Genome-wide identification and analysis of Lateral Organ Boundaries Domain (LBD) transcription factor gene family in melon (Cucumis melo L.)

Genome-wide identification and functional characterization of LBD gene family in four Cymbidium species (Orchidaceae) and potential regulatory role of CsiLBD27 in floral development of Cymbidium sinense

BACKGROUND

The Lateral Organ Boundaries Domain (LBD) gene family, encompassing plant-specific LOB domain proteins, plays essential roles in various aspects of plant growth and development, and has continuously diversified its functions across numerous species. However, studies on LBD genes in the Orchidaceae family remain limited. To our knowledge, this is the first systematic investigation of the LBD gene family in Cymbidium, a genus that exhibits remarkable species and trait diversity within the Orchidaceae.

RESULTS

In this study, we identified 122 LBD genes within the genomes of four Cymbidium species, distributed on 20 chromosomes. These genes were classified into class I (109 members, including 16 in subclass Ic/d) and class II (13 members), with protein lengths ranging from 94-477 amino acids. Promoter sequences of CymLBD genes revealed various cis-elements significant for light, hormonal, biotic, and abiotic stress responses. Transcriptomic analysis revealed tissue- and stage-specific expression of CymLBD genes in Cymbidium, and RT-qPCR and yeast one-hybrid assays indicated that CsiLBD27 may regulate floral patterning by directly binding to the CsiSEP3 promoter and activating its transcription. Under ABA treatment, the genes CsiLBD13, CsiLBD19, and CsiLBD21 displayed tissue-specific expression changes, suggesting hormone-responsive regulation. In Cymbidium ensifolium, 16 CenLBD genes were differentially expressed, while in Cymbidium mannii, 9 CmaLBD gene expression exist obvious circadian rhythm. GO and KEGG enrichment of 1074 and 399 predicted target genes, respectively, indicating a diverse range of functions for LBDs.

CONCLUSIONS

Collectively, this study provides the first comprehensive insight into the evolutionary dynamics, regulatory mechanisms, and functional roles of LBD genes in Cymbidium. These findings offer a valuable genetic resource for understanding floral and vegetative development in Orchidaceae and uncover potential novel functions of LBD genes.

Identification of the lateral organ boundary domain gene family and its preservation by exogenous salicylic acid in Cerasus humilis

The gene family known as the Lateral Organ Boundary Domain (LBD) is responsible for producing transcription factors unique to plants, which play a crucial role in controlling diverse biological activities, including their growth and development. This research focused on examining Cerasus humilis'ChLBD gene, owing to its significant ecological, economic, and nutritional benefits. Examining the ChLBD gene family's member count, physicochemical characteristics, phylogenetic evolution, gene configuration, and motif revealed 41 ChLBD gene family members spread across 8 chromosomes, with ChLBD gene's full-length coding sequences (CDSs) ranging from 327 to 1737 base pairs, and the protein sequence's length spanning 109 (ChLBD30)-579 (ChLBD35) amino acids. The molecular weights vary from 12.068 (ChLBD30) to 62.748 (ChLBD35) kDa, and the isoelectric points span from 4.74 (ChLBD20) to 9.19 (ChLBD3). Categorizing them into two evolutionary subfamilies: class I with 5 branches, class II with 2, the majority of genes with a single intron, and most members of the same subclade sharing comparable motif structures. The results of collinearity analysis showed that there were 3 pairs of tandem repeat genes and 12 pairs of fragment repeat genes in the Cerasus humilis genome, and in the interspecific collinearity analysis, the number of collinear gene pairs with apples belonging to the same family of Rosaceae was the highest. Examination of cis-acting elements revealed that methyl jasmonate response elements stood out as the most abundant, extensively dispersed in the promoter areas of class 1 and class 2 ChLBD. Genetic transcript analysis revealed that during Cerasus humilis' growth and maturation, ChLBD developed varied control mechanisms, with ChLBD27 and ChLBD40 potentially playing a role in managing color alterations in fruit ripening. In addition, the quality of calcium fruit will be affected by the environment during transportation and storage, and it is particularly important to use appropriate means to preserve the fruit. The research used salicylic acid-treated Cerasus humilis as the research object and employed qRT-PCR to examine the expression of six ChLBD genes throughout storage. Variations in the expression of the ChLBD gene were observed when exposed to salicylic acid, indicating that salicylic acid could influence ChLBD gene expression during the storage of fruits. This study's findings lay the groundwork for additional research into the biological role of the LBD gene in Cerasus humilis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01438-5.