Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Three Orchids

Abstract

SPL transcription factors regulate important processes such as plant growth and development, metabolic regulation, and abiotic stress. They play crucial roles in the development of flower organs. However, little is known about the characteristics and functions of the SPLs in the Orchidaceae. In this study, Cymbidium goeringii Rchb. f., Dendrobium chrysotoxum Lindl., and Gastrodia elata BI. were used as research objects. The SPL gene family of these orchids was analyzed on a genome-wide scale, and their physicochemical properties, phylogenetic relationships, gene structures, and expression patterns were studied. Transcriptome and qRT-PCR methods were combined to investigate the regulatory effect of SPLs on the development of flower organs during the flowering process (bud, initial bloom, and full bloom). This study identifies a total of 43 SPLs from C. goeringii (16), D. chrysotoxum (17), and G. elata (10) and divides them into eight subfamilies according to the phylogenetic tree. Most SPL proteins contained conserved SBP domains and complex gene structures; half of the genes had introns longer than 10 kb. The largest number and variety of cis-acting elements associated with light reactions were enriched, accounting for about 45% of the total (444/985); 13/43 SPLs contain response elements of miRNA156. GO enrichment analysis showed that the functions of most SPLs were mainly enriched in the development of plant flower organs and stems. In addition, expression patterns and qRT-PCR analysis suggested the involvement of SPL genes in the regulation of flower organ development in orchids. There was little change in the expression of the CgoSPL in C. goeringii, but DchSPL9 and GelSPL2 showed significant expression during the flowering process of D. chrysotoxum and G. elata, respectively. In summary, this paper provides a reference for exploring the regulation of the SPL gene family in orchids.

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

“…CCCH was mutated to CCCC in Zn-1 of SbSPL7/10 (Figure S2 ). The same changes occurred in A. thaliana AtSPL7 and S. italica SiSPL8 (Lai D et al 2022 ) and CgoSPL6 , DchSPL16 , and GelSPL8 of three orchids (Zhao et al 2023 ), indicating that Zn-1 could exist in 2 types (CCCC and CCCH). The Zn-1 of SbSPL2 and the Zn-2 sequence of SbSPL4 were missing (Figure S2 ).…”

Genome-based identification of the CYP75 gene family in Orchidaceae and its expression patterns in Cymbidium goeringii

“…All experiments were conducted in triplicate, with each run consisting of three technical replicates. The relative expression of genes was determined using the 2 -ΔΔCT method ( Wang et al, 2021 ; Zhao et al, 2023 ).…”

Genome-Wide Identification and Expression Analysis of the SQUAMOSA Promoter-Binding Protein-like (SPL) Transcription Factor Family in Catalpa bungei

“…The SPL gene family has been identified in diverse plant species, such as A. thaliana [ 9 , 27 ], rice ( Oryza sativa ) [ 6 ], soybean ( Glycine max ) [ 28 ], maize ( Zea mays ) [ 29 ], tomato ( Solanum lycopersicum L.) [ 30 ], grape ( Vitis vinifera ) [ 31 ], strawberry ( Fragaria vesca ) [ 32 ], poplar ( Populus trichocarpa ) [ 33 ], tea plant ( Camellia sinensis ) [ 34 ], apple ( Malus domestica Borkh.) [ 35 ], Ziziphus jujuba [ 36 ], Fraxinus mandshurica [ 37 ], sweet cherry ( Prunus avium L.) [ 13 ], and orchids [ 38 ]. However, there have been no genome-wide identification or systematic study reports on the SPL gene family in C. bungei .…”