Genome-Wide Identification and Expression Analysis of VviYABs Family Reveal Its Potential Functions in the Developmental Switch and Stresses Response During Grapevine Development

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

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.

Genome-Wide Characterization and Identification of the YABBY Gene Family in Mango (Mangifera indica)

YABBY is a specific transcription factor gene family in plants. It has the typical N-terminal C2C2-type zinc-finger domain and the C-terminal YABBY conservative structure domain, which play an important role in the development of the leaves and floral organs. The YABBY gene family directs leaf polarity in mango, playing an important role in maintaining species specificity. In this study, a total of seven YABBY genes were identified in the mango (Mangifera indica) genome. The seven YABBY family members possessed both typical C2C2 and YABBY domains. A phylogenetic tree was constructed based on the amino acid sequences of the 42 YABBY proteins of mango, Arabidopsis, apple, grape, and peach. The phylogenetic tree indicated that the members of the mango YABBY family could be divided into three subfamilies, including CRC, YAB5, and YAB3. Quantitative real-time PCR showed that the transcription levels of the MiYABBYs were significantly different under biotic and abiotic stresses. The transcription level of MiYABBY7 was significantly down-regulated at 0–72 h after Xanthomonas campestris pv. mangiferaeindicae infection, methyl jasmonate and salicylic acid stresses. The MiYABBY1 transcription level was significantly down-regulated at 0–72 h after Colletotrichum gloeosporioides infection. MiYABBYs were expressed specifically in different leaves and fruit, and MiYABBY6 was significantly up-regulated during leaf and fruit development. However, MiYABBY5 showed a contrary transcriptional pattern during leaf and fruit development. This is first report on the mango YABBY gene family at the genome-wide level. These results will be beneficial for understanding the biological functions and molecular mechanisms of YABBY genes.