Tomato Genome Annotation and Curation at NCBI

The Eukaryotic Genome Annotation Pipeline at the National Center for Biotechnology Information (NCBI) generates annotation of coding and non-coding genes, transcripts, and proteins from finished and unfinished genome assemblies publicly available in the International Nucleotide Sequence Database Collaboration (INSDC). The primary reagents used in this pipeline are RNA-Seq data, traditional transcripts, ESTs, transcript assemblies and proteins. These annotated genomes are in scope for manual curation by the Reference Sequence (RefSeq) group at NCBI (https://www.ncbi.nlm.nih.gov/refseq/) to generate high-quality, non-redundant transcripts with accessions starting with NM_/NP_, NG_, or NR_. The curation process makes use of available transcripts, protein alignments, and publications as evidence to curate, or supplement, the pipeline generated model RefSeq records. At present, 50 plant genomes have been annotated by NCBI, of which tomato is one of the two plant genomes chosen for manual curation, the other being corn. The curated dataset defines the ‘best’ sequence representation which, in turn, is used as a primary input reagent for annotating other plant genomes, of the same or related family.

The plant genomes annotated by this pipeline are reported publicly with links to FTP, BLAST, MapViewer, and a detailed Annotation Report Summary at https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/.

RefSeq data can be accessed at the RefSeq homepage https://www.ncbi.nlm.nih.gov/refseq/, from NCBI’s Gene resource (https://www.ncbi.nlm.nih.gov/gene/), or can be downloaded from the FTP directory at ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/Solanum_lycopersicum/.