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. 2022 Jun 25;29(4):dsac027.
doi: 10.1093/dnares/dsac027.

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations

Curtis R Carlson  1 , Anneliek M Ter Horst  1 , J Spencer Johnston  2 , Elizabeth Henry  1 , Bryce W Falk  1 , Yen-Wen Kuo  1
Affiliations

High-quality, chromosome-scale genome assemblies: comparisons of three Diaphorina citri (Asian citrus psyllid) geographic populations

Curtis R Carlson et al. DNA Res. .

Abstract

The Asian citrus psyllid, Diaphorina citri, is the insect vector of the causal agent of huanglongbing (HLB), a devastating bacterial disease of commercial citrus. Presently, few genomic resources exist for D. citri. In this study, we utilized PacBio HiFi and chromatin confirmation contact (Hi-C) sequencing to sequence, assemble, and compare three high-quality, chromosome-scale genome assemblies of D. citri collected from California, Taiwan, and Uruguay. Our assemblies had final sizes of 282.67 Mb (California), 282.89 Mb (Taiwan), and 266.67 Mb (Uruguay) assembled into 13 pseudomolecules-a reduction in assembly size of 41-45% compared with previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and annotated each assembly for repetitive elements, protein-coding genes, transfer RNAs, ribosomal RNAs, piwi-interacting RNA clusters, and endogenous viral elements. Between 19,083 and 20,357 protein-coding genes were predicted. Repetitive DNA accounts for 36.87-38.26% of each assembly. Comparative analyses and mitochondrial haplotype networks suggest that Taiwan and Uruguay D. citri are more closely related, while California D. citri are closely related to Florida D. citri. These high-quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.

Keywords: California; Taiwan; Uruguay; citrus greening disease; huanglongbing.

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Figures

Figure 1
Figure 1
Assembly chromatin contact frequency maps and sequencing coverage. (a–c) Hi-C chromatin confirmation contact frequency heatmaps of D. citri collected from geographically distinct populations maintained in laboratory colonies: California (CRF-CA) (a), Taiwan (CRF-TW) (b), and Uruguay (CRF-UY) (c). (d) Short-read, mixed-sex whole-genome shotgun sequencing average coverage per superscaffold (chromosome) across 10 kb sliding windows of CRF-CA, CRF-TW, and CRF-UY.
Figure 2
Figure 2
Structural variants and superscaffold size discrepancies of CRF-TW and CRF-UY relative to CRF-CA. (a) CRF-TW structural variant counts per superscaffold. (b) CRF-UY structural variant counts per superscaffold. (c) Superscaffold size differences in megabases per assembly relative to CRF-CA. (d) Overall structural variant counts per assembly, relative to CRF-CA. DEL (small), deletions ≤100 bp; DEL (large), deletions >100 bp; DUP: duplications; INS (small): Insertions ≤100 bp; INS (large), insertions > 100 bp; INV, inversions. DEL, deletions; DUP, duplications; INS, insertions; INV, inversions.
Figure 3
Figure 3
Circos plots of chromosomal features of each Diaphorina citri geographic population, excludingunplaced scaffolds. Tracks are, from outermost to innermost: (A) ideogram of the 13 D. citri chromosome-scale scaffolds. (B) GC percentage in 100 kb sliding windows. (C) Gene density in 100 kb sliding windows; heatmap scale in circle centres showing local min to local max. (D) Repeat DNA density in 100 kb sliding windows; heatmap scale in circle centres from local min to local max. (E) rRNA (outer row dots) and tRNA (inner row dots). (F), piRNA clusters and their direction (antisense: outer row dots; ambisense: middle row dots; sense: inner row dots). (G) Endogenous viral element (EVE) locations (D. citri-specific virus-derived EVEs: outer row dots; all other EVEs: inner row dots). The circos plots represent D. citri collected from geographically distinct populations maintained in laboratory colonies: California (CRF-CA), Taiwan (CRF-TW), and Uruguay (CRF-UY).
Figure 4
Figure 4
Full mitochondrial DNA coding sequence TCS haplotype network coded by geographic region. Circle size is scaled to the number of haplotypes. Hatch marks represent single-nucleotide substitutions. CRF-CA is in haplotype 1, CRF-TW is in haplotype 16, and CRF-UY is in haplotype 17. Arrows added for emphasis. Haplotype 2 is most common (n = 6). Regions labelled ‘Taiwan’ and ‘California’ represent mitogenomes downloaded from NCBI. Accession numbers available in Supplementary Table S2.
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