The DOI matches its Crossref record; 94 of the 94 references it cites were found in a registry or an index.
Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants
Open accessAbstract
Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use whole-genome sequences from nine species of land plants and algae to define the relationships between these proteins in plants. We show that few (less than 5) bHLH proteins are encoded in the genomes of chlorophytes and red algae. In contrast, many bHLH proteins (100-170) are encoded in the genomes of land plants (embryophytes). Phylogenetic analyses suggest that plant bHLH proteins are monophyletic and constitute 26 subfamilies. Twenty of these subfamilies existed in the common ancestors of extant mosses and vascular plants, whereas six further subfamilies evolved among the vascular plants. In addition to the conserved bHLH domains, most subfamilies are characterized by the presence of highly conserved short amino acid motifs. We conclude that much of the diversity of plant bHLH proteins was established in early land plants, over 440 million years ago.
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
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
Guindon, S., & Gascuel, O. (2003) · Systematic Biology · doi:10.1080/10635150390235520 · Cited by 16,806
PAUP^* : Phylogenetic Analysis Using Parsimony (and other methods) 4.0b8
Swofford, D. L. (2001) · Cited by 12,789
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey, T. L., & Elkan, C. (1994) · PubMed · Cited by 4,982
ProtTest: selection of best-fit models of protein evolution
Abascal, F., Zardoya, R., & Posada, D. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti263 · Cited by 3,063
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
Murre, C., McCaw, P. S., & Baltimore, D. (1989) · Cell · doi:10.1016/0092-8674(89)90682-x · Cited by 2,635
Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., & Yamaguchi-Shinozaki, K. (2003) · The Plant Cell · doi:10.1105/tpc.006130 · Cited by 2,285
The Genome of the Diatom Thalassiosira Pseudonana : Ecology, Evolution, and Metabolism
Armbrust, E. V., Berges, J. A., Bowler, C., Green, B. R., Martinez, D., Putnam, N. H., Zhou, S., Allen, A. E., Apt, K. E., Bechner, M., et al. (2004) · Science · doi:10.1126/science.1101156 · Cited by 2,010
Cited by
Emms, D. M., & Kelly, S. (2015) · Genome Biology · doi:10.1186/s13059-015-0721-2 · Cited by 3,408
Kazan, K., & Manners, J. M. (2013) · Molecular Plant · doi:10.1093/mp/sss128 · Cited by 1,081
Recent advances on the regulation of anthocyanin synthesis in reproductive organs
Petroni, K., & Tonelli, C. (2011) · Plant Science · doi:10.1016/j.plantsci.2011.05.009 · Cited by 935
Fruit Development and Ripening
Seymour, G. B., Østergaard, L., Chapman, N. H., Knapp, S., & Martin, C. (2013) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-050312-120057 · Cited by 658
Mechanisms of Stomatal Development
Pillitteri, L. J., & Torii, K. U. (2012) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042811-105451 · Cited by 389
Metadata
- Authors
- Pires, N., & Dolan, L.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-11-25
- Volume
- 27
- Issue
- 4
- Pages
- 862-874
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2119078782
- Cited by
- 640
- References
- 94
- FWCI
- 18.14
- Type
- journal article
- Language
- en
- Open access
- hybrid
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: Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants. https://app.cochat.ai/papers/10.1093/molbev/msp288
- The paper
- Pires, N., & Dolan, L. (2010). Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msp288
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.
