Scientists from Embrapa Genetic Resources and Biotechnology and from the Federal University of Goiás (UFG) shave for the first time sequenced the genome of a native Cerrado species: pink ipê, also known as pink lapacho or pink trumpet tree (Handroanthus impetiginosus). The achievement is the topic of a paper published by the journal GigaScience, by the Oxford University Press, UK. The study was funded by the Distrito Federal Research Support Foundation (FAPDF) and the National Council of Scientific and Technological Development (CNPq). A possible application of the genome sequencing of the pink ipe is helping environmental agencies in forensic analysis to fight illegal logging. It is not only the beauty of Pink ipê that is attractive in the national and international markets. The tree supplies dense, high-quality timber that is resistant to insect attacks and to fire. All of such attributtes have made ipê be known today as the new mahogany, often used to manufacture of wooden decks and floors, especially in the United States. In addition, as it produces and stores chemical compounds of interest for health, the tree is targeted for the exploration of medicinal products. In Brazil, a significant fraction of logging is illicit, or without certified management. Genotyping can help environmental agencies track illegally explored trees. According to the researcher from Embrapa Genetic Resources and Biotechnology, the physicist Orzenil Silva-Júnior, first author of the article, pink ipê was chosen due its ecological importance in the biome, because they could already count on important technical information (preliminary molecular characterization and phylogeographic analysis), and also due to the large quantity of biological material acquired thanks to the comprehensive collection conducted by professor Rosane Collevatti, from UFG's Laboratory of Genetics & Biodiversity. Orzenil explains that the sequencing of the pink ipê would not have been possible without this group's expertise on native Cerrado species, which has been working for years on interpreting the distribution of the species' populations based on ecological, demographic, geographic and genetic data. The research started in 2013 and is the fruit of scientific cooperation between Rosane Collevatti and the researcher from Embrapa Genetic Resources and Biotechnology, Dario Gattapaglia, with funds from CNPq and and NEXTREE FAP-DF/Pronex network, led by the Embrapa scientist. Genomic tools are allies in the conservation of native species The genome sequencing of native Cerrado species optimizes and reduces the costs of conservation at all the stages, starting by the collection of genetic material, as Orzenil explains. In the case of pink ipê - which is a species found in the North, Northeast, Midwest and Southeast regions of Brazil, and spread from Bolivia through dry regions in the Peruvian Andes to Mexico, with a number of genetically diverse sub-groups-, genomic tools can help rationalize collecting efforsts, thus reducing costs and allowing the organization of actions according to the new knowledge of this tree's genetic diversity. For the conservation and sustainable use of pink ipê, molecular knowledge not only prevents redundancy but can also help the selection of genotypes. Stages of the genome sequencing The first stage of the genome sequencing resulted in the obtainment of continuous biological sequences, with size above 2,000 pairs of non-redundant, genetically organized bases. The assembly of gene sequences establishes a physical scale for measurements, like a “ruler”, compares Orzenil, in which, for instance, it is possible to observe the distances between the genome points where there are differences in DNA sequences between different individuals of the species under assessment. Such ruler is not perfect because these differences can be broad, but it is a useful approximation. “This is a quite interesting concept, which is called pan-genome, and it has important implications for genetic studies or in applications in breeding and biotechnology”, the researcher explains. Later, the genome's content is annotated to identify the priority genetic elements for the specific goals of further studies, such as genes and their products, DNA variants. According to the researcher, it is a long and laborious stage because it involves comparative analysis with an extensive database that is often little accurate or with low representation for the target species. In the case of the pink ipê, which is the first species in the Bignoniaceae family, the comparative analysis is not very fruitful and required the generation of new experimental data. The last stage is the publicization of the genome data in international banks, where they become accessible for the world's scientific communities. Today, there are large databases of biological sequences, such as the GenBank/NCBI, in the United States, the ENA/EMBL-EBI, in Europe, and the DDBJ, in Japan. In the case of pink ipê, the data has been filed in the National Center for Biotechnology Information (NCBI), in Maryland, USA. But the chosen bank does not make much of a difference, as Orzenil explains, since they exchange information, under the coordination of the initiative International Nucleotide Sequence Database (INSDC). Evolution of knowledge Above all, the team celebrates the fact they have managed to establish a high performance platform for the genotyping of Handroanthus species, paving the way for the genetic analysis of other native Cerrado species. “It is currently clear that each genome tells us a particular history, but the knowledge acquired facilitates new challenges, especially in the field of analysis. In less than four years, we already have a biological asset base to investigate the genetic variants discovered in about 17,000 of 28,000 well-annotated genes in the species' genome”, Orzenil asserts. Other studies are already in progress with cashew, mangaba, baru, and cagaita trees and an endangered Cerrado tree named dedaleiro. Genomic advances on native Cerrado species represent another hope for this biome, which, after the Atlantic Rainforest, is the Brazilian ecosystem that has suffered most changes from human settlement. Today, only 0.85% of the Cerrados is officially found in conservation units. About 80% has already been modified by man as a result of agricultural and urban expansion and the construction of roads, and only 19.15% of the area remains with the original vegetation. Sequencing genomes is like unveiling a galaxy Orzenil compares genome sequencing to discovering a galaxy. “If, in a galaxy, the planets are organized by gravitational forces, in genomes, the genetic information are laid out according to evolutionary forces, such as: recombination, mutation, genetic drift, gene selection and gene flows”, he compares. And he adds: “Genomic tools are like modern telescopes and allow scientists to infer the evolutionary trajectory of plant populations in the environment, from the knowledge of genes and connection to phenotypes”. The sequencing of an organism's genome results in a scale of measurements to define points that are physically spaced out, such as the SNPs (Single Nucleotide Polymorphisms), which, according to Orzenil, are variations in the DNA that help us understand aspects of the evolutional history of populations in the light of genetic science. Based on such information, and including data on geographic, demographic and ecological distribution, among others, it is possible to infer ancestral events that correlate to changes in populations. The knowledge about the plants' past offers the researchers the possibility to anticipate their future behavior at a population level, for instance, as opposed to projected environmental and climate changes in probabilistic scenarios. Anticipating such changes to populations is essential to ensure the protection of genetic resources and even plan efficient uses of genetic diversity both in conventional breeding and in biotechnology. Another important aspect, according to Orzenil, is that the spatial distribution of SNPs in the genome can be converted into genetic distance information through the genotyping of several individuals in genetic experiments. “This information is normally used by the plant breeder to monitor genetic crossings and discover genes of interest like, for instance, those related to increased productivity or resistance to diseases, with the help of biometrics,” illustrates the researcher. Additionally, when combined with genomic statistics, this information has direct applications in breeding and genetic improvement with the use of gene prediction techniques. The Embrapa researcher Dario Grattapaglia adds: “The breeding assisted by genomic data has enabled a paradigm change. We moved on from genetic inference, in which the data are observed by testing hypotheses and estimating effects, to the gene prediction of future data”. Such knowledge allows the determination of the aggregate effect of variations in the entire genome, influencing agronomic or industrial traits of interest. Translation: Mariana Medeiros