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Diaphorina citri gene sets
A gene set produced using MAKER on the Diaci1.1 genome assembly (see below) is available:
Diaphorina citri genome assemblies
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. The contig N50 for this assembly is 38 kb. Please contact Wayne Hunter or Justin Reese for access to this assembly.
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, 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
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
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.