ITV & ICMBio

Genomics of the Brazilian Biodiversity – GBB

Genomics of the Brazilian Biodiversity – GBB

Harpy eagle (Harpia harpyja)

Harpy eagle is a threatened species, classified as vulnerable (VU) by the Official List of Brazilian Fauna Species Threatened with Extinction (MMA) and the International Union for Conservation of Nature (IUCN). This classification indicates that Harpia harpyja faces a high risk of extinction in the wild due to several factors, such as a recent sharp population decline and the limited number of individuals in its current populations. Genetic studies play a crucial role in conservation efforts of species threatened with extinction, once they provide valuable information on the genetic diversity, population structure and genetic health of such species.  

In 2022, as part of the AmazOOmics project from Vale Institute of Technology, comprehensive genetic studies were conducted on the Harpy eagle. During these investigations, the Harpy Eagle’s reference genome was sequenced and assembled, representing a significant milestone. A reference genome contains the complete and near error-free sequence and genes of the DNA of an organism. In this case, the reference genome of the Harpy eagle provided a solid foundation for comparing genomic sequences among individuals from three different populations: Atlantic Forest (n=9), Northern Amazon (n=5) and South Amazon (n=35). The population genomics study has revealed that populations from Southern Amazon and Atlantic Forest regions are more similar to each other than with respect to the Northern Amazon population. This knowledge is essential, once it allows the monitoring of the genetic exchange level among populations and helps to identify potential natural barriers or human-induced factors that may restrict gene flow. Therefore, based on this genetic knowledge, specific conservation measures may be implemented to facilitate or restore the gene flow among populations, contributing to the successful preservation of the Harpy eagle and safeguarding this vulnerable species from extinction. 

 

Jaguar (Panthera onca)

The jaguar, the largest cat species in the Americas, is native to Brazil. However, its distribution extends across several countries, from the southwestern United States to Argentina, passing through Mexico and the Amazon region. Currently, this species is classified as Near-threatened (NT) by the IUCN, and as Vulnerable (VU) by the Official List of Brazilian Fauna Species Threatened with Extinction (MMA). 

In 2023, the GBB project initiated studies related to the generation of the jaguar’s reference genome. This reference genome will be essential for future population genetic research, enabling the assessment of genetic diversity and genetic health of target populations. It will provide essential guidelines for management and conservation strategies. 

To produce this reference genome, blood samples were collected from an individual originating in southwestern Pará state. These samples were run in a high-quality DNA sequencing plataform. The next research steps involve the assembly of the species’ genome using advanced bioinformatic tools, thus consolidating a valuable source of genetic information which will boost the efforts related to the preservation and research of jaguars. 

Jaborandi (Pilocarpus sp.)

Jaborandi comprises a group of species native to Brazil and Surinam, with some species of the genus currently classified as threatened with extinction (vulnerable or endangered) according to the Official List of Brazilian Flora Species Threatened with Extinction (MMA) and to IUCN. Its relevance to the bioeconomy is remarkable since it is the only natural source of pilocarpine, a compound used in the treatment of eye diseases, such as glaucoma. In addition to this, the management of jaborandi has a significant social impact, with local communities harvesting its leaves and establishing commercial partnerships with pharmaceutical companies for the extraction of pilocarpine. The ongoing genetic research in the GBB project aims to sequence the whole genome of this species, which may support the identification of key genes, optimize the extraction of pilocarpine, and select high-yield populations. This effort plays an important role in the Bioeconomics of the Amazon and in the pharmaceutical industry, with the potential to expand access to high-quality and effective medications. 

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Genomics of the Brazilian Biodiversity – GBBProject

At the end of 2022, the Vale Institute of Technology – Sustainable Development (ITV-DS), in partnership with the Chico Mendes Institute for Biodiversity Conservation (ICMBio), released a bold and innovative project, which aims the genomic map Brazilian fauna and flora species  that are threatened with extinction, exotic, or with potential to generate income for farmers involved in bioeconomy.

Entitled “Molecular research as a tool for biodiversity conservation”, or Genomics of the Brazilian Biodiversity – GBB (GBB), the project is a groundbreaking proposal in Brazil and has the participation of different national and international research institutions.

The initiative has received investment from Vale, which sees the importance of research for the preservation of the Brazilian biodiversity and values the potential of Brazilian science in producing innovative knowledge. GBB will receive US$ 25 million in investment by 2027 to conduct research on species threatened with extinction and/or in Federal Conservation Units under the responsibility of ICMBio throughout Brazil.

Purpose of the project

Initiatives related to GBB aim to identify species of Brazilian biodiversity from the DNA that is present in different environments. These studies will allow the identification of rare species, even if they are not visible in a particular location. The goal is that by 2027, at least 80 reference genomes will be generated, and another 5000 resequenced genomes (population-level).  

