Diaci v3.0: Chromosome-level assembly,de novotranscriptome and manual annotation ofDiaphorina citri,insect vector of Huanglongbing

Abstract

Hemipterans include some of the most important insect pests of agricultural systems and vectors of plant pathogens. The vector, Diaphorina citri (Asian citrus psyllid) belonging to the Psylloidae superfamily, is the primary target of approaches to stop the spread of the pathogen Ca. Liberibacter asiaticus that causes Huanglongbing or citrus greening disease. High quality genomic resources enable rapid functional discovery that can target disease transmission and control. The previous psyllid genome (Diaci v1.1) available in NCBI is missing 25% of the single copy markers conserved in other Hemipterans. Manual genome curation helped to identify a significant number of genome anomalies including misassemblies and missing genes. We present an improved and highly contiguous de novo assembly based on PacBio long reads followed by Dovetail Chicago and Hi-C based scaffolding. The current assembly (Diaci v3) has 13 chromosomal length scaffolds with a genome size of 475 Mb. This is the first report of a chromosomal length assembly in the Hemiptera order according to our knowledge. Full-length cDNA transcripts were sequenced with PacBio Iso-Seq technology from diseased and healthy tissue at multiple life stages. Iso-Seq along with diverse Illumina RNA-Seq expression data were used to predict 19,049 protein-coding genes in psyllid using MAKER annotation pipeline. We also generated a genome independent transcriptome with a comprehensive catalog of all genes in the psyllid.

Characterization of Wnt Signaling Genes inDiaphorina citri, Asian Citrus Psyllid

“…Wnt1, Wnt6, and Wnt10 typically occur in very close proximity in a highly conserved gene cluster [22,23]. Accordingly, it is believed that this cluster is also conserved in D. citri and this notion is supported by the chromosomal length genome assembly in v3.0 [24]. The close phylogenetic relationship of Wnt1, Wnt6, and Wnt10 in D. citri ( Figure 2) supports the hypothesis that this cluster is the result of an ancient duplication event, one that may predate the divergence of cnidarians and bilaterians [23].…”

Segmentation pathway genes in the Asian citrus psyllid,Diaphorina citri

“…We searched the D. citri v3 genome for orthologs of genes known to be involved in segmentation in Drosophila [10] (Table 1). We then used available evidence to manually annotate the genes that were present [11,12] (Table 1–2). Most manual annotations were straightforward and performed using our workflow [see Methods], so only those requiring additional explanation are described in detail here.…”

Characterization of chitin deacetylase genes in theDiaphorina citrigenome

“…Chitin deacetylase genes in the D. citri v3 genome [13] were identified and manually annotated. These genes were classified into groups following the precedents established in other insects [5,6].…”

“…Chitin deacetylase genes in D. citri genome v3 [13] were identified by BLAST search of D. citri sequences with chitin deacetylase orthologs from other insects. Orthology was confirmed by reciprocal BLAST of the NCBI non-redundant protein database.…”