Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes
Author and article information
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.
Cite this as
2016. Gene discovery in Atlantic Forest plant species using GR-RSC simplified genomes. PeerJ Preprints 4:e2316v1 https://doi.org/10.7287/peerj.preprints.2316v1Author 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.
Sections
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.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Marcella A A Detoni performed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Raony G C C L Cardenas analyzed the data, prepared figures and/or tables.
Marcela Uliano-Silva analyzed the data.
Mauro de Freitas Rebelo conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
1. Brazilian National Research Council (CNPq)
2. Permit: 010567/2015-1) in accordance with the Brazilian law (13.123/2012).
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Sequences are proprietary and can be available for further research at the discretion of the owner. The sequences that are used in the article to test the suitability of the database for gene discovery can be made available for the reviewers and the public at the submission for publication
Data Deposition
The following information was supplied regarding data availability:
Proprietary databank at bioinfo.biobureau.com.br
Funding
The study was funded by Votorantim Reservas. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
