bioinformática

    30. IIB-UNSAM: Genómica y Bioinformática http://genoma.unsam.edu.ar http://www.iib.unsam.edu.ar

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