The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, researchers from the University of Naples Federico II generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome. The researchers report a comprehensive analysis of the transcriptome, improved with 39,095 transcripts, which reveals previously unannotated novel transcripts, natural antisense transcripts, long non-coding RNAs and alternative splicing variants. In addition, they investigated the sequence variants between the cultivars under investigation to highlight their genetic difference. Their strand-specific analysis allowed us to expand the current tomato transcriptome annotation and it is the first to reveal the complexity of the poly-adenylated RNA world in tomato. Moreover, this work demonstrates the usefulness of strand specific RNA-seq approach for the transcriptome-based genome annotation and provides a resource valuable for further functional studies.
Summarization and visualization of enriched GO terms of NAT pairs in tomato fruits
The scatterplot shows the representative clusters in a two dimensional space derived by applying multidimensional scaling to a matrix of the GO terms’ semantic similarities (more semantically similar GO terms are closer). Bubble color indicates the p-value according to the legend in upper left-hand corner. Bubble size is scaled according to the frequency of the GO terms.