Genome-Wide Identification of <i>YABBY</i> Genes in Orchidaceae and Their Expression Patterns in <i>Phalaenopsis</i> Orchid

• Main Authors: You-Yi Chen, Yu-Yun Hsiao, Song-Bin Chang, Diyang Zhang, Si-Ren Lan, Zhong-Jian Liu, Wen-Chieh Tsai
• Format: Article
• Language: English
• Published: MDPI AG 2020-08-01
• Series: Genes
• Subjects: Orchidaceae; <i>Phalaenopsis equestris</i>; <i>YABBY</i> gene; genome-wide; expression pattern
• Online Access: https://www.mdpi.com/2073-4425/11/9/955

The plant <i>YABBY</i> 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 <i>YABBY</i> genes in orchids, although biologists have never lost their fascination with orchids. In this study, a total of 54 <i>YABBY</i> 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 <i>YABBY</i> 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 <i>Phalaenopsis</i><i>YABBY</i> 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 <i>PeINO</i> 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, <i>PeYAB2,</i><i>PeYAB3</i>, and <i>PeYAB4</i>, in the YAB2 clade could be revealed both in vegetative and reproductive tissues, and <i>PeYAB4</i> was transcribed at a relatively higher level than that of <i>PeYAB2</i> and <i>PeYAB3</i>. Together, this comprehensive analysis provides the basic information for understanding the function of the <i>YABBY</i> gene in Orchidaceae.