Genome evolution in plants and the origins of innovation

Diversification of CLE expression patterns and nonmeristematic roles for CLAVATA receptor-like kinases in a moss

The CLAVATA pathway controls meristematic cell proliferation and multiple nonmeristematic processes in Arabidopsis development. While CLAVATA ancestrally regulates meristematic proliferation in nonseed plant gametophytes, ancestral sporophytic and nonmeristematic functions in land plants are unknown. Here, we analysed the promoter activities of all peptide (PpCLE) and receptor-encoding (PpCLV1a, PpCLV1b and PpRPK2) genes throughout the moss (Physcomitrium patens) life cycle and validated our expression analyses using mutant phenotype data. In gametophore apices, PpCLE3 expression marked apical cells, and PpCLV1b and PpRPK2 overlapped. In nonmeristematic tissues, gametophytes showed highly focal PpCLE but broader receptor-encoding gene expression, and many genes were co-expressed. Mutant phenotype analysis revealed roles for PpCLV1a, PpCLV1b and PpRPK2 in fertility and male and female reproductive development. In sporophytes, no PpCLE expression specifically marked the apical cells, and PpCLV1b and PpRPK2 expression initially marked distinct apical and basal domains, but later overlapped at the intercalary meristem. Overall, fewer genes were co-expressed in sporophytes than in gametophytes, but all genes were co-expressed in guard cells. Our data indicate that nonmeristematic CLAVATA functions in gametangium development and stomatal development may be ancestral within land plants. Peptide encoding (CLE) gene copy numbers amplified in mosses, and promoter evolution was a likely driver of cell type diversification during moss evolution.

Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls

Ferns are essential for understanding plant evolution; however, their large and intricate genomes have kept their genetic landscape largely unexplored, with only a few genomes sequenced and limited transcriptomic data available. To bridge this gap, we generated extensive RNA-sequencing data across various organs from 22 representative fern species, resulting in high-quality transcriptome assemblies. These data enabled us to construct a time-calibrated phylogeny for ferns, encompassing all major clades, which revealed numerous instances of whole-genome duplication. We highlighted the distinctiveness of fern genetics, discovering that half of the identified gene families are unique to ferns. Our exploration of fern cell walls through biochemical and immunological analyses uncovered the presence of the lignin syringyl unit, along with evidence of its independent evolution in ferns. Additionally, the identification of an unusual sugar in fern cell walls suggests a divergent evolutionary trajectory in cell wall biochemistry, probably influenced by gene duplication and sub-functionalization. To facilitate further research, we have developed an online database that includes preloaded genomic and transcriptomic data for ferns and other land plants. We used this database to demonstrate the independent evolution of lignocellulosic gene modules in ferns. Our findings provide a comprehensive framework illustrating the unique evolutionary journey ferns have undertaken since diverging from the last common ancestor of euphyllophytes more than 360 million years ago.

Evolutionary insights into light-induced stomatal opening mechanisms

Light-induced stomatal opening pathways are essential for regulating gas exchange and water loss in response to dynamic environmental light cues. While stomatal signalling pathways are well characterised at the genetic level in Arabidopsis thaliana (arabidopsis), much less is known about these mechanisms in non-flowering plant groups. We discuss recent advances in our knowledge of key components - photoreceptors, mitogen-activated protein kinases (MAPKs), phosphatases, H+-ATPases and ion channels - across plant lineages, highlighting the gaps in knowledge particularly in non-flowering species. Addressing these gaps will provide valuable insights into stomatal evolution and a deeper understanding of the functional diversity of the plants alive today.

Decoding genetic diversity through genome engineering in bryophytes

Bryophytes, which include mosses, liverworts, and hornworts, have evolved a highly successful strategy for thriving in terrestrial environments, allowing them to occupy nearly every land ecosystem. Their success is due to a unique combination of biochemical adaptations, diverse structural forms, and specialized life cycle strategies. The key to their evolutionary success lies in their genomic diversity. To fully decode this diversity, the use of advanced genome engineering techniques is crucial. In this review, we explore the genomic diversity of bryophytes and the latest advancements in their genome studies and engineering, ranging from precise gene editing to whole-genome synthesis. Notably, the moss Physcomitrium patens stands out as the only land plant capable of efficiently utilizing homologous recombination for precise genome engineering. This capability has heralded a new era in plant synthetic genomics. By focusing on bryophytes, we emphasize the potential benefits of unraveling the genetic traits, which could have significant implications across various scientific fields, from fundamental biology to biotechnological applications.

