Changes in gene expression patterns can lead to the variation of morphological traits. This phenomenon is particularly evident in recent evolution events such as crop domestication and responses to environmental stress, where alterations in expression levels can efficiently give rise to domesticated syndromes and adaptive phenotypes. Rice (Oryza sativa L.), one of the world’s most crucial cereal crops, comprises two morphologically distinct subspecies, Indica and Japonica. To investigate the morphological divergence between these two rice subspecies, this study planted a total of 315 landrace individuals of both Indica and Japonica under identical cultivation conditions. Out of the 16 quantitative traits measured in this study, 12 exhibited significant differences between the subspecies. To determine the genetic divergence between Indica and Japonica at the whole-genome sequence level, we constructed a phylogenetic tree using a resequencing dataset encompassing 95 rice landrace accessions. The samples formed two major groups that neatly corresponded to the two subspecies, Indica and Japonica. Furthermore, neighbor-joining (NJ) trees based on the expression quantity of effectively expressed genes (EEGs) across five different tissues categorized 12 representative samples into two major clades aligning with the two subspecies. These results imply that divergence in genome-wide expression levels undergoes stabilizing selection under non-stressful conditions, with evolutionary trends in expression levels mirroring sequence variation levels. This study further supports the pivotal role of changes in genome-wide expression regulation in the divergence of the two rice subspecies, Indica and Japonica.

Polyploid organisms evolve from their initial doubled genomic condition through a number of processes collectively termed diploidization, whose tempo and mode remain poorly understood mainly due to the difficulty of discriminating de novo evolution subsequent to polyploidy from variation inherited from progenitors. Here, we generated chromosome-scale genome assemblies for the wild rice allopolyploid Oryza minuta and its two diploid progenitors, Oryza punctata and Oryza officinalis , and employed a population genomic approach to investigate the diploidization process in O. minuta at the sequence and transcriptomic level. We show that this wild rice allopolyploid originated around 0.7 Mya, and during subsequent diploidization, its two subgenomes have retained highly conserved synteny with the genomes of its extant diploid progenitors. This populational approach allowed us to distinguish parental legacy of inherited variation from postpolyploidy evolution, and our analyses revealed that whereas gene fractionation occurred in an early burst, accumulation of transposable elements (TEs) and homoeologous exchanges has been gradual. Patterns of homoeolog expression bias are highly variable across tissues, with no consistent subgenome expression bias. Our assessments of the impact of DNA methylation, TE distribution, and parental legacy on expression patterns provide some support for the TE load theory (the theory that the TE densities in flanking regions surrounding genes strongly influence expression levels), while also illustrating the complexity of transcription regulation.

