Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes
- Published
- Accepted
- Subject Areas
- Biodiversity, Biotechnology
- Keywords
- Conservation, Terpene, Bioprospection
- Copyright
- © 2016 Detoni et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes. PeerJ Preprints 4:e2316v1 https://doi.org/10.7287/peerj.preprints.2316v1
Abstract
The Atlantic Forest is one of the most import biodiversity hotspots in the world, nevertheless, its 20,000 plant species are poorly characterized genetically, what could undermine conservational efforts and bioprospection of natural products. We used a genome reduction using restriction site conservation (GR-RSC) technique to minimize sequencing effort and build in a short period a data bank of gene sequences from 35 plant species from the Atlantic Forest in a private natural protected area in Southwest Brazil. After Illumina sequencing and standard bioinformatics, we produced more than 66 million super reads, of which 11 million (17\%) were annotated using Diamond and UNIREF90 database and 55 million were 'No hit'. We picked 17 enzymes from 2 secondary metabolite synthesis pathways that are both important representatives of biological processes for plants and also of industrial interest, to test the usefulness of the databank we created for gene discovery. All 17 genes were detected in at least one of the 35 species and all species exhibited at least one of the genes. Eight of the 35 species exhibited all 17 genes. These results shows that genome simplification by restriction enzyme can be applied to preliminary screen thousands of species in tropical forests, generating useful databanks for scientific and entreprenurial activities both in conservational biology and bioprospection.
Author Comment
This is a preprint submission to PeerJ Preprints. The article introduces a databank of 66 million super reads of 35 Atlantic Forest plant species that can be available upon request at the discretion of the authors for researchers and entrepreneurs interested in conservation and bioprospection.
Supplemental Information
Supplementary material 1 – List of species and the respective codes for the bioproject available in Genebank
With the exception of the Solanaceae family, for which the Solanum genus was also found in our samples, all other families (but not their respective genus or species) were also found in our study. Genome sizes seem to be shared by species in the same genus but they can vary inside the same family. Species from the same family are marked with the same color and species from the same genus inside the same family are marked with the family color in a darker tone.