The information resulting from the sequencing of thousands of samples will be structured in a database with specific categorization criteria. The data collected by these studies are important for designing biodiversity conservation strategies in all Brazilian biomes and for the decision-making process of the authorities involved.

Though the studies developed within the scope of the project, it is possible to list the biomes and species that are priorities for sampling. One of the purposes of the project is to identify the genetic diversity of each studied species, which will result in a better understanding of extinction processes and the genetic health of the current populations.

The program also aims to establish a network of researchers from both ITV and ICMBio, as well as from other institutions collaborating with the project. The program expects to qualify staff and other professionals through the establishment of protocols for all stages of the different studies conducted within the scope of the project.

 

Projeto Genômica da Biodiversidade Brasileira em números

21

Number of researchers involved

24

Scholarships granted

R$ 6.207.382

Used

-

No. of qualified/trained personnel

1

No. of species studied

14

No. of ICMBio research centers

-

No. of articles

-

No. of established protocols

16

No. of partners

1

No. of genomes produced

* Dados atualizados em 22 de setembro de 2023.

Equipe

ITV Management Committee Researchers

Alexandre Aleixo

Coordinator of ITV

Currículo Lattes

Valeria Tavares

Currículo Lattes

Gisele Nunes​

Currículo Lattes

Santelmo Vasconcelos​

Currículo Lattes

ITV Collaborating Researchers

Guilherme Oliveira

Currículo Lattes

José Augusto P. Bitencourt

Currículo Lattes

Maurício Watanabe

Currículo Lattes

Amanda Ferreira Vidal

Currículo Lattes

Carolina Carvalho

Currículo Lattes

Juliana Teixeira

Currículo Lattes

Leonardo Trevelin

Currículo Lattes

Rafael Valadares

Currículo Lattes

Cecilio Caldeira

Currículo Lattes

Sibelle Torres Vilaça

Currículo Lattes

Renato Oliveira

Currículo Lattes

ICMBio Management Committee Researchers:

Amely Martins

Coordinator of ICMBio

Currículo Lattes

Marius Belluci

Currículo Lattes

Thomas Christensen

Currículo Lattes

Paulo Jardel Braz Faiad

Currículo Lattes

Renata Rossato

Currículo Lattes
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How GBB started

The GBB is the unfolding of the AmaZOOmics project, that was conducted by ITV-DS researchers. Coordinated by Alexandre Aleixo (who is also leading the GBB, at ITV), in collaboration with the Vertebrate Genomes Project (VGP), AmaZOOmics was developed aiming to generate genetic information to implement a genetic preservation program focused on the threatened Amazon biodiversity.

The idea was to study and manage the fauna of BioParque Vale (Zoo and Botanic Garden) in Carajás using genomic tools, resulting in more accurate analyses to manage biodiversity, as well as developing the research component of BioParque Vale, providing more visibility to an important company’s asset.

During the development of the project, the researchers obtained blood and tissue samples from 12 different species in the region; extracted, quantified, and sequenced the DNA samples using high-throughput DNA sequencing from four targeted species.

The project was concluded at the end of 2022. In addition to the research outcomes, AmazOOmics was the embryo of an important partnership with the Chico Mendes Institute of Biodiversity Conservation (ICMBio) in launching the GBB.

Linha do tempo

2021

  • Beginning of the AmaZOOmics project

2022

  • Conceptualization of the GBB project
  • Start of legal proceedings for the partnership between ITV and ICMBio

2022

  • Signature of Partnership Agreement PD&I No. 01/2022 between ITV and ICMBio.
  • Publication of the Partnership Agreement PD&I No. 01/2022 between ITV and ICMBio on the D.O.U. (Federal Official Gazette) No. 194, on October 11th, 2022.

2022

  • Work Order No. 65/2022/GABIN/ICMBIO assigning employee Amely Branquinho Martins to monitor the activities regarding the Partnership Agreement PD&I No. 01/2022 between ITV and ICMBio (SEI No. 13154204 and CRC 20046411)

2023

  • Beginning of GBB
  • Shutdown of AmazOOmics project

2023

  • GBB project Kickoff

2023

  • SEI Notice No. 374/2023/GABIN/ICMBio updating the appointment of employee Amely Branquinho Martins as focus point to monitor the activities regarding the Partnership Agreement PD&I No. 01/2022 between ITV and ICMBio (SEI No. 14450378 and CRC 13F0138A).
  • Hybrid Integration Workshop between the GBB Project and GenoTropics

2023

  • Workshop to define target species and pilot projects, with the participation of ITV researchers and ICMBio employees.