Workshop TFDA Comp-Bio

Multi-omics analyses for plant genetics, food sciences, and microbiome studies

28 feb 2022, 12:50

10m

Aula Magna (Centro Congressi Partenope)

Description

Abstract:

High-throughput techniques and experiments enable researchers to investigate complex biological processes through large-scale analysis of omics data. The growth of big omics data entails continuous computational challenges in the collection, management, analysis and interpretation (mining) of data, as well as in their sharing, visualization, storage and integration to obtain emerging information necessary to understand the biology of complex systems (systems biology). Indeed, It is imperative to undertake an integrative approach that combines multi-omics data to highlight the interrelationships of different classes of biomolecules and their functions, and to investigate the biological system as a whole (holistic approach).

We present some of the research activities carried out at the Dept. of Agricultural Sciences with the aim of developing computational tools and applying multi-omics data analysis strategies for multiple purposes. The spread of increasingly efficient methods for the sequencing of DNA (genomics and metagenomics) and RNA (transcriptomics) and of NGS-based genotyping techniques allowed to (i) explore the “sequence space”; (ii) investigate genome structure and organization; (iii) characterize gene function and gene expression patterns; (iv) study food and human microbiomes, with particular focus on large-scale analyses performed at strain-level resolution; (v) provide high-resolution profiling of nucleotide variation within germplasm collections (population genomics); (vi) discover loci that are associated with key agronomic traits via genome-wide association studies; (vii) study molecular mechanisms involved in plant-microbe interaction.

Recent publications:

• Andolfo, G., Schuster, C., Gharsa, H. B., Ruocco, M., & Leclerque, A. (2021). Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola. BMC Genomics, 22(1), 708.
• Chiusano, M. L., Incerti, G., Colantuono, C., Termolino, P., Palomba, E., Monticolo, F., Benvenuto, G., Foscari, A., Esposito, A., Marti, L., de Lorenzo, G., Vega-Muñoz, I., Heil, M., Carteni, F., Bonanomi, G., & Mazzoleni, S. (2021). Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure. Plants, 10(8). https://doi.org/10.3390/plants10081744.
• Cigliano, R. A., Aversano, R., Di Matteo, A., Palombieri, S., Termolino, P., Angelini, C., Bostan, H., Cammareri, M., Consiglio, F. M., Ragione, F. D., Paparo, R., Valkov, V. T., Vitiello, A., Carputo, D., Chiusano, M. L., D’Esposito, M., Grandillo, S., Matarazzo, M. R., Frusciante, L., … Conicella, C. (2022). Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace. Horticulture Research. https://doi.org/10.1093/hr/uhab042.
• De Filippis, F., Pasolli, E., & Ercolini, D. (2020). Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease. Current Biology: CB, 30(24), 4932–4943.e4.
• De Filippis, F., Paparo, L., Nocerino, R., Della Gatta, G., Carucci, L., Russo, R., Pasolli, E., Ercolini, D., & Berni Canani, R. (2021). Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance. Nature Communications, 12(1), 5958.
• De Palma, M., Salzano, M., Villano, C., Aversano, R., Lorito, M., Ruocco, M., Docimo, T., Piccinelli, A. L., D’Agostino, N., & Tucci, M. (2019). Transcriptome reprogramming, epigenetic modifications and alternative splicing orchestrate the tomato root response to the beneficial fungus Trichoderma harzianum. Horticulture Research, 6, 5.
• Monticolo, F., & Chiusano, M. L. (2021). Computational Approaches for Cancer-Fighting: From Gene Expression to Functional Foods. Cancers, 13(16). https://doi.org/10.3390/cancers13164207.
• Monticolo, F., Palomba, E., & Chiusano, M. L. (2021). Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. Cell Death Discovery, 7(1), 17.
• Palmieri, D., Vitale, S., Lima, G., Di Pietro, A., & Turrà, D. (2020). A bacterial endophyte exploits chemotropism of a fungal pathogen for plant colonization. Nature Communications, 11(1), 5264.
• Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., Collado, M. C., Rice, B. L., DuLong, C., Morgan, X. C., Golden, C. D., Quince, C., Huttenhower, C., & Segata, N. (2019). Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell, 176(3), 649–662.e20.
• Pasolli, E., De Filippis, F., Mauriello, I. E., Cumbo, F., Walsh, A. M., Leech, J., Cotter, P. D., Segata, N., & Ercolini, D. (2020). Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications, 11(1), 2610.
• Pavan, S., Delvento, C., Ricciardi, L., Lotti, C., Ciani, E., & D’Agostino, N. (2020). Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies. Frontiers in Genetics, 11, 447.
• Vitale, S., Di Pietro, A., & Turrà, D. (2019). Autocrine pheromone signalling regulates community behaviour in the fungal pathogen Fusarium oxysporum. Nature Microbiology, 4(9), 1443–1449.
• Zotti, M., De Filippis, F., Cesarano, G., Ercolini, D., Tesei, G., Allegrezza, M., Giannino, F., Mazzoleni, S., & Bonanomi, G. (2020). One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland. The New Phytologist, 227(3), 884–898.