Determining Various Viral Sequences Associated with the Genome of Date Palm (Phoenix dactylifera L.) Using RNA-Seq Data Analysis

This chapter aims to reveal viruses in fruit tissues of date palms by developing a particular bioinformatics workflow. The study of RNA-Seq data can significantly advance our understanding of viruses and how they interact with their hosts. In order to identify the related plant viruses, the current work performed transcriptome studies of date palm (P. dactylifera) fruit from 20 public libraries. While the viruses Pittosporum cryptic virus-1 (PiCV-1) and Grapevine leafroll-associated virus (GLRaV) have been recognized previously, thirty-seven additional plant viruses have been found by using a workflow analysis constructed in this study to detect partial nucleotide sequences of their RdRp and Replicase genes. At the nucleotide level, all of the viral sequences found were nearly identical (100%) and many of the isolates had been added to GenBank. On P. dactylifera trees, however, there have been prior reports of an extremely uncommon viral infection. Therefore, it is necessary to do research in order to ascertain the virome of the date palm tree.