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U.S. Department of Agriculture

Nylanderia fulva annotations OGSv1.0

Summary
Summary
Resource Type
Genome Annotation
Name
Nylanderia fulva annotations OGSv1.0
Program, Pipeline, Workflow or Method Name
NCBI Eukaryotic Genome Annotation Pipeline (8.2); GeMoMa; exonerate; BLAST; EvidenceModeler; GFF3toolkit (v1.4.4)
Program Version
NA
Data Source
Source Name
: Nylanderia fulva genome assembly TAMU_Nfulva_1.0 (GCF_005281655.1)
Source URI
: https://i5k.nal.usda.gov/data/Arthropoda/nylful-%28Nylanderia_fulva%29/TAMU_Nfulva_1.0/
Organism
N . fulva (Tawny crazy ant)
Publication
  1. Zhou X, Rokas A, Berger SL, Liebig J, Ray A, Zwiebel LJ. Chemoreceptor Evolution in Hymenoptera and Its Implications for the Evolution of Eusociality.. Genome biology and evolution. 2015 Aug 12; 7(8):2407-16.
  2. McKenzie SK, Kronauer DJC. The genomic architecture and molecular evolution of ant odorant receptors.. Genome research. 2018 11; 28(11):1757-1765.
Description

The Nylanderia fulva OGSv1.0 is the Official Gene Set of genome assembly TAMU_Nfulva_1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_005281655.1/). It is a merge of NCBI Nylanderia fulva Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Nylanderia_fulva/100/) and semi-automated predictions of odorant receptors.

Odorant receptor predictions were based on manual curations of ORs (McKenzie & Kronauer 2018). Curated models were aligned to the genome with a combination of GeMoMa (http://www.jstacs.de/index.php/GeMoMa), exonerate (https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate) and BLAST. The exonerate alignment is based on a pipeline from Zhou et al 2015. Evidence from the different sources were combined with EvidenceModeler (https://evidencemodeler.github.io/). All gene models were checked for the 7tm6 domain against pfam using "pfam_scan.pl".

Odorant receptor predictions were merged with the NCBI Nylanderia fulva Annotation Release 100 using the GFF3toolkit software (https://github.com/NAL-i5K/GFF3toolkit).

Protein pages for the semi-automated predictions of odorant receptors can be accessed at NCBI: https://www.ncbi.nlm.nih.gov/protein?LinkName=nuccore_protein_wgs&from_u...