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Reference genome of brazil nut tree (Bertholletia excelsa Bonpl., Lecythidaceae)

Grant number: 17/06102-0
Support type:Regular Research Grants
Duration: September 01, 2017 - January 31, 2020
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal researcher:Karina Martins
Grantee:Karina Martins
Home Institution: Centro de Ciências Humanas e Biológicas (CCHB). Universidade Federal de São Carlos (UFSCAR). Sorocaba , SP, Brazil
Assoc. researchers: Georgios Joannis Pappas Junior ; Lucia Helena de Oliveira Wadt ; MARILIA DE CASTRO RODRIGUES PAPPAS ; Mateus Mondin ; Paul Gugger

Abstract

The availability of reference genomes has revolutionized the study of biology, allowing an incomparable advance in the comprehension of the relationship between genotype and phenotype. Besides this paradigm shift in biology, the quantity and availability of well annotated reference genomes are still scarce. Bertholletia excelsa Bonpl. (Lecythidaceae), popularly known as Brazil nut tree, is a tropical tree widely distributed along most of the Brazilian Amazon. Local adaptation to different environments is a consequence of natural selection and it influences the amount and distribution of genetic diversity, especially in genomic regions under selection. We have recently started a project that aims to study how the geographic history and natural selection influence genetic structure in Brazil nut. We are genotyping with thousands of SNPs Brazil nut trees widespread across its geographic range in Brazil. Recent improvements in bioinformatics algorithms have allowed the identification of genome-wide SNPs without a background reference genome. However, de novo approaches have not been quite successful in high heterozygous species, as most of trees. The present proposal aims at advancing the genomic resources of Brazil nut tree by assembling and annotating a reference genome and make it publicly available. Besides allowing a high quality SNP calling, the reference genome is the backbone of several different experiments that need genomic resources. DNA purification of one sample will be purified at the Molecular Biology Laboratory, UFSCar-Sorocaba. The preparation of whole genome shot gun and mate pair libraries will be outsourced. Bioinformatics will be done in the UFSCar-Sorocaba cluster and in a server in the University of Maryland. Additionally, based on the expertise developed during this project, we will organize one bioinformatics workshop on genome assembling and another one on SNP calling. Both will be offered annually. Researches from UFSCar, EMBRAPA Rondônia, and University of Maryland. (AU)