The DOI matches its Crossref record; 85 of the 85 references it cites were found in a registry or an index.
Evolution and diversity of the 2–oxoglutarate‐dependent dioxygenase superfamily in plants
Open accessAbstract
Summary: The 2–oxoglutarate‐dependent dioxygenase (2 OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2 OGD s remains to be accomplished. We present a phylogenetic classification of 479 2 OGD s in six plant models, ranging from green algae to angiosperms. These were classified into three classes –DOXA,DOXB and DOXC– based on amino acid sequence similarity. The DOXA class includes plant homologs ofE scherichia coli A lk B, which is a prototype of 2 OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4–hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2 OGD s from land plants were classified into the DOXC class, but only seven fromC hlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC‐class 2 OGD s to 57 phylogenetic clades. 2 OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm‐specific clades were found to be involved in various lineage‐specific specialized metabolisms, but 31 of the 57 DOXC‐class clades were only found in a single species. Therefore, the evolution and diversification of DOXC‐class 2 OGD s is partly responsible for the diversity and complexity of specialized metabolites in land plants.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,355
The Pfam Protein Families Database
Bateman, A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,000
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp348 · Cited by 12,751
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
Phytozome: a comparative platform for green plant genomics
Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr944 · Cited by 5,420
The Pfam protein families database
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719
An Improved General Amino Acid Replacement Matrix
Le, S. Q., & Gascuel, O. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn067 · Cited by 3,127
P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature
Nelson, D. R., Koymans, L., Kamataki, T., Stegeman, J. J., Feyereisen, R., Waxman, D. J., Waterman, M. R., Gotoh, O., Coon, M. J., Estabrook, R. W., et al. (1996) · Pharmacogenetics · doi:10.1097/00008571-199602000-00002 · Cited by 2,945
The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., Terry, A., Salamov, A., Fritz-Laylin, L. K., Maréchal-Drouard, L., et al. (2007) · Science · doi:10.1126/science.1143609 · Cited by 2,691
Cited by
Houben, M., & Van de Poel, B. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00695 · Cited by 420
The regulation of ethylene biosynthesis: a complex multilevel control circuitry
Pattyn, J., Vaughan‐Hirsch, J., & Van de Poel, B. (2021) · New Phytologist · doi:10.1111/nph.16873 · Cited by 398
Casanova-Sáez, R., Mateo-Bonmatí, E., & Ljung, K. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a039867 · Cited by 285
Melatonin metabolism, signaling and possible roles in plants
Back, K. (2021) · The Plant Journal · doi:10.1111/tpj.14915 · Cited by 281
Salminen, A., Kauppinen, A., & Kaarniranta, K. (2015) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-015-1978-z · Cited by 99
Metadata
- Authors
- Kawai, Y., Ono, E., & Mizutani, M.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2014-04
- Volume
- 78
- Issue
- 2
- Pages
- 328-343
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W2156654220
- Cited by
- 386
- References
- 85
- FWCI
- 19.82
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Evolution and diversity of the 2–oxoglutarate‐dependent dioxygenase superfamily in plants. https://app.cochat.ai/papers/10.1111/tpj.12479
- The paper
- Kawai, Y., Ono, E., & Mizutani, M. (2014). Evolution and diversity of the 2–oxoglutarate‐dependent dioxygenase superfamily in plants. The Plant Journal. https://doi.org/10.1111/tpj.12479
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
