Comparative analysis of the Squamosa Promoter Binding-Like (SPL) gene family in Nicotiana benthamiana and Nicotiana tabacum

Identification and Characterization of SQUAMOSA Promoter Binding Protein-like Transcription Factor Family Members in Zanthoxylum bungeanum and Their Expression Profiles in Response to Abiotic Stresses

Plant-specific transcription factors known as SQUAMOSA promoter binding protein-like (SPL) genes are essential for development, growth, and abiotic stress responses. While the SPL gene family has been extensively studied in various plant species, a systematic characterization in Zanthoxylum bungeanum (Zb) is lacking. This study used transcriptomic and bioinformatics data to conduct a thorough genomic identification and expression investigation of the ZbSPL gene family. Eight subfamilies including 73 ZbSPL members were identified, most of which are predicted to be localized in the nucleus. Ka/Ks ratio analysis indicates that most ZbSPL genes have undergone purifying selection. According to evolutionary research, segmental duplication is a major factor in the amplification of the ZbSPL gene family. Gene structures, conserved motifs, and domains were found to be highly conserved among paralogs. Cis-element research revealed that ZbSPLs may be implicated in hormone and abiotic stress responses. Codon usage pattern analysis showed that the ZbSPL gene family was more inclined to A/T base endings; the higher the A/T content, the stronger the preference of the codons; and the use pattern was mainly affected by natural selection. Additionally, 36 ZbSPLs were found to be potential targets of miR156. RNA-seq demonstrated that SPL genes in Zb are differentially expressed in response to distinct abiotic stressors. Two ZbSPL genes (ZbSPL10 and ZbSPL17) were implicated in the response to salt stress, while four ZbSPL genes (ZbSPL06, ZbSPL43, ZbSPL60, and ZbSPL61) showed response to drought stress, based on a qRT-PCR investigation of the ZbSPL genes under various abiotic stress conditions. This study will help us gain a deeper understanding of the functions of ZbSPLs and lay a genetic foundation for future breeding of high-quality, highly abiotic resistant varieties of Z. bungeanum.

Identification and expression analysis of the SPL gene family during flower bud differentiation in Rhododendron molle

BACKGROUND

The family of SQUAMOSA promoter binding protein-like (SPL) transcription factors is essential for regulating plant growth and development. While this SPL gene functional research has been limited in Rhododendron molle (R. molle).

OBJECTIVE

To preliminarily explore the regulatory mechanism of the SPL gene in flower bud development of R. molle.

METHODS

In this study, for R. molle, the flower bud differentiation period was determined by observing the morphological anatomy of the flower bud. The SPL gene family members were identified based on the R. molle genome, Additionally, the expressions of RmSPL genes at five flower bud differentiation stages were analyzed via Quantitative reverse transcription PCR (RT-qPCR).

RESULTS

We first characterized 20 SPL family members in the reference genome of R. molle. The phylogenetic analysis of plant SPL proteins separated them into eight subfamilies (G1-G8) according to conserved gene structures and protein motifs. Cis-elements of promoter region analysis showed that RmSPL genes were regulated by light, phytohormones, stress response, and plant growth and development and may play a critical role in the photoresponse, abasic acid, anaerobic induction, and meristematic expression. Gene expression analysis showed that 18 RmSPL genes were differentially expressed in different developing flower buds. In particular, RmSPL1/7/8/12/13 exhibited significantly different expressions, suggesting that they were likely essential genes for regulating the differentiation of flower buds.

CONCLUSION

In conclusion, our analysis of RmSPL genes provides a theoretical basis and reference for future functional analysis of RmSPL genes in the flower bud differentiation of R. molle.

Engineering Nicotiana benthamiana as a platform for natural product biosynthesis

Nicotiana benthamiana is a model plant, widely used for research. The susceptibility of young plants to Agrobacterium tumefaciens has been utilised for transient gene expression, enabling the production of recombinant proteins at laboratory and commercial scales. More recently, this technique has been used for the rapid prototyping of synthetic genetic circuits and for the elucidation and reconstruction of metabolic pathways. In the last few years, many complex metabolic pathways have been successfully reconstructed in this species. In addition, the availability of improved genomic resources and efficient gene editing tools have enabled the application of sophisticated metabolic engineering approaches to increase the purity and yield of target compounds. In this review, we discuss recent advances in the use of N. benthamiana for understanding and engineering plant metabolism, as well as efforts to improve the utility of this species as a production chassis for natural products.

Harnessing miRNA156: A molecular Toolkit for reshaping plant development and achieving ideal architecture

Achieving ideal plant architecture is of utmost importance for plant improvement to meet the demands of ever-increasing population. The wish list of ideal plant architecture traits varies with respect to its utilization and environmental conditions. Late seed development in woody plants poses difficulties for their propagation, and an increase in regeneration capacity can overcome this problem. The transition of a plant through sequential developmental stages e.g., embryonic, juvenile, and maturity is a well-orchestrated molecular and physiological process. The manipulation in the timing of phase transition to achieve ideal plant traits and regulation of metabolic partitioning will unlock new plant potential. Previous studies demonstrate that micro RNA156 (miR156) impairs the expression of its downstream genes to resist the juvenile-adult-reproductive phase transition to prolonged juvenility. The phenomenon behind prolonged juvenility is the maintenance of stem cell integrity and regeneration is an outcome of re-establishment of the stem cell niche. The previously reported vital and diverse functions of miR156 make it a more important case of study to explore its functions and possible ways to use it in molecular breeding. In this review, we proposed how genetic manipulation of miR156 can be used to reshape plant development phase transition and achieve ideal plant architecture. We have summarized recent studies on miR156 to describe its functional pattern and networking with up and down-stream molecular factors at each stage of the plant developmental life cycle. In addition, we have highlighted unaddressed questions, provided insights and devised molecular pathways that will help researchers to design their future studies.

Genome-wide investigation of SQUAMOSA promoter binding protein-like genes in Liriodendron and functional characterization of LcSPL2

The plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play a pivotal role in various developmental processes, including leaf morphogenesis and vegetative to reproductive phase transition. Liriodendron chinense and Liriodendron tulipifera are widely used in landscaping due to their tulip-like flowers and peculiar leaves. However, the SPL gene family in Liriodendron has not been identified and systematically characterized. We systematically identified and characterized the SPL family members in Liriodendron, including phylogeny, gene structure and syntenic analyses. Subsequently, we quantified the expression patterns of LcSPLs across various tissue sites through transcription-quantitative polymerase chain reaction (RT-qPCR) assays and identified the target gene, LcSPL2. Finally, we characterized the functions of LcSPL2 via ectopic transformation. Altogether, 17 LcSPL and 18 LtSPL genes were genome-widely identified in L. chinense and L. tulipifera, respectively. All the 35 SPLs were grouped into 9 clades. Both species had three SPL gene pairs arising from segmental duplication events, and the LcSPLs displayed high collinearity with the L. tulipifera genome. RT-qPCR assays showed that SPL genes were differentially expressed in different tissues, especially. Because LcSPL2 is highly expressed in pistils and leaves, it was selected to describe the SPL gene family of L. chinense by ectopic expression. We showed that overexpression of LcSPL2 in Arabidopsis thaliana resulted in earlier flowering and fewer rosette leaves. Moreover, we observed that overexpression of LcSPL2 in A. thaliana up-regulated the expression levels of four genes related to flower development. This study identified SPL genes in Liriodendron and characterized the function of LcSPL2 in advancing flower development.