Fungal genomes: suffering with functional annotation errors

Abstract Background 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 also continue to accumulate at a rapid...

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Autores principales:	Tapan Kumar Mohanta, Ahmed Al-Harrasi
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Fungal genome Fungi Genome Annotation Selenoprotein WRKY Botany QK1-989
Acceso en línea:	https://doaj.org/article/105ab0df42914ac9ad0a1f0e2836af58
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spelling	oai:doaj.org-article:105ab0df42914ac9ad0a1f0e2836af582021-11-08T10:45:14ZFungal genomes: suffering with functional annotation errors10.1186/s43008-021-00083-x2210-6359https://doaj.org/article/105ab0df42914ac9ad0a1f0e2836af582021-11-01T00:00:00Zhttps://doi.org/10.1186/s43008-021-00083-xhttps://doaj.org/toc/2210-6359Abstract Background 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 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. Results An 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. Conclusion The presence of functional annotation errors in fungal genome and proteome databases is of considerable concern and needs to be addressed in a timely manner.Tapan Kumar MohantaAhmed Al-HarrasiBMCarticleFungal genomeFungiGenomeAnnotationSelenoproteinWRKYBotanyQK1-989ENIMA Fungus, Vol 12, Iss 1, Pp 1-7 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Fungal genome Fungi Genome Annotation Selenoprotein WRKY Botany QK1-989
spellingShingle	Fungal genome Fungi Genome Annotation Selenoprotein WRKY Botany QK1-989 Tapan Kumar Mohanta Ahmed Al-Harrasi Fungal genomes: suffering with functional annotation errors
description	Abstract Background 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 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. Results An 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. Conclusion The presence of functional annotation errors in fungal genome and proteome databases is of considerable concern and needs to be addressed in a timely manner.
format	article
author	Tapan Kumar Mohanta Ahmed Al-Harrasi
author_facet	Tapan Kumar Mohanta Ahmed Al-Harrasi
author_sort	Tapan Kumar Mohanta
title	Fungal genomes: suffering with functional annotation errors
title_short	Fungal genomes: suffering with functional annotation errors
title_full	Fungal genomes: suffering with functional annotation errors
title_fullStr	Fungal genomes: suffering with functional annotation errors
title_full_unstemmed	Fungal genomes: suffering with functional annotation errors
title_sort	fungal genomes: suffering with functional annotation errors
publisher	BMC
publishDate	2021
url	https://doaj.org/article/105ab0df42914ac9ad0a1f0e2836af58
work_keys_str_mv	AT tapankumarmohanta fungalgenomessufferingwithfunctionalannotationerrors AT ahmedalharrasi fungalgenomessufferingwithfunctionalannotationerrors
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Fungal genomes: suffering with functional annotation errors

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