Readme file for Dcitr_OGSv1.0

Description: 

This Official Gene Set was generated as a merge of NCBI's Diaphorina citri Annotation Release 100 (available here: ftp://ftp.ncbi.nlm.nih.gov/genomes/Diaphorina_citri/ARCHIVE/ANNOTATION_RELEASE.100/) and a gff3 file resulting from manual curation efforts of the Diaphorina citri annotation community in the Apollo software (Apollo URL: https://apollo.nal.usda.gov/diacit/jbrowse/). Initially, QC of the manually curated genes was performed using the NAL's QC prototype software (description is available here: https://github.com/NAL-i5K/I5KNAL_OGS/wiki/QC-phase; software is available on request). Then, the cleaned manual annotations were merged with the protein-coding genes from the NCBI Diaphorina citri Annotation Release 100 using the NAL's Merge prototype software (description is available here:https://github.com/NAL-i5K/I5KNAL_OGS/wiki/Merge-phase; software is available on request). Non-coding RNAs from the NCBI Diaphorina citri Annotation Release 100 were added to the OGS after this merge. New consortium IDs for the OGS were generated, but Dbxref attributes referring to the original NCBI accessions were maintained when the model was not altered manually. CDS sequences for all protein-coding models, and protein and rna sequences from manually curated models were generated from the OGS gff3 file using the NAL's gff3_to_fasta.py program (available here: https://github.com/NAL-i5K/GFF3toolkit) and the underlying genome sequence (https://i5k.nal.usda.gov/data/Arthropoda/diacit-(Diaphorina_citri)/Current%20Genome%20Assembly/1.Genome%20Assembly/NCBI_RefSeq_diaci1.1/Contigs/121845_ref_Diaci_psyllid_genome_assembly_version_1.1_chrUn.fa.gz). All other sequences were derived from NCBI's Diaphorina citri Annotation Release 100 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Diaphorina_citri/ARCHIVE/ANNOTATION_RELEASE.100/), primarily because some protein and rna sequences predicted by NCBI contain additional sequence not present in the genome sequence. Note and exception attributes from NCBI were ported to the OGS gff3 file when sequence not derived from the genome sequence was used for the final model. 

Files included in this Official Gene Set:

Gff3 file: Dcitr_OGSv1.0.gff3
Protein fasta: Dcitr_OGSv1.0_pep.fa
RNA fasta: Dcitr_OGSv1.0_rna.fa
CDS fasta: Dcitr_OGSv1.0_cds.fa
Mapping file: Dcitr_NCBI_to_OGSv1.0_id_mapFile_MCOT-Dmel.txt (describes the changes between the original NCBI annotations and the OGSv1.0, MCOTv1.0 >65% coverage and Dmel >50% coverage )
Light Gff3 file without CDS and polypeptide rows. No Dbxref: Dcitr_OGSv1.0_light.gff3