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Diaphorina citri gene sets

NCBI annotations of the NCBI Diaci1.1 genome assembly, including gene sets, are available here.

Diaphorina citri genome assemblies

Diaci1.1 can be downloaded from NCBI here. Diaci1.1 is an assembly of the Diaphorina citri psyllid genome based on Diaci1.0, with approximately 12 fold coverage of PacBio reads incorporated into the assembly using PBJelly by Adam English and Stephen Richards at Baylor College of Medicine. Click here to download an older version of Diaci1.1 before processing by NCBI here. THIS IS PROVIDED FOR ARCHIVAL PURPOSES - USE THE NCBI VERSION OF THE ASSEMBLY ABOVE. 

Diaci1.0, an assembly of the Psyllid Diaphorina citri genome can be downloaded here. This assembly was produced by Nan Leng in October, 2011 with VELVET. Contigs were filtered for vector and wolbachia contamination. Some statistics for this assembly: 

 

163023 scaffolds
Max : 1101023
Min : 179
Total number of bp: 486947366
Total number N base: 29349593
Total number base without N: 457597773
Total GC: 174054882
%GC: 38.0366540813563%
N50 : 110293 (1097 scaffolds).
N50 scaffold average : 222031.063810392
Average scaffold size : 2986.98567686768

Diaci0.5, an assembly of the Psyllid Diaphorina citri genome can be downloaded here. This assembly was produced by Nan Leng in November, 2010 with VELVET, using short insert data (average insert size = 231bp) combined with 2Kb mate pair data, and used a Kmer size of 59. Some statistics for this assembly: 

153717 contigs
Max : 322695 
Min : 120
Total number of bp: 338559347
Total number N base: 76458764
Total number base without N: 262100583
Total GC: 99379781
%GC: 37.9166577435656%
N50 : 25120 (3413 contigs).
N50 contigs average : 49601.11221799
Average contig size : 2202.48474144044

Diaci0.1, a preliminary assembly of the Psyllid Diaphorina citri genome can be downloaded here. This assembly was produced by Nan Leng using VELVET. Some statistics for this assembly: 

199128 contigs
Max : 77169
Min : 120
Total number of bp: 227473101
Total number N base: 5974172
Total number base without N: 221498929
Total GC: 83950847
%GC: 37.9012428543165%
N50 : 2701 (20769 contigs).
N50 contigs average : 5476.34012229766
Average contig size : 1142.34613414487 

This assembly version 0.1 and 0.5 are not intended for annotation use, and are provided to allow Psyllid researchers to conduct preliminary analysis of the psyllid genome. A high quality assembly, currently in production, will be used for annotation.

 

Diaphorina citri transcriptome assemblies

Diaci_transcriptome_0.9, a transcriptome assembly constructed by Nan Leng of Illumina using VELVET and OASES, can be downloaded here. This de novo transcriptome assembly was produced using as input RNA reads from adult, egg and nymph tissue. Preliminary analysis indicates that this assembly is of a higher quality than the Diaci0.1 transcriptome assembly below. Separate transcriptome assemblies for adult, egg and nymph tissues were also constructed by Nan Leng using VELVET and OASES using only RNA reads from adult, egg and nymph tissues respectively. 

Diaci_transcriptome_0.1, a transcriptome assembly constructed using CUFFLINKS, can be downloaded here. This transcriptome assembly was produced using the Diaci0.5 genome assembly as a guide, and using as input RNA reads from adult, egg and nymph tissue. Note that since Diaci0.5 is a preliminary genome assembly, this transcriptome is also preliminary and will be updated and improved when an improved genome assembly is available. Liberibacter solanacearum

 

Supplemental data - D. citri transcriptome publication

Predicted expression levels in RPKM by tissue (egg, nymph and adult)

Transcripts predicted to be differentially expressed in maturing tissue (egg/nymph)

Bactericera cockerelli transcriptome assemblies

Fasta files for two assemblies of the Bactericera cockerelli transcriptome are available for download. Both were produced by Cecilia Tamborideguy at Texas A&M University and based on Illumina 105 nucleotide paired end sequencing and assembled using Trinity. 0074-L04-B01.fasta.gz is a gzipped file containing fasta-formatted contigs assembled from RNA sequencing reads from adult insects harboring Candidatus Liberibacter solanacearum, the causative agent of zebra chip disease. 0074-L04-B02.fasta.gz is a gzipped file containing fasta-formatted contigs assembled from RNA sequencing reads from adult insects not haboring Candidatus Liberibacter solanacearum.