Abstract
The Dof (DNA binding with one finger) genes encode a family of plant-specific transcription factors and play critical roles in numerous biological processes in plants. Piper nigrum L. (black pepper) is a popular spice crop with high economic value. Phytophthora capsici infection has become a key problem in P. nigrum industry, but the molecular studies about P. capsici have been rarely performed. This study aimed to conduct a genome-wide identification and characterization of the Dof gene family in P. nigrum, and provide some candidates differentially expressed genes under P. capsica infection. A total of 46 Dof genes were identified in the P. nigrum genome, and these genes were unevenly distributed on 20 chromosomes. Afterward, a phylogenetic tree was constructed by the N-J (neighbor-joining) method, and seven groups (not including one group that was not present in P. nigrum but present in Arabidopsis thaliana (L.) Heynh.) were obtained. The Dof genes in the same group had similar gene and protein structures. Selection pressure analysis indicated that duplicated genes underwent purification selection during evolution. Tissue expression analysis showed that P. nigrum Dof genes had significant tissue-specific expression characteristics, and they also expressed significantly different among different groups. In addition, according to the RNA-seq sequence data of Dof genes under the infection of P. capsici, a large number of Dof genes were found with differential expression profiles, and several genes with high response to P. capsici were screened out. This study revealed evolutionary and functional characteristics of P. nigrum Dof genes, and provided important references for the follow-up study of Dof genes in response to the biological stress of P. capsici.
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Abbreviations
- A. thaliana :
-
Arabidopsis thaliana
- CDF3 :
-
Cycling DOF factor 3
- HMM:
-
Hidden Markov Model
- MW:
-
Molecular Weight
- N-J:
-
Neighbor-joining
- P. capsici :
-
Phytophthora capsici
- PI:
-
Isoelectric point
- P. nigrum :
-
Piper nigrum
- TAIR:
-
The Arabidopsis Information Resource
- TDDF1 :
-
Tomato Dof Daily Fluctuations 1
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Acknowledgments
We are very grateful to the spice and Beverage Research Institute of Chinese Academy of Tropical Agricultural Sciences for the technical support, and to all the members of our laboratory.
Funding
This research was founded by the Innovation Platform for Academicians of Hainan Province (No. YSPTZX202154), and China Agriculture Research System of MOF and MARA (NO. CARS-11). We would to thank all authors contributing to this manuscript.
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J.L. conceived and supervised this study. J.L., and F.Z. designed the experiments. F.Z. carried out the experiments. F.Z. analyzed and interpreted the data. D.Y. and F.Z. conduct data collation and chart modification. J.L., R.F., L.Y., L.H., and F.S. participated in the discussion and provided valuable advice and practical contributions. J.L. and F.Z. wrote the manuscript. All authors reviewed, edited, and approved the final manuscript. All authors have read and agreed to the published version of the manuscript.
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Zhang, F., Fan, R., Yan, L. et al. Genome-wide identification of black pepper (Piper nigrum L.) Dof gene family and the differential gene screening in resistance to Phytophthora capsici. Biologia 78, 655–666 (2023). https://doi.org/10.1007/s11756-022-01232-2
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DOI: https://doi.org/10.1007/s11756-022-01232-2