Dcitr_OGSv2.0

Description: 

This Official Gene Set with 25,292 mRNAs was generated using the Maker pipeline and multiple evidence sources. All predicted genes have supporting evidence from RNAseq data or orthologs which is denoted by the annotation edit distance or AED (Eilbeck 2009) score. An AED of 0.0 implies that the entire gene model agrees with evidence. eAED is the annotation edit distance at an exon level and is inferred from RNAseq only. The quality string contains even more information:
(Adapted from Cantarel, Genome Research 2008. Table 2. Maker quality index summary)
Length of the 5 UTR
Fraction of splice sites confirmed by an EST/transcript alignment
Fraction of exons that overlap an EST/transcript alignment
Fraction of exons that overlap EST/transcript or Protein alignments
Fraction of splice sites confirmed by a ab initio gene prediction
Fraction of exons that overlap a ab initio prediction
Number of exons in the mRNA
Length of the 3 UTR
Length of the protein sequence produced by the mRNA

Functional annotation was done using the AHRD pipeline and Interproscan. Some of the genes have also been manually curated. Please see the following page if you are interested to join the community curation initiative.
https://citrusgreening.org/annotation/index


Files included in this Official Gene Set:
Gff3 file: Dcitr_OGSv2.0.gff3
Protein fasta: Dcitr_OGSv2.0_pep.fa
RNA fasta: Dcitr_OGSv2.0_rna.fa
CDS fasta: Dcitr_OGSv2.0_cds.fa
The protein names start with DcitrP while the corresponding mRNA transcript is prefixed with DcitrM and the CDS with DcitrC.

CITATION:
Saha S, Hosmani P, Flores M, et al (2017) Using long reads, optical maps and long-range scaffolding to improve the Diaphorina citri genome. doi: 10.6084/m9.figshare.5375116.v1
https://figshare.com/articles/Using_long_reads_optical_maps_and_long-range_scaffolding_to_improve_the_Diaphorina_citri_genome/5375116

Please contact us using the following page if you have any questions.
https://citrusgreening.org/contact/form