Biocuration and improvement of the Diaphorina citri draft genome assembly with long reads, optical maps and long-range scaffolding

Authors: SAHA, SURYA - Boyce Thompson Institute; HOSMMANI, PRASHANT - Boyce Thompson Institute; FLORES-GANZALEZ, MIRELLA - Boyce Thompson Institute; Hunter, Wayne; D'ELIA, TOM - Indian River State College; BROWN, SUSAN - Kansas State University; MUELLER, LUKAS - Boyce Thompson Institute

Submitted to: Arthropod Management Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 5/3/2017
Publication Date: 6/8/2017
Citation: Saha, S., Hosmmani, P.S., Flores-Ganzalez, M., Hunter, W.B., D'Elia, T., Brown, S.J., Mueller, L.A. 2017. Biocuration and improvement of the Diaphorina citri draft genome assembly with long reads, optical maps and long-range scaffolding. In: Proceedings of the 2017 10th Arthropod Genomics Symposium, June 8-11, 2017, Notre Dame, Indiana

Interpretive Summary: The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the spread of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods. The draft genome was annotated with automated pipelines. Knowledge transfer from well-curated reference genomes like Drosophila to a newly sequenced insect is challenging due to the diversity and complexity among all insect genomes. Thus we conducted manual curation of gene families that have key functional roles in Diaphorina citri biology and pathology. The community effort resulted in Official Gene Set v1.0 (Saha 2017a) with more than 500 manually curated gene models across developmental, Ribonucleic acid interference (RNAi)regulatory, and immune-related pathways (Saha 2017b). Curators included undergraduate and graduate students from multiple institutions as well as expert annotators from the i5k community. More information about our annotation initiative is available here https://citrusgreening.org/annotation/index.

Technical Abstract: The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the spread of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods. The draft genome was annotated with automated pipelines. Knowledge transfer from well-curated reference genomes like Drosophila to a newly sequenced insect is challenging due to the diversity and complexity among all insect genomes. We opted for manual curation of gene families that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 (Saha 2017a) with more than 500 manually curated gene models across developmental, Ribonucleic acid interference (RNAi) regulatory, and immune-related pathways (Saha 2017b). Curators included undergraduate and graduate students from multiple institutions as well as expert annotators from the i5k community. More information about our annotation initiative is available here https://citrusgreening.org/annotation/index. Single copy marker analysis using BUSCO software (Simão et al., 2015) of the current genome shows a significant proportion of 3,350 single-copy markers that are conserved in Hemiptera to be missing (25%) with only 74% present in full length copies. The manual genome annotation also identified a number of mis-assemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and potentially exacerbated by the use of short reads. To improve quality of genome assembly, we have generated 36.2Gb of Pacbio long reads from 41 SMRT cells with a coverage of 80X for the 400-450Mb psyllid genome. The Canu assembler (Koren 2016) was used to create an interim assembly (Diaci v1.9) with a contig N50 of 115.8kb and 8300 contigs (Saha et al., 2017c). This will be polished with Pacbio and Illumina paired-end reads followed by scaffolding with Illumina mate-pair reads. We are employing Dovetail chicago libraries and 10X Illumina library generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. This will be the first time all these methods have been applied to resolve an insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/.