1. Introduction Plants exhibit a remarkable capacity to regenerate tissue, organs, or entirely new individuals after wounding or under in vitro conditions (Eshed Williams, 2021; Doll and Ikeuchi, 2025). Plant regeneration in vitro involves a biphasic process encompassing the acquisition of cell pluripotency and subsequent de novo shoots regeneration (DNSR) or de novo root regeneration (DNRR) (Figure 1A; Kim and Seo, 2025; Youngstrom et al., 2025). Initially, explants are cultured on an auxin-enriched callus-inducing medium (CIM) to induce the formation of a pluripotent callus. The pluripotent callus then undergoes extensive cellular reprogramming and spatial cell identities reorganization to generate shoots or roots (Figure 1A). Accumulating evidence indicates the vital involvement of phytohormones such as auxin, jasmonic acid (JA), cytokinin (CK), ethylene in regulating plant regeneration (García-Gómez, and Tusscher, 2024; Asghar et al., 2025; Xu and Yang, 2025). In addition, a couple of key transcription factors (TFs) such as WUSCHEL-RELATED HOMEOBOX (WOX), PLETHORAs (PLTs) have been reported to play a key role in plant regeneration (Islam et al., 2023; Chen et al., 2024). Although this regenerative capability has been well-documented across numerous plant species, the underlying mechanisms remain largely elusive (Eshed Williams, 2021; Chen et al., 2024). Small signaling peptides represent a novel class of plant growth regulators, typically comprising fewer than 150 amino acids. These peptides are recognized by plasma membrane-localized receptors or co-receptors, which subsequently activate or deactivate specific regulatory pathways to modulate plant growth and stress adaptions (Ji et al., 2025; Xiao et al., 2025). Notably, several small signaling peptide-encoding genes, including CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), C-TERMINALLY ENCODED PEP TIDE (CEP), phytosulfokine (PSK), and GOLVEN/ROOT MERISTEM GROWTH FACTOR/CLE-LIKE (GLV/RGF/CLEL) are differentially activated at specific stages of DNSR, as revealed by single-cell transcriptomic analysis, suggesting their potential roles in the plant shoot regeneration process (Zhai and Xu, 2021; Wang et al., 2022). Experimental data further demonstrate the regulatory functions of CLE1-CLE7 (Kang et al., 2022), CLE9/10 (Glazunova et al., 2025) and CLE46 (Ito et al., 2025), REGENERATION FACTOR1 (REF1) (Yang et al., 2024) and RAPID ALKALINIZATION FACTOR 33 (RALF33) peptides (Shen et al., 2025) in modulating plant regeneration capacity under in vitro conditions or in response to wounding signal as well as PSK peptides in the regulation of somatic embryogenesis (SE) (Hao et al., 2023; Luo et al., 2024) (Table 1; Figure 1B - E). 2. CLE-CLV1/BAM1 signaling module negatively regulates adventitious shoot regeneration The CLE genes encode precursor proteins featuring an N-terminal signal sequence that targets them to the secretory pathway, a central variable region, and a highly conserved CLE domain at the C-terminus, which frequently undergoes posttranslational modifications to produce a functional polypeptide (Xie et al., 2022; Ji et al., 2025). Consistent with their pivotal functions in stem cell regulation (Selby and Jones, 2023; Shpak and Uzair, 2025), the expressions of CLE members are differentially activated at distinct phases of shoot regeneration (Zhai and Xu, 2021; Wang et al., 2022). Specifically, CLE1-CLE7 and CLE9/10 peptides have been demonstrated to negatively influence shoot regeneration (Figure 1B; Kang et al., 2022; Glazunova et al., 2025). CLE1-CLE7 gene expression is significantly induced by CIM or shoot-inducing medium (SIM), and CRISPR-engineered cle1-7 septuple mutant exhibits an increased number of adventitious shoots (Kang et al., 2022). While most single cle mutants do not affect DNSR, the cle4 and cle7 mutants show enhanced DNSR (Kang et al., 2022). Conversely, application of synthetic CLE1-7 peptides exhibits a dose-dependent inhibition of DNSR, and overexpression of CLE4 or CLE7 also suppresses DNSR. In addition, CLE9/10 peptide also suppresses DNSR without affecting callus formation (Figure 1B; Glazunova et al., 2025). Notably, the clv1 and bam1 mutants show increased shoot regeneration capabilities and are insensitive to CLE1-CLE7 peptide-mediated inhibition of shoot regeneration, confirming that CLAVATA1 (CLV1) CLV1 and BARELY ANY MERISTEM1 (BAM1) receptors mediate the CLE1-CLE7 signal to negatively regulate DNSR. However, clv1 mutant respond normally to CLE9/10 peptide treatment, while bam1 mutant is insensitive to CLE9/10 peptide (Glazunova et al., 2025). Further studies reveal that the CLE-CLV1/BAM1 module restricts the transcriptional level of WUSCHEL (WUS), a critical regulator of plant regeneration (Ince and Sugimoto, 2023; Shpak and Uzair, 2025), thereby controlling shoot regeneration potential (Figure 1B). 3. REF1-PORK1 pathway promotes regeneration through activating WIND1 expression Recent studies have identified REF1, a Pep peptide homolog in tomato, as a crucial regulator of plant regenerative capacity (Figure 1C; Yang et al., 2024). The absence of PRP, the precursor of REF1 peptide, results in impaired callus formation and shoot regeneration, while PRP overexpression markedly enhances regenerative capacity (Yang et al., 2024). The exogenous application of synthetic REF1 peptide also enhances callus formation and shoot regeneration in wild-type (WT) plants in a dose-responsive manner, and compensates for the regenerative deficits observed in prp mutants. These findings collectively underscore the key role of REF1 peptide in regulating plant regeneration (Yang et al., 2024). Additionally, mutation in PEPR1/2 ORTHOLOG RECEPTOR-LIKE KINASE 1 (PORK1) result in similar defects in callus formation and shoot regeneration that are observed in prp mutants. While PORK1 overexpression significantly boosts regenerative capacity. Additionally, pork1 mutant exhibits insensitivity to REF1 peptide...

Freshwater fungi are characterized by their high species diversity and perform vital ecological roles. During our survey of Chinese aquatic microfungal diversity, four fungal strains were isolated from freshwater environments in Jiangxi and Guizhou Provinces, China. Through comprehensive morphological assessment and multi-locus phylogenetic analyses based on combined ITS, LSU, SSU, RPB2 , and TEF1-α sequences, two new species, Acrogenospora bambusae and A. lignicola , were introduced. In addition, two previously described species, A. taiwanica and A. thailandica , originally described from China (Taiwan), and Thailand, respectively, are newly reported from mainland China. This study provides detailed morphological descriptions, photographic illustrations, and phylogenetic placements for each taxonomic novelty.

Drought stress is increasingly recognized as a major abiotic constraint on rice (Oryza Sativa L.) productivity and yield stability, posing a significant threat to global food security under rapidly changing and increasingly complex climatic conditions. To acclimate to water deficit, rice plants dynamically activate or suppress coordinated stress-perception systems, signal-transduction cascades, and multilayered regulatory networks. Over recent decades, extensive research has identified and characterized numerous drought-responsive genes, quantitative trait loci (QTLs), and drought-tolerant rice cultivars. Concurrently, small signaling peptides have emerged as pivotal regulatory molecules that orchestrate plant growth, development, and abiotic/biotic stress responses through binding with their cognate receptors. Nevertheless, the functional significance and underlying regulatory mechanisms of small signaling peptides in rice plant adaptation to drought stress remain insufficiently elucidated. To bridge this knowledge gap, this review summarizes recent progress in elucidating the roles and regulatory mechanisms of small signaling peptides in rice drought responses and outlines future research directions aimed at resolving outstanding unanswered issues and facilitating their application in the genetic development of water-efficient and drought-resilient rice cultivars.