Journal Article Research Support, Non-U.S. Gov't Ppublish 3 citations
PubMed: 38837946 DOI: 10.1093/gigascience/giae027
Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation.
Gigascience 13
Authors: Rafael Moysés Alves, Vinicius A C de Abreu, Rafaely Pantoja Oliveira, João Victor Dos Anjos Almeida, Mauro de Medeiros de Oliveira, Saura R Silva, Alexandre R Paschoal, Sintia S de Almeida, Pedro A F de Souza, Jesus A Ferro, Vitor F O Miranda, Antonio Figueira, Douglas S Domingues, Alessandro M Varani
Affiliations
- Embrapa Amazônia Oriental, 66095-903 Belém, PA, Brazil.
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, 66075-110 Belém, PA, Brazil.
- Departamento de Biotecnologia Agropecuária e Ambiental, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil.
- Departamento de Biologia, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, 14884-900 Jaboticabal, SP, Brazil.
- Departamento de Ciência da Computação (DACOM), Grupo de e Bioinformática e Reconhecimento de Padrões (bioinfo-cp), Universidade Tecnológica Federal do Paraná (UTFPR), 80230-901 Cornélio Procópio, PR, Brazil.
- Artificial Intelligence and Informatics, The Rosalind Franklin Institute, OX110QX Didcot, UK.
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, 13416-000 Piracicaba, SP, Brazil.
- Departamento de Genética, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), 13418-900 Piracicaba, SP, Brazil.
Abstract
BACKGROUND
Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family.
FINDINGS
The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species.
CONCLUSIONS
The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.
MeSH
Medical Informatics, Genes, Genome, Seeds, Fruit, Telomere