Land plants underpin civilization and planetary health, yet their genomic diversity remains largely uncharted. Current resources are unstandardized and scarce, lacking reference genomes for 95% of genera, 70% of families, and 51% of orders, impeding evolutionary and functional insight. We thus propose the PLANeT initiative, an international effort to generate high-quality, standardized genomes across the plant tree of life. Integrating artificial intelligence (AI) with genomics, we will decode conserved principles to advance fundamental plant biology, biodiversity conservation, crop improvement, and natural product discovery. Engaging around 100 labs to train 1,000 scientists, we will tackle pivotal questions for a sustainable future.

Fruits are a key feature defining angiosperms, yet how local growth is coordinated during development to generate diverse fruits remains unclear. Here, we demonstrate that the Capsella rubella C2H2-zinc finger transcription factor JAGGED (CrJAG) controls fruit shape determination by promoting both cell division and anisotropic growth. At the molecular level, CrJAG physically interacts with members of the Capsella rubella MULTICOPY SUPPRESSOR OF IRA1 (CrMSI)  histone chaperone family, increasing the chromatin accessibility and thereby sustaining the expression of genes involved in fruit morphogenesis. The resulting closed chromatin state in Crjag fruits is characterized by a reduction of the active histone marker (H3K18ac) and an increase of the repressive marker (H3K27me3). Further expression and pharmacological treatment analyses indicate that the developmental defects in Crjag fruits are largely attributable to down-regulation of the key cell-cycle regulator CrAUR2. Collectively, our findings therefore suggest that fine-tuning the cell cycle via epigenetic modification represents an additional, essential layer of regulation critical to organ development and diversification.

How organs partition themselves into discrete domains with distinct functions is a fundamental question in biology. The gynoecium of flowering plants provides an excellent system to address this question. Here, we show that the boundary between the stigma and style at the gynoecium apex is established by the complementary distribution of the phytohormone auxin and the Auxin Response Factor (ARF), ETTIN (ETT). Mechanistically, auxin induces ETT protein destabilization via the ubiquitin-proteasome pathway. A short sequence motif within an intrinsically disordered region is required for this auxin-triggered degradation. Disruption of this motif leads to ectopic ETT accumulation at the gynoecium apex and consequently abolishes stigma-style boundary development. We further demonstrate that this previously unrecognized mode of auxin-induced ARF instability is evolutionarily conserved among ETT orthologs across angiosperms. In summary, this study reveals how graded auxin distribution affects ARF transcription factor activity, contributing to the establishment of the stigma-style boundary, ensuring correct gynoecium formation and reproductive success in flowering plants.

Maize is amongst the most agriculturally and economically important crops to human beings. It was domesticated from a wild relative called teosinte. During domestication, maize has experienced drastic morphological transformations, such that it produces fewer ears, each of which bears many more kernels covered by soft and reduced glumes. The striking differences between maize and teosinte make the origin of maize ear a fascinating question, which has been fiercely and actively debated for more than a century. Over the past few decades, the discovery of numerous key genes and genetic pathways has greatly deepened our understanding of the mechanisms underlying maize ear development and domestication. In this review, by providing an overview of the morphogenetic processes of maize and teosinte ears, and the molecular mechanisms of maize ear development, we highlight key morphodynamical distinctions between maize and teosinte ears. By recapitulating historical accounts and summarizing recent advances regarding maize domestication, we present the current understanding and propose a model for the origin of maize ear.

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary diversity in floral traits with unclear genetic bases. To address this problem, we assemble a haplotype-resolved, chromosome-level genome for an aneuploid cultivar ‘Santiago’. We reveal pervasive variation in the number and sequence among homoeologous genes (HGs) and demonstrate proportional expression dosage effects of both chromosome and HG counts. This genome facilitates deciphering the genetic variation that contribute to trait polymorphisms in a hybrid population, some of which are also observed among HGs in P . ‘Santiago’. Specifically, nucleotide polymorphisms in a region that includes two tandemly arranged PsAGL6-2 genes account for lip morphology variation. Presence/absence of PsMYB12 genes determines presence/absence of venation-associated stripes. The b -type HG of PsMYB2 is associated with the pink color of sepals/petals. PsMYBx1 represses anthocyanin biosynthesis in multiple regions, in addition to inter-spot regions. Our study advances the genetic understanding of trait diversity in Phalaenopsis . ### Competing Interest Statement The authors have declared no competing interest. National Natural Science Foundation of China, 32370241 Kunpeng Institute of Modern Agriculture at Foshan, KIMAQD2022003 National Key R&D Program of China, 2023YFD1600505 Project supported by the Foundation for Innovative Research Groups of the National Natural Science Foundation of China, 32221001 Chinese Universities Scientific Fund, 2452024391

