Genomics and transcriptomics of Theobroma grandiflorum (cupuassu): a comparative, evolutive and functional approach

Abstract

Theobroma grandiflorum, (cupuassu) is a member of the Malvaceae family, and one of the most popular species in the Brazilian Amazon. The cupuassu fruit pulp is much appreciated for the preparation of juices, jams, liqueurs, jellies, ice cream, and others. The seeds are used in the manufacture of chocolate powder and tablets (cupulate) and the cosmetics industry. Although fruit growers are increasingly taking advantage of cupuassu resources, encouraging a productive chain in the Amazon region, the cupuassu culture is still little explored and its products are little known on a national scale. In addition, several diseases affect the crop, including witches' broom, caused by Moniliophthora perniciosa, responsible for large losses in productivity. In this sense, breeding programs have already obtained resistant and more productive genotypes (fruits), but other studies on the molecular scale are still needed, mainly to elucidate questions regarding the biology and evolution of this culture. For instance, although cupuassu belongs to the same genus as cocoa (Theobroma cacao), a species from which chocolate is obtained, and has been extensively studied from a molecular, genomic and functional point of view over the past decades; little is known about its cupuaçu genome, only that it has 2n = 40 and an estimated genome size of 448-Mb. Thus, cupuassu emerges as an excellent candidate for molecular and comparative genomics studies, especially concerning its similar species, cocoa. Comparative genomics has been widely used to identify patterns among different species, is considered a powerful tool for unraveling evolutionary processes, genomic trends, and generating potentially applicable knowledge in breeding programs. Therefore, this research proposal has the goal to deep sequencing the genomic and transcriptomic by high performance second (Illumina) and third (Pacbio) generation platforms of Theobroma grandiflorum (resistant C174 and C1074 susceptible to witches broom) genotypes, comparing against the sequenced genomes of the congener species T. cacao (genotypes Criollo and Matina) available in public databases. The main objective of this project is to generate new knowledge about the organization, evolution and genomic functions of T. grandiflorum, exploring the evolution of fruit-related gene families and mechanisms related to plant-pathogen interaction, thus generating new subsidies for sustainable exploitation of Amazonian biodiversity. This proposal will be in line with the requirements and standardization of the Earth Biogenome Project, an international initiative that aims to sequence, catalog and characterize the genomes of all Earth's eukaryotic biodiversity. The completion of this research project will also allow collaboration between two groups with complementary expertise. Prof.'s Alessandro Varani group from UNESP with experience in molecular genetics, plant genomics, and bioinformatics, and Prof.'s Vinícius Abreu group from UFPA with experience in comparative genomics, databases, bioinformatics, and genetics, and cupuassu breeding. We hope that this interaction will generate impacts related to the quality and quantity of scientific publications of both groups involved, nucleating scientific research groups in the field of bioinformatics and plant genomics in Pará and São Paulo states. (AU)