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

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.

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

“…In this study, six DchYABBYs, nine DhuYABBYs, and nine DnoYABBYs were identified from the three Dendrobium species genomes. On the basis of previous research on YABBY genes in orchids, the number of YABBY genes in Dendrobium orchids is similar to other orchid species, such as Cymbidium ensifolium (7), Cymbidium goeringii (9), Cymbidium sinense (8), Dendrobium catenatum (8), Gastrodia elata (5), Apostasiashenzenica (6), Phalaenopsis equestris (8), Platanthera zijinensis (7), Platanthera guangdongensis (6), Vanilla shenzhenica (7), and Vanilla pompona (7) [27,28]. However, the number of YABBY genes in Zea mays (13) [29], Gossypium arboreum (12), Gossypium raimondii (12), Gossypium hirsutum (23) [14], and Triticum aestivum (20) [30] is more than that in the Dendrobium species, which demonstrates that genome size, chromosome number, and gene duplication are responsible for the differences.…”

“…The results show a total of 43 orchid YABBY genes are classified into four subfamilies (CRC/DL, INO, YAB2, and FIL/YAB3), and no orchid YABBY gene was found in the YAB5 subfamily. For further confirmation, we combined the classification of other orchid YABBY genes, including V. shenzhenica , V. pompona , C. ensifolium , C.goeringii , and C.sinense [ 27 , 28 ], and found that none of these YABBY genes belonged to the YAB5 clade. Moreover, the results are consistent with some other monocot species.…”