Genome-wide identification and expression characterization of the DoG gene family of moso bamboo (Phyllostachys edulis)

Genome-wide identification and expression analysis of the WRKY transcription factors related to sesquiterpenes biosynthesis in Atractylodes lancea

Introduction

Atractylodes lancea (Thunb.) DC., a widely utilized herb in traditional Chinese medicine, contains sesquiterpenoids and polyacetylenes as its primary bioactive components. The WRKY gene family plays a critical role in regulating various biological processes in plants. However, the molecular mechanism underlying AlWRKY regulation of terpenoid synthesis unclear.

Methods

The AlWRKY gene family members were identified through bioinformatics approaches. Gene structures, motifs, and phylogenetic relationships were analyzed. Subsequently, their expression profiles across different geographical origins were investigated using transcriptome data. Furthermore, preliminary validation was performed via methyl jasmonate treatment and molecular docking, with a focus on the AlWRKY20 and AlWRKY37 genes.

Results

In this study, 65 AlWRKY genes with conserved domains were identified in A. lancea and classified into three groups: Group I (17 members), Group II (33 members), and Group III (15 members). Tissue-specific expression profiling revealed five rhizome-enriched AlWRKY genes (AlWRKY13, AlWRKY20, AlWRKY21, AlWRKY37, and AlWRKY49) were highly expressed in Hubei accessions compared to Jiangsu accessions, and co-expression analysis demonstrated their strong correlation with 16 AlTPS genes. Quantitative PCR (qPCR) validation confirmed the specific upregulation of AlWRKY20, AlWRKY21, AlWRKY37, and AlWRKY49 in Hubei rhizomes, consistent with the accumulation patterns of sesquiterpenes (hinesol, γ-eudesmol, and elemol). Methyl jasmonate (MeJA) induction experiments (12 h) revealed coordinated upregulation of AlWRKY20, AlWRKY37, AlTPS70, AlTPS71, concomitant with significantly increased cis-β-farnesene and α-curcumene content. Molecular docking analysis revealed strong binding affinities of AlWRKY20 to the AlTPS70/AlTPS71 promoter and of AlWRKY37 to the AlTPS70 promoter. Subcellular localization analysis demonstrated that both AlWRKY20 and AlWRKY37 are localized in the nucleus. These results suggest that AlWRKY20 and AlWRKY37 likely function as regulators of sesquiterpene biosynthesis, positively regulating cis-β-farnesene and α-curcumene production through AlTPS gene modulation.

Discussion

This study lays the groundwork for further exploration of the molecular mechanisms and functional validation of WRKY transcription factors in A. lancea.

Evolutionary and functional analysis of the DIR gene family in Moso bamboo: insights into rapid shoot growth and stress responses

Dirigent (DIR) proteins are key regulators of lignin and lignan biosynthesis and play critical roles in plant hormone responses, abiotic stress tolerance, and growth and development. This study identified and characterized 47 PeDIR genes in Moso bamboo, classifying them into three groups. Phylogenetic and comparative analyses revealed strong evolutionary conservation, with the Moso bamboo PeDIR genes being most closely related to those in rice and maize. DIR proteins within each subfamily exhibited high conservation in motif composition, domain structure, and 3D configuration. Subcellular localization and protein interaction studies further elucidated PeDIR gene functions. Specifically, PeDIR02 primarily localized to the cell membrane and was shown to be unable to form homodimers in yeast two-hybrid (Y2H) assays. Transcriptome and expression analyses revealed the involvement of PeDIR genes in rapid shoot growth, indicating roles in lignin biosynthesis and cell wall modification. Transcriptome and qRT-PCR data also demonstrated the responsiveness of these genes to hormones and abiotic stresses, such as drought and salinity. This study constructed the first comprehensive regulatory network between transcription factors (TFs) and PeDIR genes, identifying ERF, DOF, and MYB TFs as key synergistic regulators of PeDIR gene expression.

Analysis of the CHS Gene Family Reveals Its Functional Responses to Hormones, Salinity, and Drought Stress in Moso Bamboo (Phyllostachys edulis)

