Using Long Reads, Optical Maps and Long-Range Scaffolding to Improve the Diaphorina citri Genome

Huanglongbing (HLB) is considered to be the most devastating of all citrus diseases, where the insect Asian citrus psyllid (Diaphorina citri, ACP) vectors the phloem-restricted bacterial pathogen Candidatus Liberibacter asiaticus (CLas). The current draft genome assembly was sequenced with Illumina and low coverage Pacbio for scaffolding (163,023 scaffolds, scaffold N50: 109.8kb). A BUSCO analysis shows a significant number of conserved single-copy markers either missing (26%) or fragmented (22%). A community-driven annotation project has also identified a number of misassemblies and fragmentation in the genome. This is, in-part, due to the complexity introduced when assembling DNA from a heterogeneous population and potentially exacerbated by the use of short reads. We have generated 36.2Gb of Pacbio long reads from 41 SMRT cells with a 80X coverage of the genome. The Canu assembler was used to create an Pacbio only assembly with 8300 contigs and N50 of 115.8kb. This will be polished with Pacbio and Illumina paired-end reads followed by scaffolding with Illumina mate-pair reads. Chicago libraries (Dovetail) utilize chromatin crosslinks to associate sequences originating from the same large DNA fragment and will also be used for scaffolding. BioNano optical maps generated using high molecular weight DNA from adult psyllid tissue will be used to provide long-range scaffolding. This will be the first time all these methods will be applied to resolve an insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/.