Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)

Ruifang Ma; Bin Huang; Zhinuo Huang; Zhijun Zhang

doi:10.7717/peerj.11780

Genome-wide identification and analysis of the YABBY gene family in Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz)

PeerJ. 2021 Jul 22:9:e11780. doi: 10.7717/peerj.11780. eCollection 2021.

Authors

Ruifang Ma^{1

2}, Bin Huang^{1

2}, Zhinuo Huang^{1

2}, Zhijun Zhang^{1

2}

Affiliations

¹ State Key Laboratory of Subtropical Forest Cultivation, Zhejiang A&F University, Hangzhou, Lin'an, China.
² School of Forestry and Biotechnology, ZhejiangA&F University, Zhejiang, Lin'an, China.

Abstract

Background: The YABBY gene family is a family of small zinc finger transcription factors associated with plant morphogenesis, growth, and development. In particular, it is closely related to the development of polarity in the lateral organs of plants. Despite being studied extensively in many plant species, there is little information on genome-wide characterization of this gene family in Moso bamboo.

Methods: In the present study, we identified 16 PeYABBY genes, which were unequally distributed on 11 chromosomes, through genome-wide analysis of high-quality genome sequences of M oso bamboo by bioinformatics tools and biotechnological tools. Gene expression under hormone stress conditions was verified by quantitative real-time PCR (qRT-PCR) experiments.

Results: Based on peptide sequences and similarity of exon-intron structures, we classified the PeYABBY genes into four subfamilies. Analysis of putative cis-acting elements in promoters of these genes revealed that PeYABBYs contained a large number of hormone-responsive and stress-responsive elements. Expression analysis showed that they were expressed at a high level in Moso bamboo panicles, rhizomes, and leaves. Expression patterns of putative PeYABBY genes in different organs and hormone-treated were analyzed using RNA-seq data, results showed that some PeYABBY genes were responsive to gibberellin (GA) and abscisic acid (ABA), indicating that they may play an important role in plant hormone responses. Gene Ontology (GO) analyses of YABBY proteins indicated that they may be involved in many developmental processes, particularly high level of enrichment seen in plant leaf development. In summary, our results provide a comprehensive genome-wide study of the YABBY gene family in bamboos, which could be useful for further detailed studies of the function and evolution of the YABBY genes, and to provide a fundamental basis for the study of YABBY in Gramineae for resistance to stress and hormonal stress.

Keywords: Expression analysis; Gene family; Phyllostachys edulis; Phylogenetic analysis; Genome-wide analysis.

Grants and funding

The work was funded by the National Natural Science Foundation of China (NNSFC, Project grant: 31770721). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.