Tropical plant genome sequencing is already underway in Brazil

Tropical plant genome sequencing is already underway in Brazil

Alessandro M. Varani¹, Douglas S. Domingues², Alexandre Aleixo³, Amanda Vidal³, Ana Maria Benko-Iseppon⁴, Andrea Pedrosa Harand⁵, Bianca Baccili Zanotto Vigna⁶, Bruno Cesar Rossini⁷, Carolina Carvalho³, Celso Luis Marino⁸, Damares de Castro Monte⁹, Daniela Matias de Carvalho Bittencourt¹⁰, Diego Mauricio Riaño Pachón¹¹, Felipe Rodrigues da Silva⁹, Francisco Prosdocimi¹², Georgios Pappas Jr¹³, Guilherme Oliveira³, Isabel Rodrigues Gerhardt⁹, Karina Martins¹⁴, Leila do Nascimento Vieira¹⁵, Marco Pessoa-Filho¹⁶, Maria Imaculada Zucchi¹⁷, Maria Lucia Carneiro Vieira², Mariana Cabral de Oliveira¹⁸, Mariana Pires de Campos Telles^19,20, Mario Luiz Teixeira de Moraes²¹, Mauricio Watanabe³, Natoniel Franklin de Melo²², Paula Kuser-Falcão⁹, Renato M. Moreira-Oliveira³, Ricardo A. Dante⁹, Rosana Pereira Vianello²³, Santelmo Vasconcelos³, Sibelle Vilaça³, Sylvia Morais de Sousa Tinoco²⁴, Thannya Nascimento Soares²⁵, Valdir Marcos Stefenon²⁶, Vinícius A. C. Abreu²⁷, Vitor F. O. Miranda²⁸, Vitor Trinca¹, Clarisse Palma-Silva²⁹, Marie-Anne Van Sluys^18*

1 Department of Agricultural and Environmental Biotechnology, School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Brazil.

2 Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, São Paulo, Brazil.

3 Vale Institute of Technology (ITV), Belém, Pará, Brazil.

4 Genetics Department, Center of Biosciences, Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil.

5 Department of Botany, Biosciences Center, Federal University of Pernambuco (UFPE), Recife, Pernambuco, Brazil.

6 Embrapa Southeastern Livestock, São Carlos, São Paulo, Brazil.

7 Department of Bioprocesses and Biotechnology, Faculty of Agricultural Sciences (FCA), São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

8 Department Of Genetics, Microbiology and Immunology, Biotechnology Institute (IBTEC), São Paulo State University (UNESP), Botucatu, São Paulo, Brazil. 

9 Embrapa Digital Agriculture, Campinas, São Paulo, Brazil.

10 Embrapa Genetic Resources & Biotechnology, Brasília, Brazil.

11 Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Piracicaba, São Paulo, Brazil.

12 Institute of Medical Biochemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.

13 Department of Cell Biology, University of Brasília (UnB), Brasília, Brazil.

14 Department of Biology, Federal University of São Carlos (UFSCar), Brazil.

15 Department of Botany, Federal University of Paraná (UFPR), Curitiba, Paraná, Brazil.

16 Embrapa Genetic Resources & Biotechnology, Brasília, DF, Brazil.

17 Secretariat of Agriculture and Food Supply of São Paulo State (APTA) Piracicaba, São Paulo, Brazil.

18 Department of Botany, Institute of Biosciences (IB), University of São Paulo (USP), São Paulo, SP, Brazil.

19 Center of Excellence in Genetics and Genomics, Pontifical Catholic University of Goiás (PUC), Goiânia, Goiás, Brazil.

20 Laboratório de Genética & Biodiversidade, Federal University of Goiás (UFG), Goiânia, Goiás, Brazil.

21 Faculty of Engineering, São Paulo State University (UNESP), Ilha Solteira, São Paulo, Brazil.

22 Embrapa Semi-Arid Region, Petrolina, Pernambuco, Brazil.

23 Embrapa Rice & Beans, Santo Antônio de Goiás, Goiás, Brazil.

24 Embrapa Maize & Sorghum, Sete Lagoas, Minas Gerais, Brazil.

25 Laboratório de Genética & Biodiversidade, Institute of Biological Sciences I, Federal University of Goiás (UFG), Goiânia, Goiás, Brazil.

26 Department of Plant Sciences, Federal University of Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil.

27 Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Federal University of Pará (UFPA), Belém, Pará, Brazil.

28 Department of Biology, School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil.

29 Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.

