Synthetic Long Read Technologies and the Assembly and Investigation of Highly Repetitive Non-Model Plant Genomes

Plant species challenge existing assembly and characterisation methodologies as they are often highly complex - with varying ploidy, generally high heterozygosity and having large repetitive element content. The relatively narrow interest in any plant species also generally means that the interested communities are small compared to model species and human communities, and likewise the funding available is often at the low end for undertaking genome scale work.  Longer read lengths have proven useful in the assembly of plant genomes drastically increasing assembly metrics and often spanning over problematic repetitive regions. Here we explore and assess data generated using the Truseq Synthetic Long read Protocol (TSSLR) protocol from a highly heterozygous and repetitive tree genome. TSSLR uses extremely high quality short reads from Illumina sequencing to create synthetic long reads ranging in size from ~1 to 20 kb. Our results show that these reads provide a high fidelity alternative to existing long read technologies and should be especially useful in non-model species genome projects.