High quality, chromosome-scale genome assemblies: Comparisons of three Diaphorina citri (Asian Citrus Psyllid) geographic populations
Data files
Jun 02, 2022 version files 752.08 MB
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2021_viral_db_no_prok_no_chord_no_TE_usearch_100.fa
83.12 MB
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CA_braker.gff3
21.43 MB
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CA_final_annotations_lvl0.tsv
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CA_final_annotations_lvl1.tsv
33.09 MB
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CA_piRNA.results.txt
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CA_rnammer.gff
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CA_tRNA.gff
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CA.asm.fa.out
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CA.asm.fa.tbl
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CA.asm.rc_2022_remove_drosophila_hits.csv
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README.txt
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TW_braker.gff3
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TW_final_annotations_lvl0.tsv
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TW_final_annotations_lvl1.tsv
32.40 MB
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TW_piRNA.results.txt
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TW_rnammer.gff
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TW_to_CA_variants.vcf
24.36 MB
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TW_tRNA.gff
7.37 MB
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TW.1.reorder.asm_2022_remove_drosophila_hits.csv
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TW.asm.fa.out
116.27 MB
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TW.asm.fa.tbl
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UY_braker.gff3
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UY_final_annotations_lvl0.tsv
32.14 MB
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UY_final_annotations_lvl1.tsv
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UY_piRNA.results.txt
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UY_rnammer.gff
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UY_to_CA_variants.vcf
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UY_tRNA.gff
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UY.1.reorder.asm_2022_remove_drosophila_hits.csv
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UY.asm.fa.out
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UY.asm.fa.tbl
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Jun 21, 2022 version files 986.86 MB
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2021_viral_db_no_prok_no_chord_no_TE_usearch_100.fa
83.12 MB
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CA_augustus.gtf
53.79 MB
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CA_braker.gtf
60.35 MB
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CA_final_annotations_lvl0.tsv
33.64 MB
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CA_final_annotations_lvl1.tsv
33.09 MB
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CA_piRNA.results.txt
18.91 KB
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CA_rnammer.gff
78.98 KB
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CA_tRNA.gff
7.47 MB
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CA.asm.fa.out
116.41 MB
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CA.asm.fa.tbl
2.45 KB
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CA.asm.rc_2022_remove_drosophila_hits.csv
4.91 KB
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README.txt
1.62 KB
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TW_augustus.gtf
43.35 MB
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TW_braker.gtf
51.05 MB
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TW_final_annotations_lvl0.tsv
32.95 MB
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TW_final_annotations_lvl1.tsv
32.40 MB
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TW_piRNA.results.txt
28.06 KB
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TW_rnammer.gff
76.93 KB
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TW_to_CA_variants.vcf
24.36 MB
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TW_tRNA.gff
7.37 MB
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TW.1.reorder.asm_2022_remove_drosophila_hits.csv
6.48 KB
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TW.asm.fa.out
116.27 MB
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TW.asm.fa.tbl
2.45 KB
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UY_augustus.gtf
41.67 MB
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UY_braker.gtf
49.52 MB
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UY_final_annotations_lvl0.tsv
32.14 MB
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UY_final_annotations_lvl1.tsv
31.61 MB
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UY_piRNA.results.txt
9.58 KB
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UY_rnammer.gff
71.01 KB
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UY_to_CA_variants.vcf
23.09 MB
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UY_tRNA.gff
6.80 MB
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UY.1.reorder.asm_2022_remove_drosophila_hits.csv
5.27 KB
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UY.asm.fa.out
106.08 MB
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UY.asm.fa.tbl
2.45 KB
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. 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% to 45% compared to previous assemblies which we validated using flow cytometry. We identified the X chromosome in D. citri and found it to use an XX/X0 sex-determination system. Annotation of repetitive elements revealed differing repeat class content between assemblies and showed that the bulk of repeat DNA is found on chromosomes 8 through 13. We annotated between 19,083 and 20,357 protein-coding genes and orthologous clustering of these suggested Taiwan and Uruguay D. citri are more closely related. Structural variant analyses identified chromosome 1 as having the largest variation in size between assemblies. We provide new python scripts to predict and filter endogenous viral elements (EVEs), finding 30 EVEs in California, 40 EVEs in Taiwan, and 32 EVEs in Uruguay, including a large, conserved integration with a closest BLASTx hit to Diaphorina citri flavi-like virus (DcFLV). We predicted differing numbers and sizes of piwi-interacting RNA (piRNA) clusters in each assembly, identifying 29 clusters in California, 41 in Taiwan, and 11 in Uruguay. Mitochondrial haplotype networks indicate that Taiwan and Uruguay D. citri are closely related, while California is related to Florida D. citri. These high quality, chromosome-scale assemblies provide new genomic resources to researchers to further D. citri and HLB research.