Brachypodium distachyon is emerging as a widely recognized model plant that has very close relations with several economically important Poaceae species. MAPK cascade is known to be an evolutionarily conserved signaling module involved in multiple stresses. Although the gene sequences of MAPK and MAPKK family have been fully identified in B. distachyon, the information related to the upstream MAPKKK gene family especially the regulatory network among MAPKs, MAPKKs and MAPKKKs upon multiple stresses remains to be understood. In this study, we have identified MAPKKKs which belong to the biggest gene family of MAPK cascade kinases. We have systematically investigated the evolution of whole MAPK cascade kinase gene family in terms of gene structures, protein structural organization, chromosomal localization, orthologs construction and gene duplication analysis. Our results showed that most BdMAPK cascade kinases were located at the low-CpG-density region, and the clustered members in each group shared similar structures of the genes and proteins. Synteny analysis showed that 62 or 21 pairs of duplicated orthologs were present between B. distachyon and Oryza sativa, or between B. distachyon and Arabidopsis thaliana respectively. Gene expression data revealed that BdMAPK cascade kinases were rapidly regulated by stresses and phytohormones. Importantly, we have constructed a regulation network based on co-expression patterns of the expression profiles upon multiple stresses performed in this study. BdMAPK cascade kinases were involved in the signaling pathways of multiple stresses in B. distachyon. The network of co-expression regulation showed the most of duplicated BdMAPK cascade kinase gene orthologs demonstrated their convergent function, whereas few of them developed divergent function in the evolutionary process. The molecular evolution analysis of identified MAPK family genes and the constructed MAPK cascade regulation network under multiple stresses provide valuable information for further investigation of the functions of BdMAPK cascade kinase genes.

Phenylalanine ammonia-lyase (PAL) is the core branch-point enzyme connecting plant primary aromatic amino acid metabolism to the phenylpropanoid pathway, which determines carbon flux redistribution between growth and defense and is essential for plant adaptation to various environments. Extensive research has clarified PAL’s conserved homotetrameric structure, MIO cofactor-dependent catalytic mechanism, and its roles in plant growth, development, and stress responses. However, there is a lack of comprehensive review studies focusing on PAL-mediated carbon metabolic flux redistribution, specifically covering its structural and evolutionary foundations, the links between this flux regulation and plant growth/development, its multi-layered regulatory network, and its roles in stress adaptation, limiting a comprehensive understanding of its evolutionary and functional diversity. This review systematically covers four core aspects: first, the molecular foundation, encompassing PAL’s structural features and catalytic specificity governed by the MIO cofactor; second, evolutionary diversity spanning from algae to angiosperms, with emphasis on unique regulatory mechanisms and evolutionary significance across lineages; third, the multi-layered regulatory network, integrating transcriptional control, post-translational modifications, epigenetic regulation, and functional crosstalk with phytohormones; and fourth, functional dynamics, which elaborate PAL’s roles in organ development, including root lignification, stem mechanical strength, leaf photoprotection, flower and fruit quality formation, and lifecycle-wide dynamic expression, as well as its mediated stress adaptations and regulatory networks under combined stresses. These insights provide a theoretical basis for targeted manipulation of PAL to optimize crop carbon allocation, thus improving growth performance, enhance stress resilience, and promote sustainable agriculture.

