Abstract
BackgroundThe genome sequence data of more than 65985 species are publicly available as of October 2021 within the National Center for Biotechnology Information (NCBI) database alone and additional genome sequences are available in other databases and also continue to accumulate at a rapid pace. However, an error-free functional annotation of these genome is essential for the research communities to fully utilize these data in an optimum and efficient manner.ResultsAn analysis of proteome sequence data of 689 fungal species (7.15 million protein sequences) was conducted to identify the presence of functional annotation errors. Proteins associated with calcium signaling events, including calcium dependent protein kinases (CDPKs), calmodulins (CaM), calmodulin-like (CML) proteins, WRKY transcription factors, selenoproteins, and proteins associated with the terpene biosynthesis pathway, were targeted in the analysis. Gene associated with CDPKs and selenoproteins are known to be absent in fungal genomes. Our analysis, however, revealed the presence of proteins that were functionally annotated as CDPK proteins. However, InterproScan analysis indicated that none of the protein sequences annotated as “calcium dependent protein kinase” were found to encode calcium binding EF-hands at the regulatory domain. Similarly, none of a protein sequences annotated as a “selenocysteine” were found to contain a Sec (U) amino acid. Proteins annotated as CaM and CMLs also had significant discrepancies. CaM proteins should contain four calcium binding EF-hands, however, a range of 2–4 calcium binding EF-hands were present in the fungal proteins that were annotated as CaM proteins. Similarly, CMLs should possess four calcium binding EF-hands, but some of the CML annotated fungal proteins possessed either three or four calcium binding EF-hands. WRKY transcription factors are characterized by the presence of a WRKY domain and are confined to the plant kingdom. Several fungal proteins, however, were annotated as WRKY transcription factors, even though they did not contain a WRKY domain.ConclusionThe presence of functional annotation errors in fungal genome and proteome databases is of considerable concern and needs to be addressed in a timely manner.
Highlights
The genome sequence data of more than 65985 species are publicly available as of October 2021 within the National Center for Biotechnology Information (NCBI) database alone and additional genome sequences are available in other databases and continue to accumulate at a rapid pace
To determine the potential presence of Calcium dependent protein kinase (CDPK) genes/ proteins in fungi, the annotated proteome files of 689 fungal species were downloaded from the NCBI website
The search resulted in the identification of 521 protein sequences in 197 species annotated as a “calcium/calmodulin-dependent protein kinase” (Additional file 1)
Summary
The genome sequence data of more than 65985 species are publicly available as of October 2021 within the National Center for Biotechnology Information (NCBI) database alone and additional genome sequences are available in other databases and continue to accumulate at a rapid pace. There are several databases present in the public domain, including the National Center for Biotechnology Information (NCBI), UniProt/SwissProt (Consortium 2018), Ensembl (Hunt et al 2018), and others, that provide genome, gene, and protein sequences of thousands of species, as well as other biological data on the regulation, expression, evolution, and phylogeny of genes and proteins. These databases provide analytical tools to determine the homology of new gene/protein sequences. The use of these data for experimental validation and the discovery of novel, beneficial products is very promising, their efficient and optimal utilization can be hampered if the sequence data are prone to false positive or negative annotations
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