Diaci2.0 genome build
A new sequencing effort led by the
Mueller and
Brown labs utilized Pacbio and Dovetail technologies to create a high quality assembly. The improved v2.0 reference assembly has 1906 contigs and a contig N50 of 759Kb.
The genome and associated annotation were released on
March 5, 2018 and described in a webinar. Slides for the webinar are available
online. Please see our
slides from the ESA 2017 meeting and our
poster from the IRCHLB 2017 meeting for more details. We have released a new
Official Gene Set (v2.0) with 20,793 genes based on Illumina RNAseq and Pacbio Isoseq evidence. We have updated the
DiaphorinaCyc pathway database with OGS v2 and characterized 172 pathways that include 1477 enzymatic reactions. The ACP expression atlas (
Psyllid Expression Network) can be used to identify co-expressed gene sets.
Blast is available and you can download the data from our
FTP site.
Diaci1.9 interim genome build
Diaci1.9 is interim version of the
Diaphorina citri psyllid genome based on Pacbio long reads. We have generated 36.2Gb of Pacbio long reads from 41 SMRT cells with a coverage of 80X for the 400-450Mb psyllid genome. The
canu assembler was used to create an interim assembly with a contig N50 of 115.8kb and 8352 contigs. DIACI v1.9 has 8,352 contigs compared to 161,988 contigs in Diaci1.1 genome assembly. It has a contig N50 of 115.8kb and does not contain any Ns. Please note that this is an interim assembly so we will not be annotating it but you can
blast to it. You can download the genome from our
FTP site. We will be releasing this soon as Diaci2.0.
Diaci1.1 genome build
Diaci1.1 is the current version. It 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 scaffold N50 for this 485,705,082bp assembly is 109.8 kb. It has 161,988 scaffolds and 19,335,169 of N's. The number of contigs is 176,470 and the contig N50 is 34,407bp.
It was submitted to
NCBI and called NCBI-diaci1.1. It was annotated with the NCBI
Gnomon pipeline. This is used as the reference in
WebApollo for manual curation. The
Maker annotations from Diaci1.0 were updated to conform to the Diaci1.1 build and are also available within
WebApollo. You can find more information about our manual curation effort
here. We have created a
metabolic pathway database with 185 pathways and 1524 enzymatic reactions based on 12,548 proteins in the genome.
Diaci1.0 genome build
Diaci1.0, assembly was produced by Nan Leng in October, 2011 with
Velvet. Contigs were filtered for vector and wolbachia contamination. This assembly contains 163023 scaffolds with a total length of 486.9MB. The N50 is 110293 (1097 scaffolds) with a average scaffold size of 2986.98bp. The assembly was annotated using
Maker pipeline.
MCOT transcriptome 1.1
The
D. citri MCOT v1.0 transcriptome is a genome independent transcriptome assembly that provides a comprehensive set of gene models and was performed with the
MCOT pipeline where transcripts from
Maker,
Cufflinks,
Trinity and
Oases pipelines are combined. The
Jiang lab has kindly provided the MCOT annotations. MCOT v1.1 set has 30,562 CDS, transcripts and proteins. Combining gene models from Maker and cufflinks that are based on the genome with transcripts from
denovo transcriptome assembly from Trinity and Oases allows the identification of genes which only have transcript evidence from RNAseq.
MCOT v1.1 has been annotated with
AHRD and
Interproscan. The description includes Pfam domains, GO terms and a description generated using Uniprot, Interproscan and the AHRD pipeline. The
mapping file describes the connection between the original NCBI annotations and the OGSv1.0, MCOT, and
Drosophila orthologs. Please see the
README for more information.
Diaci transcriptome 0.9
Diaci_transcriptome_0.9, a transcriptome assembly was constructed by Nan Leng of Illumina using
Velvet and
Oasis. This
de novo transcriptome assembly was produced using as input RNA reads from adult, egg and nymph tissue. Separate transcriptome assemblies for adult, egg and nymph tissues were also constructed by Nan Leng using
Velvet and
Oasis using only RNA reads from adult, egg and nymph tissues respectively. This transcriptome assembly was used in the Maker annotation of Diaci1.1 genome build.
