To the full: the case of a virus and its host plant genomes

Advances in sequencing technologies have produced extensive data about plant genome and pathogens. When applied to plant–virus pathosystems, current sequencing technologies can facilitate the characterization of both plant and virus diversity as well as the identification of previously unknown viruses. However, the contribution of high-throughput sequencing technologies to virus detection and identification remains constrained by several technical challenges including the risk of assembling artificially chimeric viral genomes due to short sequencing read lengths. Similarly, assembly of sequences in the highly repetitive regions of plant genomes remains challenging. The study of the genomic components from the cassava – geminivirus pathosystem illustrates the current limitations and opportunities of high-throughput sequencing technologies.
Cassava geminiviruses are the causal agents of cassava mosaic disease (CMD), the most widespread and devastating disease of cassava, an important staple crop in Africa. Sequencing technologies can be instrumental to analyse the diversity of geminiviruses in the field as well as to characterize natural resistance/tolerance in cassava. For example, we have taken advantage of PacBio long read sequencing to develop a new methodology called CIDER-Seq (Circular DNA Enrichment Sequencing). The CIDER-Seq is particularly suitable to produce full-length virus genomes at relatively low cost and can be used analyse geminivirus populations in field trials of virus-resistant cassava.
Natural tolerance to cassava geminiviruses has been extensively in the African cassava cropping systems to limit the negative impact of CMD. The so-called CMD2 is a single dominant locus that confers tolerance to geminivirus infection. Despite extensive efforts to characterize the CMD2 locus, the gene(s) conferring natural tolerance has remained elusive. Genome sequencing efforts pave the way to the identification of the CMD2 genes. However, the highly repetitive nature of the CMD2 genomic region has made its assembly particularly challenging and new sequencing and bioinformatics approaches need to be implemented in order to improve the assembly of repetitive sequences and to fill the gaps between contigs.