Genome-wide characterization and expression profiling of the TGA gene family in sweet orange (Citrus sinensis) reveal CsTGA7 responses to multiple phytohormones and abiotic stresses

Citrus is widely recognized as one of the most economically important fruit crops worldwide. However, citrus growth is frequently hindered by external environmental stresses, which severely limit its development and yield. The TGA (TGACG motif-binding factor) transcription factors (TFs) are members of the bZIP family and play essential roles in plant defense responses and organ development. Nevertheless, the systematic identification and functional analysis of the TGA family in citrus remains unreported. In this study, genome-wide analysis identified a total of seven CsTGA TFs in Citrus sinensis, which were classified into five subgroups. Phylogenetic and syntenic analysis revealed that the CsTGA genes are highly conserved, with no tandem or segmental duplication events among family members. Promoter sequence analysis identified numerous cis-acting elements associated with transcriptional regulation, phytohormone response, and environmental adaptation in the promoters of CsTGA genes. The expression patterns under five phytohormones and three abiotic stresses demonstrated significant responses of multiple CsTGA genes under various forms of adversity. Among all tested treatments, CsTGA7 showed the most robust response to multiple stresses. Tissue-specific expression pattern analysis revealed potential functional biases among CsTGA genes. In-depth analysis showed that CsTGA7 localized in the nucleus and possessed transcriptional activation activity, consistent with the typical characteristic of transcriptional regulators. In summary, our research systematically investigated the genomic signature of the TGA family in C. sinensis and unearthed CsTGA7 with potential functions in phytohormone signaling transduction and abiotic stress responses. Our study establishes a basis for further exploration of the function of CsTGA genes under abiotic stress.

Genomic correlates of vascular plant reproductive complexity and the uniqueness of angiosperms

Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated in diversification rate shifts, structural innovations, and increased disparity. But the general effects of WGD are challenging to evaluate, in part due to the difficulty of directly comparing morphological patterns across disparate clades. We explored relationships between WGD and the evolution of reproductive complexity across vascular plants using a metric based on the number of reproductive part types. We used multiple regression models to evaluate the relative importance of inferred WGD events, genome size, and a suite of additional variables relating to growth habit and reproductive biology in explaining part type complexity. WGD was a consistent predictor of reproductive complexity only among angiosperms. Across vascular plants generally, reproductive biology, clade identity, and the presence of bisexual strobili (those that produce microsporangiate and megasporangiate organs) were better predictors of complexity. Angiosperms are unique among vascular plants in combining frequent polyploidy with high-reproductive complexity. Whether WGD is mechanistically linked to floral complexity is unclear, but we suggest widespread polyploidy and increased complexity were ultimately facilitated by the evolution of herbaceous growth habits in early angiosperms.

Functional characterization of Camptotheca acuminata 7-deoxyloganetic acid synthases and 7-deoxyloganetic acid glucosyltransferases involved in camptothecin biosynthesis

Camptothecin (CAM), a well-known plant-derived antitumor compound, is a structurally complex pentacyclic pyrroloquinoline monoterpene indole alkaloid (MIA) found in various plant species. As a specific MIA, CAM had been thought to share a common upstream biosynthetic pathway with other MIAs such as the antitumor vinblastine and vincristine from Catharanthus roseus. Nevertheless the key enzymes responsible for the consecutive three-step oxidation of the -CH3 of nepetalactol to form the -COOH of 7-deoxyloganetic acid and the subsequent glycosylation of 7-deoxyloganetic acid to yield 7-deoxyloganic acid have yet to be functionally characterized. Here we established an in vivo tandem catalysis assay for the enzymatic catalytic activity characterization of 7-deoxyloganetic acid synthase (7DLS) and 7-deoxyloganetic acid glucosyltransferase (7DLGT), two crucial catalytic enzymes in MIAs biosynthesis, thereby avoiding the difficulty in the detection of the unstable biosynthetic intermediates. The enzyme activity assay platform was conducted through the co-expression of functionally characterized Cr7DLS and Cr7DLGT in Saccharomyces cerevisiae WAT11, substrate feeding, and enzymatic product verification. Two cytochrome P450 enzymes (CYPs) from Camptotheca acuminata, the prestigious resource for CAM, CaCYP76A75 and CaCYP76A76, were identified and functionally characterized to be responsible for the consecutive three-step oxidation of nepetalactol to yield 7-deoxyloganetic acid through reciprocal replacement of Cr7DLS in the in vivo tandem enzyme activity assay platform. Two uridine 5'-diphosphate glycosyltransferases (UGTs), CaUGT709C10 and CaUGT709C11, were functionally characterized to be capable of glycosylating 7-deoxyloganetic acid to yield 7-deoxyloganic acid. This study provides two CYPs as 7DLSs and two UGTs as 7DLGTs, offering potential applications in MIAs biosynthesis.

