Genome-Wide Identification and Expression Analysis of the PHD Finger Gene Family in Pea (Pisum sativum)

Mingli Liu; Wenju Li; Xiaoling Zheng; Zhuo Yuan; Yueqiong Zhou; Jing Yang; Yawen Mao; Dongfa Wang; Qing Wu; Yexin He; Liangliang He; Dan Zong; Jianghua Chen

doi:10.3390/plants13111489

Genome-Wide Identification and Expression Analysis of the PHD Finger Gene Family in Pea (Pisum sativum)

Plants (Basel). 2024 May 28;13(11):1489. doi: 10.3390/plants13111489.

Authors

Mingli Liu^{1

2}, Wenju Li^{1

2}, Xiaoling Zheng^{2

3}, Zhuo Yuan^{2

3}, Yueqiong Zhou^{2

3}, Jing Yang^{2

4}, Yawen Mao^{2

3}, Dongfa Wang^{2

5}, Qing Wu^{2

3}, Yexin He², Liangliang He^{2

3}, Dan Zong¹, Jianghua Chen^{2

3}

Affiliations

¹ School of Life Sciences, Southwest Forestry University, Kunming 650224, China.
² CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence for Molecular Plant Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China.
³ University of Chinese Academy of Sciences, Beijing 100049, China.
⁴ School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China.
⁵ School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.

Abstract

The plant homeodomain finger (PHD finger) protein, a type of zinc finger protein extensively distributed in eukaryotes, plays diverse roles in regulating plant growth and development. While PHD finger proteins have been identified in various species, their functions remain largely unexplored in pea (Pisum sativum). In this study, we identified 84 members of the PHD finger gene family in pea, which displayed an uneven distribution across seven chromosomes. Through a comprehensive analysis using data from Arabidopsis thaliana and Medicago truncatula, we categorized the PHD finger proteins into 20 subfamilies via phylogenetic tree analysis. Each subfamily exhibited distinct variations in terms of quantity, genetic structure, conserved domains, and physical and chemical properties. Collinearity analysis revealed conserved evolutionary relationships among the PHD finger genes across the three different species. Furthermore, we identified the conserved and important roles of the subfamily M members in anther development. RT-qPCR and in situ hybridization revealed high expression of the pea subfamily M members PsPHD11 and PsPHD16 in microspores and the tapetum layer. In conclusion, this analysis of the PHD finger family in pea provides valuable guidance for future research on the biological roles of PHD finger proteins in pea and other leguminous plants.

Keywords: PHD finger; Pisum sativum; anther development; gene family.

Grants and funding

This research was funded by the National Natural Science Foundation of China grants (32170839, 32200290, 32170360, U2102222, and 32070204), and the China Postdoctoral ScieChina Postdoctoral Science Foundation (2022M713344).