Background: Ca²⁺ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca²⁺ sensors, which could directly translate Ca²⁺ signals into downstream phosphorylation signals. Considering the importance of CDPKs as Ca²⁺ effectors for regulation of plant stress tolerance and few studies on Brachypodium distachyon were available, it was of interest for us to isolate CDPKs from B. distachyon. Results: A systemic analysis of 30 CDPK family genes in B. distachyon was performed. Results showed that all BdCDPK family members contained conserved catalytic Ser/Thr protein kinase domain, autoinhibitory domain, and EF-hand domain, and a variable N-terminal domain, could be divided into four subgroup (I-IV), based upon sequence homology. Most BdCDPKs had four EF-hands, in which EF2 and EF4 revealed high variability and strong divergence from EF-hand in AtCDPKs. Synteny results indicated that large number of syntenic relationship events existed between rice and B. distachyon, implying their high conservation. Expression profiles indicated that most of BdCDPK genes were involved in phytohormones signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. Moreover, the co-expression network implied that BdCDPKs might be both the activator and the repressor involved in WRKY transcription factors or MAPK cascade genes mediated stress response processes, base on their complex regulatory network. Conclusions: BdCDPKs might play multiple function in WRKY or MAPK mediated abiotic stresses response and phytohormone signaling transduction in B. distachyon. Our genomics analysis of BdCDPKs could provide fundamental information for further investigation the functions of CDPKs in integrating Ca²⁺ signalling pathways in response to environments stresses in B. distachyon.

Background: Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. Results: A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. Conclusions: This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.

The heat shock protein 70s (Hsp70s) and heat shock factors (Hsfs) play key roles in protecting plant cells or tissues from various abiotic stresses. Brachypodium distachyon, recently developed an excellent model organism for functional genomics research, is related to the major cereal grain species. Although B. distachyon genome has been fully sequenced, the information of Hsf and Hsp70 genes and especially the regulatory network between Hsfs and Hsp70s remains incomplete. Here, a total of 24 BdHsfs and 29 BdHsp70s were identified in the genome by bioinformatics analysis and the regulatory network between Hsfs and Hsp70s were performed in this study. Based on highly conserved domain and motif analysis, BdHsfs were grouped into three classes, and BdHsp70s divided into six groups, respectively. Most of Hsf proteins contain five conserved domains: DBD, HR-A/B region, NLS and NES motifs and AHA domain, while Hsp70 proteins have three conserved domains: N-terminal nucleotide binding domain, peptide binding domain and a variable C-terminal lid region. Expression data revealed a large number of BdHsfs and BdHsp70s were induced by HS challenge, and a previous heat acclimation could induce the acquired thermotolerance to help seedling suffer the severe HS challenge, suggesting that the BdHsfs and BdHsp70s played a role in alleviating the damage by HS. The comparison revealed that, most BdHsfs and BdHsp70s genes responded to multiple abiotic stresses in an overlapping relationship, while some of them were stress specific response genes. Moreover, co-expression relationships and predicted protein-protein interaction network implied that class A and B Hsfs played as activator and repressors, respectively, suggesting that BdHsp70s might be regulated by both the activation and the repression mechanisms under stress condition. Our genomics analysis of BdHsfs and BdHsp70s provides important evolutionary and functional characterization for further investigation of the accurate regulatory mechanisms among Hsfs and Hsp70s in herbaceous plants.

Seasonal radial-increment records can help to elucidate how tree growth responds to climate seasonality. Such knowledge is critical for understanding the complex growth-climate relationships in subtropical China. We hypothesize that under subtropical monsoon climate characterized by mild winters and hot summers, summer drought constrains stem radial increment, which generally results in growth-limiting factors switching from temperatures in spring and early summer to precipitation in summer and autumn. Here, we monitored intra-annual dynamics of stem radial increment with band dendrometers in a montane stand of Taiwan pine (Pinus taiwanensis Hayata) from Lushan Mountains for two consecutive years (2016–2017). A pronounced bimodal seasonal pattern of stem radial increment was observed in 2016. However, it was less clear in 2017 when late-summer rainfall events occurred in early August. Changing growth-climate relationships were detected throughout the two growing seasons. Stem increments were consistently positively correlated with temperatures before early July, whereas the growth-temperature dependency was gradually weakened and more variable after early July. Conversely, stem increments were significantly correlated with precipitation and soil moisture since early July, indicating that moisture variables were the main factor limiting stem increments in dry period. More precipitation was received in the dry period (July–November) of 2017 as compared with the year 2016, which favoured a wider annual increment in 2017, although growing-season temperature and precipitation was similar between years. Our study suggests a seasonal shift in growth-limiting factors in subtropical forests, which should be explicitly considered in forecasting responses of tree growth to climatic warming.