Adaptive evolution of chloroplast division mechanisms during plant terrestrialization

Ecotype-specific phenolic acid accumulation and root softness in Salvia miltiorrhiza are driven by environmental and genetic factors

Salvia miltiorrhiza Bunge, a renowned medicinal herb in traditional Chinese medicine, displays distinctive root texture and high phenolic acid content, traits influenced by genetic and environmental factors. However, the underlying regulatory networks remain unclear. Here, we performed multi-omics analyses on ecotypes from four major Chinese regions, focusing on environmental impacts on root structure, phenolic acid accumulation and lignin composition. Lower temperatures and increased UV-B radiation were associated with elevated rosmarinic acid (RA) and salvianolic acid B (SAB) levels, particularly in the Sichuan ecotype. Structural models indicated that the radial arrangement of xylem conduits contributes to greater root hardness. Genomic assembly and comparative analysis of the Sichuan ecotype revealed a unique phenolic acid metabolism gene cluster, including SmWRKY40, a WRKY transcription factor essential for RA and SAB biosynthesis. Overexpression of SmWRKY40 enhanced phenolic acid levels and lignin content, whereas its knockout reduced root hardness. Integrating high-throughput (DNA affinity purification sequencing) and point-to-point (Yeast One-Hybrid, Dual-Luciferase and Electrophoretic Mobility Shift Assay) protein-DNA interaction detection platform further identified SmWRKY40 binding sites across ecotypes, revealing specific regulatory networks. Our findings provide insights into the molecular basis of root texture and bioactive compound accumulation, advancing breeding strategies for quality improvement in S. miltiorrhiza.

The complete chloroplast genomes of four Aspidopterys species and a comparison with other Malpighiaceae species

The genus Aspidopterys has multiple functions in medicine, food and ecological restoration. Due to the similar morphological characteristics of some species and the limited genomic information hinder the studies on germplasm identification and molecular phylogeny analysis. In this study, we compared and explored the six complete chloroplast (cp) genomes including four Aspidopterys species (A. glabriuscula, A. concava, A. cavaleriei, A. obcordata), Banisteriopsis caapi and Bunchosia argentea. Their cp genomes in length were 158,473 to 161,091 bp, displaying the high conserved degree in the structure, gene arrangement and GC content. Moreover, 57-80 long repeats and 61-92 SSRs were identified, most of which were forward or palindromic repeats and mononucleotides, respectively. Eleven non-coding regions and 12 coding regions, especially ndhH_ndhA, rpl32_ndhF and ycf1, had the higher nucleotide diversity values that could can be regarded as DNA barcodes of Malpighiaceae species. In addition, the 9 genes (like accD, atpE, atpF, clpP) were conducted positive selection (Ka/Ks > 1). As indicated by phylogenetic analysis, those four Aspidopterys were clustered into single clade with other Malpighiaceae species and were closely related to B. caapi and B. argentea. This study sheds more lights on further phylogenetic, evolutionary and genetic diversity studies on the genus Aspidopterys and even the Malpighiaceae species.

Hierarchical Regulatory Networks Reveal Conserved Drivers of Plant Drought Response at the Cell-Type Level

Drought is a critical environmental challenge affecting plant growth and productivity. Understanding the regulatory networks governing drought response at the cellular level remains an open question. Here, a comprehensive multi-omics integration framework that combines transcriptomic, proteomic, epigenetic, and network-based analyses to delineate cell-type-specific regulatory networks involved in plant drought response is presented. By analyzing nearly 30 000 multi-omics data samples across species, unique insights are revealed into conserved drought responses and cell-type-specific regulatory dynamics, leveraging novel integrative analytical workflows. Notably, CIPK23 emerges as a conserved protein kinase mediating drought tolerance through interactions with CBL4, as validated by yeast two-hybrid and BiFC assays. Experimental validation in Arabidopsis thaliana and Vitis vinifera confirms the functional conservation of CIPK23, which enhances drought resistance in overexpression lines. In addition, the authors' causal network analysis pinpoints critical regulatory drivers such as NLP7 and CIPK23, providing insights into the molecular mechanisms of drought adaptation. These findings advance understanding of plant drought tolerance and offer potential targets for improving crop resilience across diverse species.

Polyploidy drives autophagy to participate in plant-specific functions

Polyploidization promotes the functional diversification of autophagy in plants, expanding autophagy-associated genes (AAGs) to support processes like chloroplast division and flowering. Analysis of 92,967 AAGs in Arabidopsis thaliana, Solanum lycopersicum, Camellia oleifera, and 74 other plant species shows that 45.69% of AAGs are polyploidy-related, highlighting polyploidy's role in linking autophagy to plant-specific functions.

Evolution and Functional Differentiation of the C-terminal Motifs of FtsZs During Plant Evolution

Filamentous temperature-sensitive Z (FtsZ) is a tubulin-like GTPase that is highly conserved in bacteria and plants. It polymerizes into a ring at the division site of bacteria and chloroplasts and serves as the scaffold protein of the division complex. While a single FtsZ is present in bacteria and cyanobacteria, there are two subfamilies, FtsZ1 and FtsZ2 in the green lineage, and FtsZA and FtsZB in red algae. In Arabidopsis thaliana, the C-terminal motifs of AtFtsZ1 (Z1C) and AtFtsZ2-1 (Z2C) display distinct functions in the regulation of chloroplast division. Z1C exhibits weak membrane-binding activity, whereas Z2C engages in the interaction with the membrane protein AtARC6. Here, we provide evidence revealing the distinct traits of the C-terminal motifs of FtsZ1 and FtsZ2 throughout the plant evolutionary process. In a range of plant species, the C-terminal motifs of FtsZ1 exhibit diverse membrane-binding properties critical for regulating chloroplast division. In chlorophytes, the C-terminal motifs of FtsZ1 and FtsZ2 exhibit both membrane-binding and protein interaction functions, which are similar to those of cyanobacterial FtsZ and red algal FtsZA. During the transition from algae to land plants, the functions of the C-terminal motifs of FtsZ1 and FtsZ2 exhibit differentiation. FtsZ1 lost the function of interacting with ARC6 in land plants, and the membrane-binding activity of FtsZ2 was lost in ferns. Our findings reveal the functional differentiation of the C-terminal motifs of FtsZs during plant evolution, which is critical for chloroplast division.