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MSc in Biochemistry Dissertation Project – 2nd Cycle Student´s Name: Student email address: No. Supervisor(s): Rita Sobral andSusana Gaudêncio Supervisor(s) email address:[email protected] and [email protected] Lab/Institution: Lab of Molecular Microbiology of Bacterial Pathogens (Lab333), DCV, UNL and Lab 202, DQ, UNL TITLE:A genome-wide approach to understand the diversity of marine bacteria and identify new producer species BACKGROUND Ocean environments constitute a major source of biodiversity, harboring marine life forms capable of producing a variety of molecules with unique features, unmatched biochemical diversity and structural complexity. Marine bacteria are an exceptional source of bioactive chemical diversity, especially actinomycetes, providing a high number of lead-like compounds for drug discovery. Due to the dramatic increase of infectious diseases and mutiresistant bacteria, the need to discover and develop new drugs has never been greater. The sequencing and annotation of the genome of bacteria that are known producers of new chemical structures will reveal new biosynthetic pathways of secondary metabolism responsible for the synthesis of such compounds. S. Gaudêncio has gathered a diverse collection of 400 taxonomically described marine-sedimentderived bacteria, collected from the Madeira Archipelago. Several of these strains have revealed new phylogeny, exclusive adaptation to sea-life conditions and biological activities (antimicrobial, antibiofilm, antifouling and proteasome inhibition). OBJECTIVES We aim to perform whole-genome sequencing of pre-selected strains of Salinispora genus and Streptomyces aculeolatus species, that were identified as prolific producers of compounds with antimicrobial and anti-biofilm activity. Through a genome-based approach we aim to identify new clusters of genes involved in the production of these new compounds. Furthermore, results from 16SRNA sequencing suggest that, strains representative of new unidentified species of Micromonospora, Verrucosispora, Stackebrandtia, Actinocorallia, among others, exist among our collection. These strains are also producers of compounds with biological activity. We aim to characterize such strains in order to define them as new species. 1 MSc in Biochemistry Dissertation Project – 2nd Cycle PROJECT DESCRIPTION - The genomic DNA of theSalinispora and Streptomyces strains will be extracted through the CTAB/phenol/chloroform method(Task 1). The yield of the extraction procedure and the integrity of the DNA will be assessed using Qubit Fluorometer, agarose gel electrophoresis and NanoDrop Spectrophotometer. Genome sequencing will be performed using the MiSeq (Illumina) platform(Task 2). Preliminary annotation of the sequence will be performed using a reference genome in CLC Genomics Workbench(Task 3). - For the characterization of the new species, several phenotypic traits will be explored(Task 4), including optimum growth conditions, microscopic morphology (SEM), hydrolysis of complex polymers, metabolic patterns (Biolog), etc. Also the composition of the cell wall and the genome GC content will be evaluated(Task 5). TIMELINE(use fill tool for the cells) Month 1 Month 2 Month 3 Month 4 Month 5 Month 6 Month 7 Month 8 Month 9 Month 10 Task 1 Task 2 Task 3 Task 4 Task 5 Thesis 2