Chalcone synthase (CHS), the first key structural enzyme in the flavonoid biosynthesis pathway, plays a crucial role in regulating plant responses to abiotic stresses and hormone signaling. However, its molecular functions remain largely unknown in Phyllostachys edulis, which is one of the most economically and ecologically important bamboo species and the most widely distributed one in China. This study identified 17 CHS genes in Phyllostachys edulis and classified them into seven subgroups, showing a closer evolutionary relationship to CHS genes from rice. Further analysis of PeCHS genes across nine scaffolds revealed that most expansion occurred through tandem duplications. Collinearity analysis indicated strong evolutionary conservation among CHS genes. Motif and gene structure analyses confirmed high structural similarity, suggesting shared functional characteristics. Additionally, cis-acting element analysis demonstrated that PeCHS genes are involved in hormonal regulation and abiotic stress responses. RNA-Seq expression profiles in different bamboo shoot tissues and heights, under various hormone treatments (gibberellin (GA), naphthaleneacetic acid (NAA), abscisic acid (ABA), and salicylic acid (SA)), as well as salinity and drought stress, revealed diverse response patterns among PeCHS genes, with significant differential expression, particularly under hormone treatments. Notably, PeCHS14 consistently maintained high expression levels, suggesting its key role in stress response mechanisms. qRT-PCR analysis further validated the expression differences in five PeCHS genes under GA and ABA treatments. Subcellular localization analysis demonstrated that PeCHS14 and PeCHS15 proteins are localized in the nucleus. This study provides a foundation for investigating the potential functions of PeCHS genes and identifies candidate genes for future research on the responses of Phyllostachys edulis to abiotic stresses and hormone signaling.

Genome-wide analysis of the KNOX gene family in Moso bamboo: insights into their role in promoting the rapid shoot growth

BACKGROUND

KNOTTED1-like homeobox (KNOX) genes, plant-specific homologous box transcription factors (TFs), play a central role in regulating plant growth, development, organ formation, and response to biotic and abiotic stresses. However, a comprehensive genome-wide identification of the KNOX genes in Moso bamboo (Phyllostachys edulis), the fastest growing plant, has not yet been conducted, and the specific biological functions of this family remain unknown.

RESULTS

The expression profiles of 24 KNOX genes, divided into two subfamilies, were determined by integrating Moso bamboo genome and its transcriptional data. The KNOX gene promoters were found to contain several light and stress-related cis-acting elements. Synteny analysis revealed stronger similarity with rice KNOX genes than with Arabidopsis KNOX genes. Additionally, several conserved structural domains and motifs were identified in the KNOX proteins. The expansion of the KNOX gene family was primarily regulated by tandem duplications. Furthermore, the KNOX genes were responsive to naphthaleneacetic acid (NAA) and gibberellin (GA) hormones, exhibiting distinct temporal expression patterns in four different organs of Moso bamboo. Short Time-series Expression Miner (STEM) analysis and quantitative real-time PCR (qRT-PCR) assays demonstrated that PeKNOX genes may play a role in promoting rapid shoot growth. Additionally, Gene Ontology (GO) and Protein-Protein Interaction (PPI) network enrichment analyses revealed several functional annotations for PeKNOXs. By regulating downstream target genes, PeKNOXs are involved in the synthesis of AUX /IAA, ultimately affecting cell division and elongation.

CONCLUSIONS

In the present study, we identified and characterized a total of 24 KNOX genes in Moso bamboo and investigated their physiological properties and conserved structural domains. To understand their functional roles, we conducted an analysis of gene expression profiles using STEM and RNA-seq data. This analysis successfully revealed regulatory networks of the KNOX genes, involving both upstream and downstream genes. Furthermore, the KNOX genes are involved in the AUX/IAA metabolic pathway, which accelerates shoot growth by influencing downstream target genes. These results provide a theoretical foundation for studying the molecular mechanisms underlying the rapid growth and establish the groundwork for future research into the functions and transcriptional regulatory networks of the KNOX gene family.

Unraveling the Guardians of Growth: A Comprehensive Analysis of the Aux/IAA and ARF Gene Families in Populus simonii

The auxin/indole-3-acetic acid (Aux/IAA) and auxin response factor (ARF) genes are two crucial gene families in the plant auxin signaling pathway. Nonetheless, there is limited knowledge regarding the Aux/IAA and ARF gene families in Populus simonii. In this study, we first identified 33 putative PsIAAs and 35 PsARFs in the Populus simonii genome. Analysis of chromosomal location showed that the PsIAAs and PsARFs were distributed unevenly across 17 chromosomes, with the greatest abundance observed on chromosomes 2. Furthermore, based on the homology of PsIAAs and PsARFs, two phylogenetic trees were constructed, classifying 33 PsIAAs and 35 PsARFs into three subgroups each. Five pairs of PsIAA genes were identified as the outcome of tandem duplication, but no tandem repeat gene pairs were found in the PsARF family. The expression profiling of PsIAAs and PsARFs revealed that several genes exhibited upregulation in different tissues and under various stress conditions, indicating their potential key roles in plant development and stress responses. The variance in expression patterns of specific PsIAAs and PsARFs was corroborated through RT-qPCR analysis. Most importantly, we instituted that the PsIAA7 gene, functioning as a central hub, exhibits interactions with numerous Aux/IAA and ARF proteins. Furthermore, subcellular localization findings indicate that PsIAA7 functions as a protein localized within the nucleus. To conclude, the in-depth analysis provided in this study will contribute significantly to advancing our knowledge of the roles played by PsIAA and PsARF families in both the development of P. simonii tissue and its responses to stress. The insights gained will serve as a valuable asset for further inquiries into the biological functions of these gene families.