Tissue specific global gene expression profile in Yerba Mate (Ilex paraguariensis)

KRISHNA SHRESTHA, R.; FAY, J.; WATKINS, C.; LITWINIUK, S.; TALAVERA STEFANI, L.; ROJAS, C.; ARGÜELLES, C.; CACCAMO, M.; MIRETTI, M.

Foz do Iguaçu

Congreso; 11th International Plant and Molecular Biology Congress; 2015

International Society for Plan Molecular Biology

Transcriptome data provide direct insight into the global gene expression at specific time and space. Yerba Mate (Ilex paraguariensis, Aquifoliaceae) represents the foremost regional economy produce in northeast Argentina. However, it was not until recently that has been granted access to biotechnology and genetic studies applied to Yerba Mate (YM) production. Here we present the first tissue specific transcription profile in YM. Tissue samples were stored in liquid nitrogen until RNA extraction. Total RNA extracted from leaves and roots was quality-assessed and 500ng was used for the RNA-Sequencing library construction (100bp paired-ends reads) in triplicates. Libraries were then sequenced in two Illumina HiSeq 2500 lanes. Denovo-assembly from sequence reads was done using the Trinity assembler. Short contigs were filtered out and incomplete genes were extended to full-length RNA transcripts using the software Full-lengther based on full-length UniprotKB plant proteins. We obtained 119,285 protein sequences, though only 24,612 were complete. Assembled sequences were used as reference sequence and tissue specific sequence reads were then mapped to the reference sequence using bowtie2. Sequencing three libraries per sample gave consistency to our results. Analyses from the previously available transcriptome data are based on a single RNA-Seq library, and therefore prone to inconsistencies. Our results represent the first step to tissue specific expression profiling in YM, essential to explore effects of diseases, abiotic stress and microorganism interactions on YM production. Further investigations are necessary to expand these analyses covering other tissues and conditions.