Evolution analysis of FRIZZY PANICLE (FZP) orthologs explored the mutations in DNA coding sequences in the grass family (Poaceae)

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Plant Biology

Main article text

 

Introduction

Materials and Methods

Identification of the FZP gene in Poaceae

Analysis of conserved motifs and multiple sequence alignment of the FZP gene in Poaceae species

Phylogenetic analysis of the FZP gene in Poaceae species

Selection pressure analysis of the FZP gene in Poaceae species

Predict the impact of amino acid substitutions or indels on the biological functions of FZP gene protein

Protein 3D structure prediction

Results and Analysis

Identification of the FZP gene in Poaceae species

Analysis of conserved domains of the FZP gene in Poaceae species

Phylogenetic analysis of the FZP gene in Poaceae species

Detection of selection pressure of the FZP gene in Poaceae species

Predict the impact of amino acid substitutions or indels on the biological functions of FZP gene protein

Protein 3D structure prediction

Discussion

Conclusion

Supplemental Information

Multiple sequence alignment of amino acid of FZP orthologs gene in Poaceae

The red and orange frames indicate AP2/ERF domain and acidic domain of FZP orthologs gene. Amino acids residues with asterisks indicate that they confer specific GCC box binding. The amino acid residues with brown, blue, green and red arrows indicate mutation sites that can cause supernumerary spikelets (SSs) phenotype in maize, Brachypodiumdistachyon, bread wheat and rice, respectively. An amino acid substitution is shown at positions 157 (Y157C: Y at position 157 is changed to C) and 183 (L183P: L at position 39 is changed to P) of the QBI22216.1 and QBI22219.1 genes, respectively. The amino acid residues with red triangle, diamond and box indicate significant positive selection sites in a branch of Triticeae, Oryza, and C4 plants, respectively.

DOI: 10.7717/peerj.12880/supp-1

Phylogenetic analysis of the FZP orthologsgene in Poaceae (BI tree)

The numbers above the branches indicate the posterior probability. The branch labels are tagged with gene ID numbers and Latin names of species (inside brackets).

DOI: 10.7717/peerj.12880/supp-2

The parameters of the top 5 final models of the 5 genes predicted by I-TASSER

a The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [ −5, 2], where a C-score of a higher value signifies a model with a higher confidence and vice-versa (https://zhanggroup.org/I-TASSER/). b, c TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. The first model has a better quality in most cases (https://zhanggroup.org/I-TASSER/).

DOI: 10.7717/peerj.12880/supp-3

FZP orthologous gene CDS sequence

DOI: 10.7717/peerj.12880/supp-4

FZP orthologous gene protein sequence

DOI: 10.7717/peerj.12880/supp-5

Phylogenetic tree of FZP orthologous genes in Gramineae (ML tree)

DOI: 10.7717/peerj.12880/supp-6

Phylogenetic tree of FZP orthologous genes in Gramineae (BI tree)

DOI: 10.7717/peerj.12880/supp-7

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Jia Li and Ahmed H. El-Sappah conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Litian Zhang conceived and designed the experiments, prepared figures and/or tables, and approved the final draft.

Rania G. Elbaiomy, Bo Chen and Na Lin analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Lilan Chen, Zhenrong Wang and Jie Jiao performed the experiments, prepared figures and/or tables, and approved the final draft.

Jiliang Zhu and Wanhai Zhou performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Salma A. Soaud and Manzar Abbas analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw data is available in the Supplemental Files.

Funding

Open Access funding was provided by Yibin Science and Technology Plan (Key) Project (No. 2018JY002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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