Genome-Wide Identification of YABBY Genes in Orchidaceae and Their Expression Patterns in Phalaenopsis Orchid.

You-Yi Chen,Song-Bin Chang,Si-Ren Lan,Zhong-Jian Liu,Wen-Chieh Tsai,Diyang Zhang,Yu-Yun Hsiao

doi:10.3390/genes11090955

Abstract

The plant YABBY transcription factors are key regulators in the lamina development of lateral organs. Orchid is one of the largest families in angiosperm and known for their unique floral morphology, reproductive biology, and diversified lifestyles. However, nothing is known about the role of YABBY genes in orchids, although biologists have never lost their fascination with orchids. In this study, a total of 54 YABBY genes, including 15 genes in CRC/DL, eight in INO, 17 in YAB2, and 14 in FIL clade, were identified from the eight orchid species. A sequence analysis showed that all protein sequences encoded by these YABBY genes share the highly conserved C2C2 zinc-finger domain and YABBY domain (a helix-loop-helix motif). A gene structure analysis showed that the number of exons is highly conserved in the same clades. The genes in YAB2 clade have six exons, and genes in CRC/DL, INO, and FIL have six or seven exons. A phylogenetic analysis showed all 54 orchid YABBY genes could be classified into four major clades, including CRC/DL, INO, FIL, and YAB2. Many of orchid species maintain more than one member in CRC/DL, FIL, and YAB2 clades, implying functional differentiation among these genes, which is supported by sequence diversification and differential expression. An expression analysis of Phalaenopsis YABBY genes revealed that members in the CRC/DL clade have concentrated expressions in the early floral development stage and gynostemium, the fused male and female reproductive organs. The expression of PeINO is consistent with the biological role it played in ovule integument morphogenesis. Transcripts of members in the FIL clade could be obviously detected at the early developmental stage of the flowers. The expression of three genes, PeYAB2, PeYAB3, and PeYAB4, in the YAB2 clade could be revealed both in vegetative and reproductive tissues, and PeYAB4 was transcribed at a relatively higher level than that of PeYAB2 and PeYAB3. Together, this comprehensive analysis provides the basic information for understanding the function of the YABBY gene in Orchidaceae.

Highlights

The small plant-specific YABBY gene family, belonging in the subfamily of the zinc-finger superfamily, plays important roles in the development of lateral organs [1], establishment of adaxial–abaxial polarity [2], leaf margin establishment [3], and stress response [4]
Seven and six YABBY genes could be identified from P. zijinensis and P. guangdongensis, respectively
We found that the orchids YABBY genes in the CRABS CLAW (CRC)/DL, INNER NOOUTER (INO), YAB2, and FIL clades have six to seven exons (Table 1)

Summary

Introduction

The small plant-specific YABBY gene family, belonging in the subfamily of the zinc-finger superfamily, plays important roles in the development of lateral organs [1], establishment of adaxial–abaxial polarity [2], leaf margin establishment [3], and stress response [4]. The genome of Arabidopsis thaliana encodes for six YABBY members (FIL, CRC, INO, YAB2, YAB3, and YAB5), and Orzya sativa has eight. Among the members of YABBY gene family, functional and expression characterizations suggest that CRC plays as a carpel development regulator across angiosperms [10,11] and nectaries in the core eudicots [12]. Vegetative YABBY genes show functional redundancy during leaf development in Arabidopsis [18], as well as in other core eudicots [5] and monocots [19]. Various expression patterns could be observed in vegetative YABBY genes among monocot species

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