*Corresponding author: mavsluys@usp.br

doi: 10.5281/zenodo.17536760

Abstract
Bedoya, Zapata and Sanín (2025) urge the inclusion of tropical plants in genome sequencing. We agree, emphasizing that this transformation is already underway in Brazil through coordinated, locally led initiatives delivering chromosome-scale assemblies. Aligned with the Earth BioGenome Project and the Kunming–Montreal Global Biodiversity Framework, these efforts build equitable collaborations and capacity, exemplifying how tropical plant genomics can advance from the Global South.

Main Text

Bedoya, Zapata, and Sanín¹ highlight a critical gap in plant genome sequencing: the underrepresentation of tropical species, despite their ecological, cultural, and global relevance. We agree, and emphasize that in Brazil—one of the world’s most megadiverse countries—tropical plant genomics is rapidly maturing, with coordinated, locally led efforts already producing high-quality, chromosome-scale assemblies.

Across universities (e.g., the CBioClima initiative²), state-owned companies and institutes (e.g., Embrapa and ICMBio), and private partners (e.g., Instituto Tecnológico Vale, through the GBB consortium³), groups are acting on these priorities: sequencing hyperdominant and endangered species from Amazonian forests and other biomes, alongside cultural keystones and crops that sustain biodiversity and local livelihoods. Most projects align with Earth BioGenome Project (EBP) recommendations⁴ and are led by Brazil-based teams; importantly, several are integrating genomic, ecological, physiological, and remote-sensing data to connect genes, traits, and ecosystem processes—exactly the translational arc the community needs.

These efforts also operationalize the Kunming–Montreal Global Biodiversity Framework (KMGBF) by generating genomic baselines and building regional capacity through equitable, locally anchored collaborations (Targets 4 and 20)^5,6, while addressing the historical pattern whereby tropical genomes were often sequenced outside their countries of origin⁷, and directly advance the call by Bedoya et al. for inclusive tropical genomics.

Momentum across Brazilian biomes

Examples across the major biomes illustrate this progress (Figure 1). Additionally, several Brazilian-led projects target non-native or model species, mostly agriculture-oriented with a focus on breeding and climate-change adaptation⁸. Notably, twenty-six ongoing projects on native taxa have already reached chromosome scale, which will more than triple the number of Brazilian-led tropical plant genomes. These projects span fruit trees and palms; morning glories, orchids and bromeliads; hardwoods and medicinal plants; crops; forage grasses relevant to rangeland restoration; conifers and marine and freshwater algae. By linking genomic resources to traditional knowledge, local livelihoods, conservation, carbon storage, and climate resilience, these initiatives provide actionable tools to anticipate tropical biodiversity responses to rapid environmental change—moving beyond a strict “crop vs. non-crop” framing that poorly fits the tropics and extending the forum opened by Bedoya et al. Nonetheless, available reference genomes, and population-scale datasets still underrepresent biodiversity across Brazilian biomes (e.g., species native to the Pantanal wetlands remain unrepresented, despite taxa from other biomes).

Path forward

Advancing from here will require nationally coordinated programmes anchored in the Global South, clear access-and-benefit-sharing (ABS) arrangements, and sustained investment in people and infrastructure to ensure regional scientific leadership—imperatives that mirror updated EBP priorities on equitable partnerships, workforce development, and coordination at scale⁹. Tropical plant genomics in Brazil has matured into an established field, driving innovation and informing policy frameworks. A vibrant, locally led community is consolidating, capacity for long-term progress is being built, and many sequencing projects are nearing publication, advancing alignment with the KMGBF and the EBP. Endorsing and adequately resourcing Brazilian-led initiatives would directly advance the agenda articulated by Bedoya et al. and help accelerate delivery of a truly global, equitable reference library of tropical plant genomes.

Acknowledgements
The Brazilian Plant Genomes Database is hosted and supported by the Center for Scientific Computing (NCC/GridUNESP), São Paulo State University (UNESP).

Competing interests

The authors declare no competing interests.

References

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Figure Legend

Figure 1. Tropical plant genome sequencing initiatives in Brazil. The map is stratified by biome, marking the primary biome of origin for each native species (a species may occur in multiple biomes, but only its primary biome is shown here) and highlighting only Brazilian-led initiatives and remaining gaps—reinforcing calls for coordinated funding, fair ABS, and local capacity building, as emphasized by Bedoya et al. An interactive version of the map is available at https://plantgenomics.ncc.unesp.br/Brazil_Plant_Genomes