Giant genomes, generally dominated by transposable elements (TEs), have evolved repeatedly in angiosperms. The role of TEs in the evolution of giant genomes, however, remains largely unclear. Here, by ancestral genome size reconstruction, whole-genome sequencing, and comparative genomic and transcriptomic analyses, we reveal the processes, drivers, and consequences of genomic gigantism in the buttercup family (Ranunculaceae). We find that the giant diploid genome of Nigella damascena (10.84 Gb, ~35 times that of columbine) has evolved from an ~1.46 Gb ancestral genome by persistent TE accumulation over 60 million years. TE insertions in genic regions have generated genes with ultra-long introns or altered coding sequences, as well as Nigella-specific TE-derived genes, collectively accounting for ~20% of protein-coding genes in the N. damascena genome. TE-mediated regulatory changes and gene duplications/losses likely underpin the evolution of elaborate petals, fused carpels, and specialized secondary metabolites in N. damascena. These findings reveal how TEs drive genomic gigantism and shape specialized traits, advancing our understanding of genome size evolution.

Conical cells (CCs), trichomes, and hairs are all protrusive epidermal cells of plants, yet the differences and relationships among them remain largely unclear. Here, we show that the unicellular long hairs (LHs) and short trichomes (STs) on Nigella damascena petals differ from CCs in shape, length, number, distribution pattern, relative nuclear size, ploidy level, developmental process, and molecular basis. Specifically, NidaMIXTA, an ortholog of the famous CC/trichome identity gene in many species, is involved in CC development but does not affect STs and LHs. The identities of STs and LHs, however, are specified by genes encoding components in the MYB-bHLH-WDR (MBW) complex-GL2 module. STs, which serve as tiny pillars to prop open the upper and lower petal lips and facilitate pollinators' access to nectar, require the function of NidaMYB5-1, NidaGL3, NidaTT8, and NidaGL2, whereas the formation of LHs is determined by NidaMYB5-1/-2, NidaGL3, and NidaGL2. The evolution of STs and LHs from LH-like ancestors in the genus Nigella, therefore, was likely caused by independent co-option of the TT8 and MYB5-2 genes, respectively, followed by refining of their expression patterns.

As some of the earliest evolving flowering plants, waterlilies offer unique insights into angiosperm evolution. Giant Amazonian waterlilies (genus Victoria) are of particular interest due to their production of the world's largest floating leaves and gigantic flowers that entrap pollinating beetles. Here, we report chromosome-level genome assemblies of Victoria cruziana and three related waterlilies: Euryale ferox, Nymphaea mexicana, and Brasenia schreberi. We found an ancient whole-genome duplication event specific to the Nymphaeales. We reveal major gene duplication and loss events throughout the evolution of angiosperms, with substantial implications for flower development and the biosynthesis of floral volatile organic compounds (FVOCs) in waterlilies. Importantly, we report a unique division of labor in the stamen function of V. cruziana linked to beetle attraction by FVOCs. This is related to the ultra-high expression of VicSABATHa along with Vicchitinase, possibly linked to protection from damage by trapped beetles. Overexpression of VicSABATHa in tobacco leaves reveals a capacity to produce volatile fatty acids, confirming its role in their catalytic synthesis. Overall, these findings provide novel insights into the evolution and adaptations of waterlilies and flowering plants in general.

Plant development is a serial and dynamic process that encompasses various stages, from embryogenesis to senescence, influenced by both genetic and environmental factors. This review provides an in-depth exploration of the mechanisms underlying plant growth and development, highlighting key morphogenesis processes such as photomorphogenesis, plant growth, shoot branching, floral transition, flower development, fruit development and reproductivity specification. We delve into the molecular genetics of plant development, focusing on regulator and signaling pathways that govern critical developmental events. Furthermore, we discuss the role of phytohormones, including auxins, cytokinins, gibberellins, abscisic acid, and ethylene, in regulating developmental transitions. The interaction between plants and their environment, particularly light, temperature, and nutrient availability, is also examined, emphasizing how these external cues impact developmental pathways. Overall, this comprehensive overview offers insights into the intricate interplay between genetic programs and environmental stimuli in shaping plant architecture and life cycle, which will facilitate smart breeding and intelligent cultivation.

