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Study of genome instability of Halobacterium salinarum NRC-1 by long reads sequencing

Grant number: 18/25329-9
Support type:Scholarships in Brazil - Scientific Initiation
Effective date (Start): September 01, 2019
Effective date (End): August 31, 2021
Field of knowledge:Biological Sciences - Biochemistry - Molecular Biology
Principal Investigator:Tie Koide
Grantee:Vinícius Henrique Franceschini dos Santos
Home Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

Halobacterium salinarum NRC-1 is an extremophile halophile, and as an archaeon organism has characteristics shared by eukaryotes and bacteria. Since it is easy to manipulate H. salinarum in the laboratory, it has become a model for genetic studies, most of which characterized its genome as highly unstable due to the high frequency of spontaneous mutations. Our research group study different H. salinarum strains with chromosomal genes knocked out and analyzing RNA-Seq data, we identified a new genome instability phenomenon: a ~30 kb deletion in one of their plasmids. In this project we aim to study the genetic instability of H. salinarum NRC-1, with an emphasis in the plasmids, using genome sequencing of the knockout strains. MinION platform (Oxford Nanopore Technologies) will be used to generate long reads that facilitate genome assembly and deletions and other structural variant identification. Bioinformatics tools will be used to identify these structural variants and relate them to direct and indirect fall of gene expression using existing RNA-Seq data. This project is a starting point to study the genome instability mechanisms and their relationship with the regulation of gene expression. The current project will be performed as part of Alan Lorenzetti PhD project (FAPESP 2017/03052-2), with emphasis in the study of the plasmids.