Diaphorina citri genome assembly Diaci 1.1
Principal Investigator(s): View help for Principal Investigator(s) US Department of Agriculture; National Agricultural Library
Version: View help for Version V1
Project Citation:
US Department of Agriculture, and National Agricultural Library. Diaphorina citri genome assembly Diaci 1.1. Ann Arbor, MI: Inter-university Consortium for Political and Social Research [distributor], 2026-06-26. https://doi.org/10.3886/E250257V1
Project Description
Project Title:
View help for Project Title
Diaphorina citri genome assembly Diaci 1.1
Summary:
View help for Summary
The International Psyllid Genome Consortium has generated a genome assembly Diaci 1.1 of the Asian citrus psyllid (Diaphorina citri). This assembly is also available and accessioned at the National Center for Biotechnology Information:
https://www.ncbi.nlm.nih.gov/assembly/GCF_000475195.1/.
DNA extraction and library preparation
High-molecular weight DNA was extracted using the BioRad AquaPure Genomic DNA isolation kit from fresh intact D. citri collected from a citrus grove in Ft. Pierce, FL and reared at the USDA, ARS, U.S. Horticultural Research Laboratory, Ft. Pierce, FL. To generate PacBio libraries, DNA was sheared using a Covaris g-Tube and SMRT-bell library was prepared using the 10Kb protocol (PacBio DNA template prep kit 2.0; 3-10Kb), cat #001-540-835.
Genome sequencing and assembly
Samples were prepared for sequencing using the TruSeq DNA library preparation kits for paired-end as well as long-insert mate-pair libraries. All were sequenced on the Illumina HiSeq2000 using 100bp or longer reads. Seven libraries were sequenced, with inserts ranging from "short" (ca. 275bp) to 10Kb. These are available in NCBI SRA and included 99.7 million paired-end reads (NCBI SRA:SRX057205), 35.1 million 2kb mate-pair reads (NCBI SRA: SRX057204), 30 million 5kb mate-pair reads (NCBI SRA: SRX058250) and 30 million 10kb mate-pair reads (NCBI SRA: SRX216330). A second round of DNA sequencing was done with PacBio at 12X coverage (NCBI SRA: SRX218985) for scaffolding the Diaci1.0 Illumina assembly to create the Diaci1.1 version of the D. citri genome. Thirty-nine SMRTcells of the library were sequenced, all with 2×45 minute movies. A total of 2,750,690 post-filter reads were generated, with an average of 70,530 reads per SMRTcell. The post-filter mean read length was 2,504 bp with an error rate of 15%.
Velvet was used with kmer 59 for generating the original assembly. PacBio long reads were mapped to the draft assembly using blasr with the folowing parameters: -minMatch 8 -minPctIdentity 70 -bestn 5 -nCandidates 30 -maxScore -500 -nproc 8 -noSplitSubreads. These alignments were parsed using PBJelly with default parameters.
Resources in this dataset:
Resource Title: Diaphorina citri genome assembly Diaci 1.1. File Name: 121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.mfa_.gzResource Description: This resource contains a fasta file of the Diaphorina citri genome assembly Diaci 1.1.
Resource Title: Diaphorina citri genome assembly Diaci 1.1.
File Name: 121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.mfa_.gz
Resource Description: This resource contains a fasta file of the Diaphorina citri genome assembly Diaci 1.1.
DNA extraction and library preparation
High-molecular weight DNA was extracted using the BioRad AquaPure Genomic DNA isolation kit from fresh intact D. citri collected from a citrus grove in Ft. Pierce, FL and reared at the USDA, ARS, U.S. Horticultural Research Laboratory, Ft. Pierce, FL. To generate PacBio libraries, DNA was sheared using a Covaris g-Tube and SMRT-bell library was prepared using the 10Kb protocol (PacBio DNA template prep kit 2.0; 3-10Kb), cat #001-540-835.
Genome sequencing and assembly
Samples were prepared for sequencing using the TruSeq DNA library preparation kits for paired-end as well as long-insert mate-pair libraries. All were sequenced on the Illumina HiSeq2000 using 100bp or longer reads. Seven libraries were sequenced, with inserts ranging from "short" (ca. 275bp) to 10Kb. These are available in NCBI SRA and included 99.7 million paired-end reads (NCBI SRA:SRX057205), 35.1 million 2kb mate-pair reads (NCBI SRA: SRX057204), 30 million 5kb mate-pair reads (NCBI SRA: SRX058250) and 30 million 10kb mate-pair reads (NCBI SRA: SRX216330). A second round of DNA sequencing was done with PacBio at 12X coverage (NCBI SRA: SRX218985) for scaffolding the Diaci1.0 Illumina assembly to create the Diaci1.1 version of the D. citri genome. Thirty-nine SMRTcells of the library were sequenced, all with 2×45 minute movies. A total of 2,750,690 post-filter reads were generated, with an average of 70,530 reads per SMRTcell. The post-filter mean read length was 2,504 bp with an error rate of 15%.
Velvet was used with kmer 59 for generating the original assembly. PacBio long reads were mapped to the draft assembly using blasr with the folowing parameters: -minMatch 8 -minPctIdentity 70 -bestn 5 -nCandidates 30 -maxScore -500 -nproc 8 -noSplitSubreads. These alignments were parsed using PBJelly with default parameters.
Resources in this dataset:
Resource Title: Diaphorina citri genome assembly Diaci 1.1. File Name: 121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.mfa_.gzResource Description: This resource contains a fasta file of the Diaphorina citri genome assembly Diaci 1.1.
Resource Title: Diaphorina citri genome assembly Diaci 1.1.
File Name: 121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.mfa_.gz
Resource Description: This resource contains a fasta file of the Diaphorina citri genome assembly Diaci 1.1.
Original Distribution URL:
View help for Original Distribution URL
https://agdatacommons.nal.usda.gov/articles/dataset/Diaphorina_citri_genome_assembly_Diaci_1_1/24660609
Scope of Project
Subject Terms:
View help for Subject Terms
genome assembly;
Diaphorina citri;
Asian citrus psyllid
Data Type(s):
View help for Data Type(s)
observational data
Collection Notes:
View help for Collection Notes
DOI: 10.15482/USDA.ADC/1342728
Citation: Leng, Nan; English, Adam; Johnson, Shannon; Richards, Stephen; Hunter, Wayne B.; Saha, Surya (2017). Diaphorina citri genome assembly Diaci 1.1. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1342728 (Downloaded 2026-06-26)
Related Publications
Published Versions
Report a Problem
Found a serious problem with the data, such as disclosure risk or copyrighted content? Let us know.
This material is distributed exactly as received from the data depositor. ICPSR has not reviewed, checked, or processed this material. For additional information about the study, please contact the investigator(s) directly. If you have questions about the accessibility of materials distributed by ICPSR or require further assistance, please visit ICPSR's Accessibility Center.