Chapter 4 - Viral metagenomics for the analysis of the Begomovirus genome

Abstract

The genus Begomovirus comprises a diverse group of economically important plant viruses infecting several crop species such as papaya, tomato, cotton, pulses, and cucurbits. They are single-stranded DNA virus belonging to the family geminiviridae and are transmitted by whiteflies. Most of the viruses in the genus Begomovirus comprise ssDNA(+), with a circular, bipartite genome with components A and B of about ~2.6–2.8kb per component. The begomovirus genome may also consist of subviral particles (satellite DNA) along with its mono- or bipartite genome. The diverse group of viruses in the Begomovirus genus can be determined through several molecular techniques such as polymerase chain reaction and rolling circle amplification. Here, we discuss the new insights to begomovirus life deduced from the studies of metagenomics, as well as the extensive set of analytical tools that facilitates the exploration of the diversity and function of begomovirus in plants. While metagenomics is shaping our interpretation of begomovirus in ecosystems via gene-centric and genome-centric approaches, annotating functions, metagenome assembly, and binning in heterogeneous samples remain challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to enhance our knowledge in begomoviral taxonomy virus at species level, and in phylogenetic and recombination analyses and evolution of the virus.