The Aga, also known as the Mariana Crow, is an endangered endemic crow of the Northern Mariana Islands, a Commonwealth of the United States of America. The only known population currently extant is on the island of Rota and has been in decline over the past two decades. Unknown pathogens are among the factors that may be contributing to this decline. To support metagenomic and transcriptomic analysis of potential disease agents, a reference genome was generated and gene features comprehensively annotated. The methods used and data availability are described. This data release consists of: 1. Gene annotations for the endangered Aga or Mariana Crow, including summary statistics, that are available from the National Center for Biotechnology Information (NCBI) at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Corvus_kubaryi/100/ 2. Raw.data.accessions.txt. A summary of raw data accessions deposited in NCBI databases used to complete the reference genome and gene annotation. The format is tab-delimited text, available at https://doi.org/10.5066/P9XSS01V.
3. Supernova.assembly.report.txt. A table describing the input data for genome assembly and output statistics of the final assembly, as computed by the supernova assembly program, in tab-delimited text and available at https://doi.org/10.5066/P9XSS01V. Additional information about these assembly parameters, including the algorithms used to compute them and expected ranges, are described in Weisenfeld et al. 2017.