ArticleFrontiers in plant science2016
Misannotation Awareness: A Tale of Two Gene-Groups.
Article in Frontiers in plant science, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 36 citations in OpenAlex.
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- Genome-wide identification of AOX family genes in Moso bamboo and functional analysis of PeAOX1b_2 in drought and salinity stress tolerance.Plant cell reports · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- The Azurin Coding Gene: Origin and Phylogenetic Distribution.Microorganisms · 2021Article
- CarrotPlants (Basel, Switzerland) · 2021Article
- Flavonone 3-hydroxylase Relieves Bacterial Leaf Blight Stress in Rice via Overaccumulation of Antioxidant Flavonoids and Induction of Defense Genes and Hormones.International journal of molecular sciences · 2021Article
- Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis.Heliyon · 2021Article
- Functional Relationship of Arabidopsis AOXs and PTOX Revealed via Transgenic Analysis.Frontiers in plant science · 2021Article
- Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing.Biology · 2020Review
- Article
- Identification and Expression Profiling of Toll-Like Receptors of Brown Trout (International journal of molecular sciences · 2020Article
- Whole Proteome Clustering of 2,307 Proteobacterial Genomes Reveals Conserved Proteins and Significant Annotation Issues.Frontiers in microbiology · 2019Article
- Considerations of AOX Functionality Revealed by Critical Motifs and Unique Domains.International journal of molecular sciences · 2018Article
- AOX1-Subfamily Gene Members in Olea europaea cv. "Galega Vulgar"-Gene Characterization and Expression of Transcripts during IBA-Induced in Vitro Adventitious Rooting.International journal of molecular sciences · 2018Article
- Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat.PloS one · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Incorrectly or simply not annotated data is largely increasing in most public databases, undoubtedly caused by the rise in sequence data and the more recent boom of genomic projects. Molecular biologists and bioinformaticists should join efforts to tackle this issue. Practical challenges have been experienced when studying the alternative oxidase (AOX) gene family, and hence the motivation for the present work. Commonly used databases were screened for their capacity to distinguish AOX from the plastid terminal oxidase (also called plastoquinol terminal oxidase; PTOX) and we put forward a simple approach, based on amino acids signatures, that unequivocally distinguishes these gene families. Further, available sequence data on the AOX family in plants was carefully revised to: (1) confirm the classification as AOX and (2) identify to which AOX family member they belong to. We bring forward the urgent need of misannotation awareness and re-annotation of public AOX sequences by highlighting different types of misclassifications and the large under-estimation of data availability.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.