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

Abstract

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 Identification of the ARF Gene Family in Three Dendrobium Species and Its Expression Pattern Analysis in D. nobile Flower

“…To determine the chromosomal localization information of the ARF genes, the genome files (fasta files) and annotation files (gff files) for D. nobile, D. huoshanense, and D. chrysotoxum were subjected to TBtools. Comparative genome data analyses were then performed between the three species for collinearity assessment using One Step MCScanx [18]. The collinearity results were visualized using TBtools with Dual Synteny Plot for MCscanX [21].…”

“…These species include A. thaliana (23), Ap. shenzhenica (17), P. equestris (16), P. aphrodite (18), D. catenatum (21), as well as D. nobile, D. huoshanense, and D. chrysotoxum (Figure 1). Notably, members of the ARF genes family in D. chrysotoxum, D. huoshanense, and D. nobile were identified for the first time in this study.…”

“…Dendrobium, the second-largest genus of Orchidaceae, is notable for its aesthetic and medicinal value [18]. Flowers exhibit a rich array of colors, including yellow, white, and purple.…”

Genome-Wide Identification of the PEBP Family Gene in Three Cymbidium Species and Its Expression Patterns Analysis in C. ensifolium

“…The PEBP genes were named and classified according to the naming rules of A. thaliana. Finally, the ExPASy website (https://www.expasy.org/, accessed on 20 August 2023) was used to calculate the amino acid (aa), isoelectric point (pI), molecular weight (MW), grand average hydrophilicity (GRAVY), instability index (II), and lipid index (AI) of the PEBP proteins [32,33].…”

“…Based on the Taq Pro Universal SYBR qPCR Master Mix kit (Vazyme, Nanjing, China), the ABI 7500 Real-Time System (Applied Biosystems, Foster City, CA, USA) was used to analyze the RT-qPCR. Finally, the 2 −∆∆CT method was used to calculate the expression level [26,33,38].…”