A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes

Abstract

Genome annotation errors are a persistent problem that impede research in the biosciences. A manual curation effort is described that attempts to produce high-quality genome annotations for a set of haloarchaeal genomes (Halobacterium salinarum and Hbt. hubeiense, Haloferax volcanii and Hfx. mediterranei, Natronomonas pharaonis and Nmn. moolapensis, Haloquadratum walsbyi strains HBSQ001 and C23, Natrialba magadii, Haloarcula marismortui and Har. hispanica, and Halohasta litchfieldiae). Genomes are checked for missing genes, start codon misassignments, and disrupted genes. Assignments of a specific function are preferably based on experimentally characterized homologs (Gold Standard Proteins). To avoid overannotation, which is a major source of database errors, we restrict annotation to only general function assignments when support for a specific substrate assignment is insufficient. This strategy results in annotations that are resistant to the plethora of errors that compromise public databases. Annotation consistency is rigorously validated for ortholog pairs from the genomes surveyed. The annotation is regularly crosschecked against the UniProt database to further improve annotations and increase the level of standardization. Enhanced genome annotations are submitted to public databases (EMBL/GenBank, UniProt), to the benefit of the scientific community. The enhanced annotations are also publically available via HaloLex.

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

“…Additionally, curated H. salinarum R1 annotation from HaloLex database [95] was considered when RefSeq CDS were missing. iTSS located within 90 bp or 10% of CDS’ annotated edges were disregarded as intraRNA’s TSS and filtered out in next steps to avoid simple downstream gene promoters.…”

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

“…If we considered our annotation superior, we sent feedback to KEGG. In our report of the manual curation strategy (Pfeiffer & Oesterhelt, ), we have pointed to the severe problems caused by overannotation (assignment of a specific protein function while there is only support for a general function assignment; see also Schnoes, Brown, Dodevski, and Babbitt () for this subject). We consider some of the specific function assignments by KEGG as overannotations, which seems to be caused by relaxed conditions for some of the KEGG orthology assignments.…”

“…salinarum R1 genome reflects an extensive Gold Standard Protein based manual curation (Pfeiffer & Oesterhelt, ) and is used as a reference for the strain 91‐R6 annotation. This annotation is regularly and systematically kept up‐to‐date, based on principles published in 2015 (Pfeiffer & Oesterhelt, ). This also includes regular systematic correlation with a high‐level database (SwissProt).…”

Revision and reannotation of the Halomonas elongata DSM 2581T genome

“…In the original sequencing report, we applied a stringent annotation strategy only to proteins directly connected to ectoine metabolism, while the remainder of the genome was left as predicted by an annotation robot (Schwibbert et al, 2011). In the meantime, we have applied the stringent annotation strategy (Pfeiffer & Oesterhelt, 2015) to one-third of the genome. This detailed postannotation was performed during a study concerned with detailed analysis of osmoregulation in H. elongata (Kindzierski et al, 2017).…”