Let them eat cake: when the small aims at being LARGE or the empowering effects of bioinformatics in NGS wonderland

Abstract

This report summarizes the path (and pitfalls) in the way of the Genetic Resources Laboratory (LARGE-UFSJ), trailed with the aid of bioinformatics, in the field of massive DNA data analyses and its application in the field of conservation of biodiversity, particularly of Neotropical migratory fish. We use the metaphor of DNA sequencing as the cake, both as a prized delicacy formerly inaccessible to the masses, as in the infamous "let them eat cake", scornfully exclaimed by Marie-Antoinette during bread shortage in the French Revolution, but also as a means to achieve rapid growth for small research groups, as the plot device in Lewis Carroll' Alice in Wonderland. Next-Generation Sequencing (NGS) methods have been known to promote a true revolution in the Life Sciences, empowering groups with limited resources to explore the relatively new, still unknown and often surprising world of genetic sequences. Indeed, we argue for the inertia breaking potential of NGS and give our group's trajectory as a testimony. It all begun with the fortuitous union of providential fish DNA big-data gathered by Genetics professor, Dr. Yazbeck, and Computer Science professor, Dr. Sachetto's curiosity onto biological research, along the wit of some young researchers. Our initial NGS challenge was to provide the assembly and annotation of the first mitochondrial genome for the Anostomidae fish family. The LARGE's NGS research program was able to promote the characterization of what was then arguably the highest number of microsatellite DNA markers for the flagship species, Salminus brasiliensis (dourado) and Brycon orbignyanus (piracanjuba), useful in environmental applications for conservation (green biotechnology). We also have provided this large raw datasets, as well as elaborated massive results, freely available to the scientific community in data repositories such as GenBank, SRA and FigShare, such as genomic assemblies and gene annotation in these fish. Technological spin offs with application in the environmental protection and food production fields have also been devised as direct consequence of the availability of such rich and diverse data.