Data analysis by imputation of EXTREME-LOW coverage sequencing (EXL-WGS): markers detection and population genetics

• Grant number: 18/07406-6
• Support Opportunities: Scholarships in Brazil - Master
• Start date: June 01, 2018
• End date: April 30, 2020
• Field of knowledge: Biological Sciences - Parasitology - Entomology and Malacology of Parasites and Vectors
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Paulo Eduardo Martins Ribolla
• Grantee: Marcus Vinicius Niz Alvarez
• Host Institution: Instituto de Biotecnologia (IBTEC). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil

Abstract

Projects demanding for large scale whole genome sequencing (WGS) are often impractical due to the cost of the technique when applied in large sample quantities. Therefore, studies are needed to find new viable and low-cost strategies that can be adopted to circumvent the situation. The objective of this project is to study different methods of obtaining genomic information from WGS of extreme low coverage (EXL-WGS) to study populations. Larvae and adults of Anopheles Darlingi in different environment conditions were captured in Mâncio Lima - AC. The Nextera XT (Illumina) protocol was performed with 1/5 of the volume suggested by the standard protocol and the DNA sequenced by the NextSeq500 (Illumina). Genotyping by sequencing and imputation of the markers will be performed for population study, correlating with different collection conditions, such as time and location of capture. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

NIZ ALVAREZ, MARCUS VINICIUS; ALONSO, DIEGO PERES; KADRI, SAMIR MOURA; RUFALCO-MOUTINHO, PAULO; FERRARI BERNARDES, ISABELLA ARIADNE; FLORINDO DE MELLO, ANA CAROLINA; SOUTO, ANA CAROLINA; CARRASCO-ESCOBAR, GABRIEL; MORENO, MARTA; GAMBOA, DIONICIA; et al. Nyssorhynchus darlingi genome-wide studies related to microgeographic dispersion and blood-seeking behavior. PARASITES & VECTORS, v. 15, n. 1, p. 11-pg., 2022-03-28. (18/07406-6)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

ALVAREZ, Marcus Vinicius Niz. Low coverage sequencing data analysis using imputation: Marker selection and population genetics.. 2020. Master's Dissertation - Universidade Estadual Paulista (Unesp). Instituto de Biociências. Botucatu Botucatu.