Genome-Wide Identification of the YABBY Gene Family in Dendrobium Orchids and Its Expression Patterns in Dendrobium chrysotoxum

Qinyao Zheng; Xuewei Zhao; Ye Huang; Meng-Meng Zhang; Xin He; Shijie Ke; Yuanyuan Li; Cuili Zhang; Sagheer Ahmad; Siren Lan; Minghe Li; Zhong-Jian Liu

doi:10.3390/ijms241210165

Genome-Wide Identification of the YABBY Gene Family in Dendrobium Orchids and Its Expression Patterns in Dendrobium chrysotoxum

Int J Mol Sci. 2023 Jun 15;24(12):10165. doi: 10.3390/ijms241210165.

Authors

Qinyao Zheng¹, Xuewei Zhao², Ye Huang¹, Meng-Meng Zhang², Xin He², Shijie Ke², Yuanyuan Li¹, Cuili Zhang¹, Sagheer Ahmad¹, Siren Lan¹, Minghe Li¹, Zhong-Jian Liu^{1

2}

Affiliations

¹ Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
² College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Abstract

The small plant-specific YABBY gene family plays key roles in diverse developmental processes in plants. Dendrobium chrysotoxum, D. huoshanense, and D. nobile are perennial herbaceous plants belonging to Orchidaceae with a high ornamental value. However, the relationships and specific functions of the YABBY genes in the Dendrobium species remain unknown. In this study, six DchYABBYs, nine DhuYABBYs, and nine DnoYABBYs were identified from the genome databases of the three Dendrobium species, which were unevenly distributed on five, eight, and nine chromosomes, respectively. The 24 YABBY genes were classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3) based on their phylogenetic analysis. A sequence analysis showed that most of the YABBY proteins contained conserved C2C2 zinc-finger and YABBY domains, while a gene structure analysis revealed that 46% of the total YABBY genes contained seven exons and six introns. All the YABBY genes harbored a large number of Methyl Jasmonate responsive elements, as well as anaerobic induction cis-acting elements in the promoter regions. Through a collinearity analysis, one, two, and two segmental duplicated gene pairs were identified in the D. chrysotoxum, D. huoshanense, and D. nobile genomes, respectively. The Ka/Ks values of these five gene pairs were lower than 0.5, indicating that the Dendrobium YABBY genes underwent negative selection. In addition, an expression analysis revealed that DchYABBY2 plays a role in ovary and early-stage petal development, while DchYABBY5 is essential for lip development and DchYABBY6 is crucial for early sepal formation. DchYABBY1 primarily regulates sepals during blooming. Furthermore, there is the potential involvement of DchYABBY2 and DchYABBY5 in gynostemium development. The results of a comprehensive genome-wide study would provide significant clues for future functional investigations and pattern analyses of YABBY genes in different flower parts during flower development in the Dendrobium species.

Keywords: D. chrysotoxum; D. huoshanense; D. nobile; Dendrobium orchid; YABBY transcription factor; expression pattern.

MeSH terms

Dendrobium* / genetics
Dendrobium* / metabolism
Flowers / metabolism
Gene Expression Regulation, Plant
Genome-Wide Association Study
Phylogeny
Plant Proteins / metabolism

Substances

Plant Proteins

Grants and funding

This work was supported by the National Natural Science Foundation of China (KAy22014XA) and the Forestry Peak Discipline Construction Project of Fujian Agriculture and Forestry University (72202200205).