In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome

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

lncRNA

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.

Scarano D, Rao R, Corrado G (2017) In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits. PLoS ONE 12(2): e0171504. [article]

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