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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Deep Sequencing of Diaphorina Citri

Location: Subtropical Insects and Horticulture Research

2013 Annual Report


1a.Objectives (from AD-416):
Produce better annotation of Asian citrus psyllid genome, Diaphorina citri, by producing a deep sequencing run.


1b.Approach (from AD-416):
Using psyllid DNA and RNA, as provided by ARS, conduct a deep sequencing run to aid validation and fill gaps in alignments for psyllid genome.


3.Progress Report:

This research relates to inhouse project objective #2: Biological Control: Develop new and improve existing biological control methods for psyllids and sharpshooter species. #2a. Virus propagation in insect cell cultures.

Deep sequencing of psyllid genome increased sequence accuracy and gene predictions. Genomics provides insights into insect biology, pathology, and management. The Asian citrus psyllid genome is the first genome from any psyllid species. The draft genome of D. citri (DIACI_1.0) was completed in 2011 (ARS, Ft. Pierce, FL), however, gaps in the assembly prompted the need for additional sequencing, conducted at the Los Alamos National Lab, New Mexico. The new revised genome (DIACI_1.1) was improved N50 of 38 kb (up from 25 kb) and an increase of over 10 million resolved bases. The genome and transcriptome have been submitted into the public domain at the National Center for Biotechnology Information, NCBI, to be made available by the larger research community Bioproject: [http://www.ncbi.nlm.nih.gov/genome?LinkName=bioproject_genome&from_uid=29447]. The psyllid transcriptome is supported by an additional 19,598 EST’s, with life-stage specific transcripts being identified for adults, nymphs and eggs for a refined transcriptome of 18,300 predicted proteins. BlastX analyses resulted in the greatest homologies between the psyllid and the Pea Aphid, Acyrthosiphon pisum, another hemipteran. The transcriptome data was provided to the Innocentive® Challenge Program to advance efforts for Ribonucleic Acid Interference (RNAi) development against psyllids. Efforts are now focused on annotation of the psyllid genome which will provide more information on the genetic basis of psyllid biology. Characterization of the psyllid transcriptome was submitted for publication.


Last Modified: 9/10/2014
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