U.S. flag

An official website of the United States government

Other Access

The information on this page (the dataset metadata) is also available in these formats:

JSON RDF

via the DKAN API

Diaphorina citri genome assembly Diaci 1.1

Asian citrus psyllid (Diaphorina citri)

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.

FieldValue
Modified
2019-08-05
Release Date
2017-01-20
Identifier
1dab11ba-7b6a-40ea-9305-86c93f0e6f51
Publisher
Ag Data Commons
License
Contact Name
Saha, Surya
Contact Email
Bureau Code
005:00 - Department of Agriculture