De novo annotation of long noncoding RNAs in tomato and eggplant

A large fraction of the genomes of multicellular organisms contain genes specifying many classes of RNAs, inducing the complexity of the transcriptome. Long noncoding RNAs (lncRNAs) have increasingly been recognized to play essential functional roles in a diverse number of processes. Often lncRNAs are lowly or tissue-specifically expressed, show low levels of sequence conservation, and can even be translated into proteins, making high confidence identification difficult and contentious. To begin asking questions centered around lncRNAs in Solanaceous crop species, I have created a de novo annotation of lncRNAs for Solanum lycopersicum (tomato) cv. M82, and Solanum melongena (eggplant) cv. BARI06. The selected cultivars serve as both agriculturally and scientifically significant varieties. This de novo annotation will provide a foundational resource; being the first annotation of lncRNAs for each of these varieties serving as the basis of future research. In this analysis I used rigorous filtering to identify 3,224 and 6,012 high-confidence lncRNAs for tomato and eggplant, respectively, from paired-end Illumina short-read sequencing data generated from homografted (self-grafted) plants and tissue atlases. One such application of these annotations is in the identification of non-cell autonomous RNAs. Noncoding RNAs have been shown as mobile across long distances (i.e., between organs) in a wide variety of vascular plants. A key research focus of the Frank Lab is identification, validation, and reprogramming of mobile signals. Novel lncRNAs found to be mobile will be studied as novel communication systems, integral for the future of programmable plant systems.

I am extremely excited to have received the opportunity to partake in plant science research at Cornell University through the Boyce Thompson Institute. Given my passion for analytical work, I sought to immerse myself in bioinformatics. Building upon my foundation and understanding of computational chemistry, I was able to bring new directions to my research in the Frank Lab. This experience has solidified my decision to pursue a future in plant genetics. It has also provided me with a support network including my amazing mentor Michelle Heeney, members of the Frank Lab, and the larger plant science community at Cornell. I also feel much more informed about the process of applying to graduate school and the experience of being a graduate student. The breadth of my skills expanded as I became more confident in molecular biology doing PCR and confocal microscopy. Additionally, I was introduced to important plant-related skills like seed extraction, cultivation, pruning, and grafting, as well as broadening my knowledge of computational biology and bioinformatics. I also feel extremely grateful for the opportunity to have met like-minded undergraduate plant scientists in the program, and enjoy Ithaca and the surrounding areas. This program has been an amazing experience!