Phalaenopsis orchids are one of the most important ornamental crops, prized for their beautiful flowers and long flowering phase. Hundreds of commercially available cultivars display a remarkable range of variation in key horticultural traits, including inflorescence type, floral size, and color patterning. While most current cultivars have been developed through cross-breeding or mutation breeding, genetic homogenization has become a growing concern. This is largely due to extensive hybridization among existing cultivars, which are predominantly derived from a limited number of parental species. Additionally, trait linkage in Phal. can hinder the integration of desirable characteristics in progeny. Therefore, there is an urgent need to decipher the genetic programs governing key horticultural traits to facilitate both conventional and molecular breeding. Despite significant research efforts, progress has been hampered by several resource limitations. These include a scarcity of high-quality genome assemblies, the lack of stable genetic transformation systems, and insufficient materials for molecular biology studies—a challenge exacerbated by the plant's relatively long life cycle. Consequently, the molecular mechanisms underlying the formation and diversity of most important horticultural traits in Phal. orchids remain largely unexplored. This review summarizes recent research advances, with a primary focus on the key floral traits in Phal. orchids, including inflorescence type, flowering time, floral organ organization, color patterning, size, longevity, scent, organ shape, cuticle production and wax biosynthesis. Furthermore, we offer perspectives on future research directions aimed at elucidating the genetic basis for the remarkable diversity of these traits and advancing molecular breeding in Phal. orchids.

Parallel evolution of the same, or at least very similar, phenotype(s) in different lineages is often interpreted as evidence for the action of natural selection. However, caution is required when inferring parallel evolution based on uncertain or potentially incorrect phylogenetic frameworks. Here, by conducting extensive phylogenomic and population genetic analyses, we aim to clarify the evolutionary history of spurless taxa within the Aquilegia ecalcarata complex. We observed substantial discordance in the phylogenetic patterns across the entire genome, primarily attributed to ancient introgression and incomplete lineage sorting. Additionally, we identified several spurless lineages whose phylogenetic positions were distorted by admixture events. Using a backbone tree and demographic modeling, we determined that these spurless taxa independently originated twice within this group. Intriguingly, our investigation revealed that the spurless taxa experienced population expansion during global cooling, while their spurred sister groups underwent population contraction. The parallel losses of petal spurs, therefore, may be linked to adaptations for low-temperature conditions. These findings emphasize the importance of comprehensive population-level analyses in phylogenetic inference and provide valuable insights into the dynamics of trait loss and its implications for the adaptive strategies.

Germline fate determination is a critical event in sexual reproduction. Unlike animals, plants specify the germline by reprogramming somatic cells at the late stages of their development. However, the genetic basis of germline fate determination and how it evolved during the land plant evolution are still poorly understood. Here, we report that the plant homeodomain finger protein GERMLINE IDENTITY DETERMINANT (GLID) is a key regulator of the germline specification in liverwort, Marchantia polymorpha. Loss of the MpGLID function causes failure of germline initiation, leading to the absence of sperm and egg cells. Remarkably, the overexpression of MpGLID in M. polymorpha induces the ectopic formation of cells with male germline cell features exclusively in male thalli. We further show that MpBONOBO (BNB), with an evolutionarily conserved function, can induce the formation of male germ cell-like cells through the activation of MpGLID by directly binding to its promoter. The Arabidopsis (Arabidopsis thaliana) MpGLID ortholog, MALE STERILITY1 (AtMS1), fails to replace the germline specification function of MpGLID in M. polymorpha, demonstrating that a derived function of MpGLID orthologs has been restricted to tapetum development in flowering plants. Collectively, our findings suggest the presence of the BNB-GLID module in complex ancestral land plants that has been retained in bryophytes, but rewired in flowering plants for male germline fate determination. The genetic module underlying germline fate determination has been rewired during the land plant evolution.

