Presentation Title

Identification of Long Non-Coding RNAs and Alternative Splicing Events During Tomato Fruit Development

Start Date

November 2016

End Date

November 2016

Location

HUB 302-#42

Type of Presentation

Poster

Abstract

Long non-coding RNAs (lncRNAs) are a class of regulatory RNA that are longer than 200 base pairs and do not code for protein. Alternative splicing (AS) is a process in gene transcription where a multi-exon gene is spliced into two or more different mature transcripts. Solanum lycopersicum, a model plant for fleshy fruit development, was studied through the use of RNA-Seq analysis for lncRNAs and AS events in order to better understand the molecular mechanisms of fleshy fruit development. Five distinct stages of tomato fruit with three biological replicates were used to monitor the changes in cell expanison, maturation, and ripening. The purpose of this project was to generate a comprehensive list of isoforms from the RNA-Seq data in order to identify lncRNAs, AS events, as well as new protein-coding genes. It was determined from this dataset that there were 565 lncRNAs with 162 of these having significant changes in expression during fruit development. It was also shown that 289 paired isoforms had significant differential expression between stages. Additionally, there were 214 new protein coding genes that were identified from the dataset. Novel results include a newly discovered lncRNA that was identified which is an example of a cis-natural antisense transcript and showed an inverted expression pattern to a zeta-carotene isomerase gene, a key component of lycopene biosynthesis, suggesting a possible regulatory role of this lncRNA in carotenogenesis. Future work will include investigation of these novel results from both bioinformatics and molecular biology approaches.

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Identification of Long Non-Coding RNAs and Alternative Splicing Events During Tomato Fruit Development

HUB 302-#42

Long non-coding RNAs (lncRNAs) are a class of regulatory RNA that are longer than 200 base pairs and do not code for protein. Alternative splicing (AS) is a process in gene transcription where a multi-exon gene is spliced into two or more different mature transcripts. Solanum lycopersicum, a model plant for fleshy fruit development, was studied through the use of RNA-Seq analysis for lncRNAs and AS events in order to better understand the molecular mechanisms of fleshy fruit development. Five distinct stages of tomato fruit with three biological replicates were used to monitor the changes in cell expanison, maturation, and ripening. The purpose of this project was to generate a comprehensive list of isoforms from the RNA-Seq data in order to identify lncRNAs, AS events, as well as new protein-coding genes. It was determined from this dataset that there were 565 lncRNAs with 162 of these having significant changes in expression during fruit development. It was also shown that 289 paired isoforms had significant differential expression between stages. Additionally, there were 214 new protein coding genes that were identified from the dataset. Novel results include a newly discovered lncRNA that was identified which is an example of a cis-natural antisense transcript and showed an inverted expression pattern to a zeta-carotene isomerase gene, a key component of lycopene biosynthesis, suggesting a possible regulatory role of this lncRNA in carotenogenesis. Future work will include investigation of these novel results from both bioinformatics and molecular biology approaches.