Plant morphology has its intellectual roots in the concept of organ metamorphosis articulated by Johann Wolfgang von Goethe, which seeks to understand plant form in terms of transformation and unity. Its development has been closely intertwined with advances in microscopy. In particular, the advent of fluorescence and confocal microscopy enabled the visualization of molecular and organelle dynamics in living plant cells, allowing morphology to be understood within a temporal framework. More recently, super-resolution microscopy and cryo-electron microscopy have made it possible to observe plant cell structures at unprecedented resolution. As a result, morphology is moving beyond the question of “what can be seen” toward addressing “how such forms are generated.” In this sense, the history of plant morphology can be regarded as the history of expanding the visible world. Microscopy is not merely a tool for the precise description of plant form, but also an intellectual framework for interrogating the principles underlying its formation. In this special issue, we revisit this historical trajectory and consider the contemporary significance of “seeing” the principles of life.

Mitochondria, which originated from an α-proteobacterial ancestor through endosymbiosis, are not formed de novo within the cell but increase in number exclusively through the division of pre-existing mitochondria. In contrast, the vast majority of mitochondrial proteins are not encoded by mitochondrial DNA but are derived from hundreds of genes encoded in the nuclear genome. Consequently, newly synthesized mitochondrial proteins translated by cytosolic ribosomes are selectively recognized based on peptide sequences appended to their amino termini and are transported into mitochondria through large protein translocase complexes embedded in the mitochondrial membranes. However, the “information” contained within these targeting peptides is cryptic, and the fundamental principles by which mitochondrial protein precursors are selected and discriminated remain incompletely understood. Here, we demonstrate that mitochondrial protein import relies on an unexpectedly simple prerequisite encoded within the targeting presequence. Using the unicellular red alga Cyanidioschyzon merolae, a eukaryote possessing a single mitochondrion, we identified the minimal essential elements required for mitochondrial targeting sequences. Our analyses revealed a remarkably simple rule governing mitochondrial protein recognition and further suggest an evolutionary potential by which novel mitochondrial proteins can arise through minimal sequence changes.

Cryo-electron microscopy (cryo-EM) is a technique that enables the visualization of biological specimens under near-physiological conditions by rapidly freezing the samples and directly observing them at cryogenic temperatures using a transmission electron microscope. Biomolecular complexes in cells exert their functions while dynamically changing their structures. We focus on the ribosome, the protein synthesis machinery at the heart of the central dogma, and aim to elucidate the behavior of molecules across multiple scales by using cryo-electron microscopy. The development of cryo-EM has been driven by the accumulation of technological advances in two major methodologies. In single-particle analysis, purified biological specimens are embedded in vitreous ice, and three-dimensional structures are reconstructed from a large number of two-dimensional projection images by image processing. Cryo-electron tomography (cryo-ET) enables three-dimensional structural analysis of larger cellular regions, by imaging frozen specimens over a range of tilt angles, and is therefore well suited for studying structures beyond individual molecules targeted in single-particle analysis. However, electron beam penetration is limited by sample thickness. In the 2000s, the introduction of cryogenic focused ion beam–scanning electron microscopy (cryo-FIB-SEM) enabled precise micromachining of targeted regions of frozen specimens while preserving the vitrified state. Subsequent technological developments have greatly expanded the applicability of cryo-electron tomography (cryo-ET). Currently, in addition to structural analysis of the ribosome by single-particle analysis, we are also trying in situ visualization of ribosomes from diverse organisms using cryo-FIB-SEM. In this article, we provide an overview of the workflow from sample preparation to data acquisition in cryo-EM.

Cryo-focused ion beam scanning electron microscopy (cryo-FIB-SEM) combined with cryo-electron tomography (cryo-ET) enables visualization of chloroplast architecture close to its native state, but vitrifying isolated organelles remains challenging. We outline practical considerations for applying cryo-FIB-SEM and cryo-ET to plant chloroplasts and compare osmolyte conditions that support vitrification without distorting membranes. Using isolated chloroplasts from an AtVIPP1-GFP transplastomic Nicotiana tabacum line to aid fluorescence-guided targeting, we found that trehalose (0.33 M) and betaine (0.66 M) maintained lamella quality and preserved grana organization, whereas mannitol and sucrose frequently produced ice artifacts. Tomograms from trehalose-treated samples showed well-resolved grana stacks and intact thylakoid networks consistent with native architecture. These observations offer practical guidance for laboratories adopting chloroplast cryo-ET and highlight sample preparation choices that improve reproducible 3D imaging at nanometer resolution.

In pollen vegetative cells, the generative cell or sperm cells are enclosed by a biomembrane that is thought to play crucial roles in protecting and transporting these germ cells. Although this membrane had long lacked an established name, forty-five researchers worldwide discussed its nomenclature and, in 2024, agreed to designate it as the “peri-germ cell membrane.” In this report, we describe the background of this nomenclatural revision and propose the Japanese translation “ 精包膜” (Sei- hō-maku) for the term peri-germ cell membrane.

Double fertilization is an innovative mechanism and trait of sexual reproduction acquired by flowering plants (angiosperms). This process must have played a pivotal role in the survival strategies and evolutionary success of flowering plants, while also being essential for human development through its contribution to food production. As a fundamental biological mechanism, double fertilization is widely recognized and taught, even at the high school level, underscoring its importance not only to researchers but also to the general public. On the other hand, although the phenomenon was first reported in 1898 and confirmed in many flowering plants subsequently, it has taken a long time to elucidate its molecular mechanism. Our understanding of cellular dynamics and molecular basis of double fertilization is progressing, and it is anticipated that the fundamental molecular and cellular mechanisms may not be far from being elucidated. In this review, we address frequently asked questions about double fertilization, provide an overview of the current understanding of its molecular and cellular mechanisms, and discuss key challenges and future directions at the forefront of research in this field.

In flowering plants, the mechanism linking fertilization to nutrient supply has long remained unclear. Here, we report the discovery of a novel structure in the chalazal region of the ovule, termed “the final form of the phloem end.” Using aniline blue staining, we found that unfertilized ovules accumulate callose in a ring-shaped pattern that blocks nutrient influx. Live imaging revealed that fertilization of the central cell triggers callose degradation, thereby opening the “gate” for nutrient flow from maternal tissues. Transcriptome analysis identified a fertilization-dependent β-1,3-glucanase gene, AtBG_ppap. Loss of AtBG_ppap impaired callose degradation and nutrient flow, whereas its overexpression enlarged seed size by approximately 16%. A conserved mechanism was also confirmed in rice. These findings represent the first discovery of a new plant tissue in 160 years since the Casparian strip and establish a new principle of fertilization-coupled nutrient regulation. This review summarizes the discovery and discusses its broad implications for understanding seed development.

Plant morphology, such as vegetative shoots, compound leaves, and inflorescence structures, exhibits self-similar structures. In shoot branching, for instance, leaves formed by the primary apical meristem bear axillary buds that themselves become new apical meristems and produce leaves in the secondary shoots, resulting in a self-similar structure. Although the secondary structures are not always identical to the primary structure in, for example, gene expression, they can share common developmental framework regardless of the chemical or genetic players. In this paper, I discuss the common developmental framework that can be applied on multiple scales in plant morphology, focusing on floral organ numbers in Ranunculaceae flowers and floret numbers in Asteraceae capitula. Although the flowers and inflorescences are differ in scales, number variations in these two structures can be explained by a common developmental framework: whorled-like arrangements of primordia and fluctuations on expression boundaries of fate determinants.