Genome-scale identification of plant defensin (PDF) family genes and molecular characterization of their responses to diverse nutrient stresses in allotetraploid rapeseed

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Plant Biology

Main article text

 

Introduction

Materials and Methods

Retrieval of gene sequences

Gene nomenclature

Physical mapping and family expansion analysis

Sequence alignment and phylogeny analysis

Analysis of evolutionary selection pressure and divergence of BnaPDFs

Molecular characterization of BnaPDFs

Conserved motif identification of BnaPDFs

Elucidation of gene structure and promoter regulatory cis-elements

Growth conditions

Reverse transcription quantitative PCR assays

Statistical data analysis

Results

Genome-wide identification of PDFs in Brassica species

Genomic distribution and expansion patterns of BnaPDFs

Phylogeny analysis of BnaPDFs

Molecular characterization of BnaPDFs

Identification of evolutionary selection pressure on BnaPDFs

Conserved domain, gene structure, protein interaction and transcriptional regulatory analysis

Transcriptional analysis of BnaPDFs under diverse nutrient stresses

Discussion

Comprehensive analysis of molecular characteristics of BnaPDFs

Potential involvement of BnaPDFs in rapeseed responses to diverse nutrient stresses

Conclusion

Supplemental Information

miRNA targeting the BnPDF genes; phosphorylation sites of the plant defensin (PDF) proteins in Arabidopsis thaliana and Brassica napus.

DOI: 10.7717/peerj.12007/supp-1

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Ying Liu performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Ying-peng Hua conceived and designed the experiments, analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Huan Chen analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Ting Zhou analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Cai-peng Yue analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Jin-yong Huang conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

Raw measurements are available in the Supplemental Files.

Funding

This study was financially supported by the National Natural Science Foundation of China (31801923), Major Collaborative Innovation Project of Zhengzhou City (Key Discipline Construction Project of Zhengzhou University) (NO. xkzdjc201905), and the Youth Innovation Project of Key discipline of Zhengzhou University (NO. XKZDQN202002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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