During the process of flower opening, most petals move downward in the direction of the pedicel (i.e., epinastic movement). In most Delphinium flowers, however, their two lateral petals display a very peculiar movement, the mirrored helical rotation, which requires the twist of the petal stalk. However, in some lineages, their lateral petals also exhibit asymmetric bending that increases the degree of mirrored helical rotation, facilitating the formation of a 3D final shape. Notably, petal asymmetric bending is a novel trait that has not been noticed yet, so its morphological nature, developmental process, and molecular mechanisms remain largely unknown. Here, by using D. anthriscifolium as a model, we determined that petal asymmetric bending was caused by the localized expansion of cell width, accompanied by the specialized array of cell wall nanostructure, on the adaxial epidermis. Digital gene analyses, gene expression, and functional studies revealed that a class I homeodomain-leucine zipper family transcription factor gene, DeanLATE MERISTEM IDENTITY1 (DeanLMI1), contributes to petal asymmetric bending; knockdown of it led to the formation of explanate 2D petals. Specifically, DeanLMI1 promotes cell expansion in width and influences the arrangement of cell wall nano -structure on the localized adaxial epidermis. These results not only provide a comprehensive portrait of petal asymmetric bending for the first time but also shed some new insights into the mechanisms of flower opening and helical movement in plants.

Peltate organs, such as the prey-capturing traps of carnivorous plants and nectary-bearing petals of ranunculaceous species, are widespread in nature and have intrigued and perplexed scientists for centuries. Shifts in the expression domains of adaxial/abaxial genes have been shown to control leaf peltation in some carnivorous plants, yet the mechanisms underlying the generation of other peltate organs remain unclear. Here, we show that formation of various peltate ranunculaceous petals was also caused by shifts in the expression domains of adaxial/abaxial genes, followed by differentiated regional growth sculpting the margins and/or other parts of the organs. By inducing parameters to specify the time, position, and degree of the shifts and growth, we further propose a generalized modeling system, through which various unifacial, bifacial, and peltate organs can be simulated. These results demonstrate the existence of a hierarchical morphospace system and pave the way to understand the mechanisms underlying plant organ diversification.

Recently,Worobey et al.(2022)pub-lished a report entitled 'The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19pan-demic'that succinctly summarizes their study[1].A pre-print version of this study had earlier elicited a series of high-profile media coverages[2,3].All these reports deliver a social-political message that the Huanan market is the epicenter of COVID-19.

Species of the tribe Delphinieae (Ranunculaceae) have long been the focus of morphological, ecological, and evolutionary studies due to their highly specialized, nearly zygomorphic (bilaterally symmetrical) spiral flowers with nested petal and sepal spurs and reduced petals. The mechanisms underlying the development and evolution of Delphinieae flowers, however, remain unclear. Here, by conducting extensive phylogenetic, comparative transcriptomic, expression, and functional studies, we clarified the evolutionary histories, expression patterns, and functions of floral organ identity and symmetry genes in Delphinieae. We found that duplication and/or diversification of APETALA3-3 (AP3-3), AGAMOUS-LIKE6 (AGL6), CYCLOIDEA (CYC), and DIVARICATA (DIV) lineage genes was tightly associated with the origination of Delphinieae flowers. Specifically, an AGL6-lineage member (such as the Delphinium ajacis AGL6-1a) represses sepal spur formation and petal development in the lateral and ventral parts of the flower while determining petal identity redundantly with AGL6-1b. By contrast, two CYC2-like genes, CYC2b and CYC2a, define the dorsal and lateral-ventral identities of the flower, respectively, and form complex regulatory links with AP3-3, AGL6-1a, and DIV1. Therefore, duplication and diversification of floral symmetry genes, as well as co-option of the duplicated copies into the preexisting floral regulatory network, have been key for the origin of Delphinieae flowers.

Complex color patterns on petals are widespread in flowering plants, yet the mechanisms underlying their formation remain largely unclear. Here, by conducting detailed morphological, anatomical, biochemical, optical, transcriptomic, and functional studies, we investigated the cellular bases, chromogenic substances, reflectance spectra, developmental processes, and underlying mechanisms of complex color pattern formation on Nigella orientalis petals. We found that the complexity of the N. orientalis petals in color pattern is reflected at multiple levels, with the amount and arrangement of different pigmented cells being the key. We also found that biosynthesis of the chromogenic substances of different colors is sequential, so that one color/pattern is superimposed on another. Expression and functional studies further revealed that a pair of R2R3-MYB genes function cooperatively to specify the formation of the eyebrow-like horizontal stripe and the Mohawk haircut-like splatters. Specifically, while NiorMYB113-1 functions to draw a large splatter region, NiorMYB113-2 functions to suppress the production of anthocyanins from the region where a gap will form, thereby forming the highly specialized pattern. Our results provide a detailed portrait for the spatiotemporal dynamics of the coloration of N. orientalis petals and help better understand the mechanisms underlying complex color pattern formation in plants.

The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionarybiogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial-temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/ Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a 'mixing-isolation-mixing (MIM)' mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Presentday island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of 'non-adaptive' radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.