EMU: acquisition of genomics equipment for next-generation sequencing - exploring historic DNA in museums: a museomics center to expand the value of biological collections and promote the discovery of biodiversity

• Grant number: 22/11560-6
• Support Opportunities: Research Infrastructure Program - Collections
• Start date: June 01, 2023
• End date: May 31, 2026
• Field of knowledge: Biological Sciences - Zoology - Taxonomy of Recent Groups
• Principal Investigator: Luís Fábio Silveira
• Grantee: Luís Fábio Silveira
• Host Institution: Museu de Zoologia (MZ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Naercio Aquino Menezes
• Associated scholarship(s): 24/15512-1 - Bioinformatics and genomic data analysis, BP.TT; 24/14408-6 - Generation, processing and bioinformatics analysis of historical DNA, BP.TT

Abstract

Due to the rapid development of evolutionary genetic studies, specimens kept in biological collections over the centuries are now accessible for molecular analysis through the sequencing of so-called historical DNA. These data have been recovered from bones, skins, muscles, teeth, hair, feathers, and the exoskeleton of invertebrates belonging to specimens deposited in museums for years, in a new and emerging area of knowledge known as museomics. The development of museomics took place mainly with the advent of Next Generation Sequencing (NGS). This is because most platforms require short stretches of DNA as a template, avoiding the fundamental problem of the fragmented nature of historical DNA, and increasing the number of loci sequenced. The development of these new technologies places scientific collections as instruments for genomic investigations in different clades of the tree of life because their collections bring together a broad temporal and spatial sampling. Brazil's participation in genomics studies, specifically in the field of biodiversity, is still low. Some of the reasons are the high cost and the difficulty in sending samples for sequencing outside Brazil. Although private companies offer NGS services, they cost 4-6 times more than it would take to generate the data in a specialized national center. These factors culminate in dependence on international collaborations and place Brazilian researchers in a position of technical and financial inequality. The equipment requested in this proposal will represent a qualitative leap for the work carried out in Brazil. These types of equipment will generate genomic DNA sequences from samples preserved in biological collections for studies associated with evolution, taxonomy, systematics, and biodiversity conservation. Within this chain of operation, we are requesting equipment necessary for the storage of samples (Liquid Nitrogen Container and Ultralow -85C Freezer), for DNA extraction and construction of genomic libraries (PippinPrep, Thermocycler, RT PCR, and Sonicator), and processing and computational storage of sequences (Computers, Storage and Software). This equipment park will be essential for building a genomics nucleus within MZUSP. The approaches and applications for research are broad and represent the new frontier of knowledge in biodiversity, placing an institution like MZUSP at the forefront of Museomics in Latin America and a prominent position before the entire Global South. Current MZUSP professors already have work in the genomics area developed in international partnerships responsible for generating this data or even acquired through purchasing services in private companies. These studies will be able to centralize their data generation in the Center of MZUSP. Specifically, concerning associated projects linked to this proposal, the Museomics Center will be fundamental to fulfilling and expanding its already established objectives and lowering the costs previously paid for genomic sequencing. The thematic project financed by FAPESP, #2017/23548-2, and led by Prof. Dr. Luis Fábio Silveira (PR of the present proposal) will use the Center to sequence genomic libraries to unravel the origin and evolution of birds at the Pernambuco Endemism Center. Another thematic project funded by FAPESP, #2016/19075-9 and led by Profs. Dr. Naércio Aquino Menezes (PP of this proposal) and Dr. Aléssio Datovo, will be able to use the Center to generate genomic libraries that will help to understand the systematics of Neotropical electric fish. In addition to these associated projects, several other projects conducted by researchers from inside and outside MZUSP will already use the MZUSP museomics center. (AU)