Hybrid De Novo Assembly of the Leafhopper Genome with SMRT Sequencing Method

The leafhopper (Nephotettix cincticeps) is one of the most destructive agricultural pests in Asia. N.cincticeps directly damages the rice plant by sucking, and causes secondary damage by transmitting viruses as a vector. The leafhopper persistently transmitted rice dwarf virus (RDV) that causes enormous grain yield reduction worldwide. Control of the insect vector is a key approach for management of plant viral disease.

The genome of N.cincticeps was sequenced and assembled using a whole-genome shotgun approach that combined more than 146 Gb of single and paired-end sequence data (~180×) obtained from single-molecule (PacBio RS II) and second-generation (Illumina Hiseq2500) sequencing platforms. Our assembly comprises 10,774 contigs totaling 862 Mb, and a maximum contig length of 1.63 Mb. In addition, we used whole-genome mapping technology to generate a restriction map of the N.cincticeps genome uing Argus (OpGen) and then assembled scaffolds into super-scaffolds.

We used three gene-prediction methods (homology-based annotation, ab initioprediction and RNA-seq-based annotation) to annotate protein-coding genes. We then merged the results from each method to obtain a consensus genes. The genomic resources described here will facilitate future studies on the molecular information between virus and its insect vectors.