Genome-wide identification of YABBY genes in three Cymbidium species and expression patterns in C. ensifolium (Orchidaceae)

Qian-Qian Wang; Yuan-Yuan Li; Jiating Chen; Meng-Jia Zhu; Xuedie Liu; Zhuang Zhou; Diyang Zhang; Zhong-Jian Liu; Siren Lan

doi:10.3389/fpls.2022.995734

Genome-wide identification of YABBY genes in three Cymbidium species and expression patterns in C. ensifolium (Orchidaceae)

Front Plant Sci. 2022 Nov 24:13:995734. doi: 10.3389/fpls.2022.995734. eCollection 2022.

Authors

Qian-Qian Wang¹, Yuan-Yuan Li¹, Jiating Chen¹, Meng-Jia Zhu², Xuedie Liu¹, Zhuang Zhou^{1

3}, Diyang Zhang¹, Zhong-Jian Liu^{1

2

3}, Siren Lan^{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, China.
² College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
³ Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China.

Abstract

Members of the YABBY gene family play significant roles in lamina development in cotyledons, floral organs, and other lateral organs. The Orchidaceae family is one of the largest angiosperm groups. Some YABBYs have been reported in Orchidaceae. However, the function of YABBY genes in Cymbidium is currently unknown. In this study, 24 YABBY genes were identified in Cymbidium ensifolium, C. goeringii, and C. sinense. We analyzed the conserved domains and motifs, the phylogenetic relationships, chromosome distribution, collinear correlation, and cis-elements of these three species. We also analyzed expression patterns of C. ensifolium and C. goeringii. Phylogenetic relationships analysis indicated that 24 YABBY genes were clustered in four groups, INO, CRC/DL, YAB2, and YAB3/FIL. For most YABBY genes, the zinc finger domain was located near the N-terminus and the helix-loop-helix domain (YABBY domain) near the C-terminus. Chromosomal location analysis results suggested that only C. goeringii YABBY has tandem repeat genes. Almost all the YABBY genes displayed corresponding one-to-one relationships in the syntenic relationships analysis. Cis-elements analysis indicated that most elements were clustered in light-responsive elements, followed by MeJA-responsive elements. Expression patterns showed that YAB2 genes have high expression in floral organs. RT-qPCR analysis showed high expression of CeYAB3 in lip, petal, and in the gynostemium. CeCRC and CeYAB2.2 were highly expressed in gynostemium. These findings provide valuable information of YABBY genes in Cymbidium species and the function in Orchidaceae.

Keywords: Cymbidium; Orchidaceae; YABBY genes; expression pattern; genome-wide.