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Inference and annotation of the sugarcane pantranscriptome

Grant number: 19/24796-5
Support Opportunities:Scholarships in Brazil - Scientific Initiation
Effective date (Start): February 01, 2020
Effective date (End): January 31, 2022
Field of knowledge:Biological Sciences - Biology
Principal Investigator:Diego Mauricio Riano Pachon
Grantee:Felipe Vaz Peres
Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil


Sugarcane (Saccharum spp.) belongs to the family Poaceae and has a large impact in the Brazilian agriculture, industry and economy, where it is a source of sugar, ethanol and electricity. Current sugarcane breeding program are increasingly exploiting molecular-based approaches in order to generate new varieties in a more targeted and faster manner. However, sugarcane has a very complex genome, due to high levels of ploidy, aneuploidy and polymorphisms among sister chromosomes. Due to this the genomes of commercial cultivars have not been completely sequenced or characterized yet. An alternative that is widely used with the goal of identifying genes responsible for the establishment of phenotypes of interest is the sequencing of messenger RNA molecules in a large scale. Many of these transcriptome sequencing datasets have been publicly released via public repositories and can be re-used in order to generate new insights.In the last decade with the development of the massively parallel nucleic acid sequencing technologies applied to genomics and transcriptome, it has been shown that the terms pangenomics and pantranscriptomics, that were thought to be restricted to prokaryotes, are actually applicable to eukaryotes as well. Briefly, it has been shown that in a given species not all individuals have the same genetic information, some individuals can have genes that are exclusively found in them. The union set of all the genes, in all the individuals of the species, is what it is called the pangenome. That part of the genetic information only shared by a subset of individuals is known as the accessory genome and that part only found in a single individual is known as the exclusive genome. These concepts applied in a similar way to the study of the transcriptomes, and then we have pantranscriptomes.In this project, our goal is to applied well established approached for the inference of eukaryotic pan-transcriptomes, to public transcriptomics data from sugarcane, and in that way generate a pan-transcriptome for sugarcane that will allow to make cross-cultivar comparisons as well as to explore, in future projects, co-expression networks that will in turn aid in the functional annotation of until then transcripts of unknown function.

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
PERES, FELIPE VAZ; RIANO-PACHON, DIEGO MAURICIO; STADLER, PF; WALTER, MEMT; HERNANDEZ-ROSALES, M; BRIGIDO, MM. ContFree-NGS: Removing Reads from Contaminating Organisms in Next Generation Sequencing Data. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, BSB 2021, v. 13063, p. 4-pg., . (19/24796-5)

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