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RNA-Seq technology allows identifying which genes are being transcribed at a specific time point and comparing their expression levels under different conditions. Usually, the "mapping first" methodology is used to filter the reads aligned in the references, although it is possible to proceed with the "assembly first", which forms contiguous sequences with the “de novo” assembly. In present study, total RNA was extracted from a susceptible cultivar of sugarcane subjected to different biotic stresses with leaf scald causing agent. Subsequently, the transcripts were sequenced by the Illumina HIGH-SEQ platform and aligned, respectively, To the references of the study comprising: rRNA, organelas genes, and bacterial genes. After the last filtering, different outputs of unmapped reads were generated, which were used as input in Trinity de novo assembly of RNA-Seq data (Galaxy Version 2.9.1) to obtain contigs. These sequences were sent to a database with genomic sequences for identification and subsequent selection. After using different packages in R Studio, it was seen that several contigs had high TPM values under all conditions. Interestingly, alignments of these sequences were identified in Saccharum and Non-Redundant taxa, including members of the Poaceae family. In addition, similarities were identified of these sequences in sugarcane transposable elements identified in the study by (DOMINGUES et al., 2012). Furthermore, our analyzes show that there is a differential distribution of Acinetobacter soli aligned contigs between treatments, suggesting a relationship between their proliferation and the designed biotic stress. Further analyses are necessary for data curation and validation, but we conclude that our pipeline for unmapped reads presents to be a relevant strategy to uncover information from transcripts that would otherwise be unnoticed remain noticed, in addition to showing the microenvironment within the sugarcane and its variation between treatments.

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#	Name
1	Joel Junior(joelnunes@usp.br)
2	Raquel Miranda(miranda.rp@usp.br)
3	Marcelo Zerillo(marcelo.zerillo@gmail.com)
4	Henrique Dias (diash@usp.br)
5	Marie-Anne Sluys(mavsluys@usp.br)

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1	Domingues, D.S., Cruz, G.M., Metcalfe, C.J. et al. (2012). Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. In: BMC Genomics 13, 137.

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