New beginnings for dead ends: polyploidy, -SSE models and the dead-end hypothesis

BACKGROUND

Since the mid-20th century, it has been argued by some that the transition from diploidy to polyploidy is an 'evolutionary dead end' in plants. Although this point has been debated ever since, multiple definitions of 'dead end' have been used in the polyploidy literature, without sufficient differentiation between alternative uses.

SCOPE

Here, we focus on the two most common conceptions of the dead-end hypothesis currently discussed: the 'lowering diversification' hypothesis and the 'rarely successful' hypothesis. We discuss the evidence for both hypotheses, and we use a recently developed method of inferring tip diversification rates to demonstrate tests for the effect of ploidy on diversification in Solanaceae.

CONCLUSIONS

We find that diversification rates in the family are not strongly correlated with ploidy or with the closely related trait of breeding system. We also outline recent work in the field that moves beyond the relatively simple question of whether polyploidy increases, decreases or does not significantly affect diversification rates in plants.

Whole-chromosome oligo-painting in licorice unveils interspecific chromosomal evolutionary relationships and possible origin of triploid genome species

Licorice is one of the most extensively studied medicinal plants in the world, whose roots and rhizomes have long been used as both a sweetener and an essential component in numerous herbal preparations. However, the genus Glycyrrhiza has a complex composition, and the interspecies chromosomal relationships, origin, and evolution are still largely unclear. Here, we develop a set of whole-chromosome painting probes that allowed identification of all eight chromosomes of licorice on same metaphase chromosomes. Comparative chromosome painting analyses in seven different Glycyrrhiza species revealed that the genus Glycyrrhiza maintained extraordinarily conserved chromosomal synteny after about 3-12 million years of divergence. No cytologically visible inter-chromosomal rearrangements were identified in any species. By comparative chromosomal karyotype analyses, we revealed interspecific chromosome evolutionary relationships and dramatic variable chromosomal karyotype after independent divergence and demonstrated that G. prostrate was the most closely related to the ancestral type among the seven Glycyrrhiza species. Furthermore, we also discovered a G. glandulosa seed with distinct triploid-genome for the first time in China, suggesting the existence of a polyploid evolutionary pathway in the genus Glycyrrhiza, which challenges the previous notion that only diploids of licorice existed in nature. This study expands our knowledge of the chromosome evolution of licorice and will lay an important foundation for the genome origin and evolution studies in the genus Glycyrrhiza.

Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism

Plant chemical diversity is largely owing to a number of enzymes which catalyse reactions involved in the assembly, and in the subsequent chemical modifications, of the core structures of major classes of plant specialized metabolites. One such reaction is acylation. With this in mind, to study the deep evolutionary history of BAHD and the serine-carboxypeptidase-like (SCPL) acyltransferase genes, we assembled phylogenomic synteny networks based on a large-scale inference analysis of orthologues across whole-genome sequences of 126 species spanning Stramenopiles and Archaeplastida, including Arabidopsis thaliana, tomato (Solanum lycopersicum) and maize (Zea mays). As such, this study combined the study of genomic location with changes in gene sequences. Our analyses revealed that serine-carboxypeptidase (SCP)/serine-carboxypeptidase-like (SCPL) genes had a deeper evolutionary origin than BAHD genes, which expanded massively on the transition to land and with the development of the vascular system. The two gene families additionally display quite distinct patterns of copy number variation across phylogenies as well as differences in cross-phylogenetic syntenic network components. In unlocking the above observations, our analyses demonstrate the possibilities afforded by modern phylogenomic (syntenic) networks, but also highlight their current limitations, as demonstrated by the inability of phylogenetic methods to separate authentic SCPL acyltransferases from standard SCP peptide hydrolases.This article is part of the theme issue 'The evolution of plant metabolism'.

Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land

Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.

Endosomal membrane budding patterns in plants

Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets.

Proteomic dynamics revealed sex-biased responses to combined heat-drought stress in Marchantia

Recent studies have documented plant responses to climate change extensively, particularly to single-stress exposures. However, critical factors for stress survival, such as sexual differentiation, are not often considered. The dioicous Marchantia polymorpha stands as an evolutionary milestone, potentially preserving ancestral traits from the early colonizers. In this study, we employed proteomic analyses complemented with physiological monitoring to investigate combined heat and drought responses in Tak-1 (male) and Tak-2 (female) accessions of this liverwort. Additionally, targeted transcriptomics was conducted using different natural populations from contrasting environments. Our findings revealed sex-biased dynamics among natural accessions, particularly evident under control conditions and during early stress responses. Although Tak-2 exhibited greater diversity than Tak-1 under control conditions, male accession demonstrated distinct and more rapid stress sensing and signaling. These differences in stress response appeared to be strongly related to sex-specific plasticity influenced by geoclimatic origin. Furthermore, we established distinct protein gene ages and genomic distribution trends, underscoring the importance of protein diversification over time. This study provides an evolutionary perspective on sexual divergence and stress emergence employing a systems biology approach, which allowed for the establishment of global and sex-specific interaction networks in the stress response.

Evolution of the sporophyte shoot axis and functions of TALE HD transcription factors in stem development

The stem is one of the major organs in seed plants and is important for plant survival as well as in agriculture. However, due to the lack of clear external landmarks in many species, its developmental and evolutionary processes are understudied compared to other organs. Recent approaches tackling these problems, especially those focused on KNOX1 and BLH transcription factors belonging to the TALE homeodomain superfamily have started unveiling the patterning process of nodes and internodes by connecting previously accumulated knowledge on lateral organ regulators. Fossil records played crucial roles in understanding the evolutionary process of the stem. The aim of this review is to introduce how the stem evolved from ancestorial sporophyte axes and to provide frameworks for future efforts in understanding the developmental process of this elusive but pivotal organ.

Deciphering the evolutionary development of the "Chinese lantern" within Solanaceae

MAIN CONCLUSION

The key genetic variation underlying the evo-devo of ICS in Solanaceae may be further pinpointed using an integrated strategy of forward and reverse genetics studies under the framework of phylogeny. The calyx of Physalis remains persistent throughout fruit development. Post-flowering, the fruiting calyx is inflated rapidly to encapsulate the berry, giving rise to a "Chinese lantern" structure called inflated calyx syndrome (ICS). It is unclear how this novelty arises. Over the past 2 decades, the role of MADS-box genes in the evolutionary development (evo-devo) of ICS has mainly been investigated within Solanaceae. In this review, we analyze the main achievements, challenges, and new progress. ICS acts as a source for fruit development, provides a microenvironment to protect fruit development, and assists in long-distance fruit dispersal. ICS is a typical post-floral trait, and the onset of its development is triggered by specific developmental signals that coincide with fertilization. These signals can be replaced by exogenous gibberellin and cytokinin application. MPF2-like heterotopic expression and MBP21-like loss have been proposed to be two essential evolutionary events for ICS origin, and manipulating the related MADS-box genes has been shown to affect the ICS size, sepal organ identity, and/or male fertility, but not completely disrupt ICS. Therefore, the core genes or key links in the ICS biosynthesis pathways may have undergone secondary mutations during evolution, or they have not yet been pinpointed. Recently, we have made some encouraging progress in acquiring lantern mutants in Physalis floridana. In addition to technological innovation, we propose an integrated strategy to further analyze the evo-devo mechanisms of ICS in Solanaceae using forward and reverse genetics studies under the framework of phylogeny.

Interspecific transfer of genetic information through polyploid bridges

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

Elucidation of arsenic detoxification mechanism in Marchantia polymorpha: The role of ACR3

The arsenic-specific ACR3 transporter plays pivotal roles in As detoxification in yeast and a group of ancient tracheophytes, the ferns. Despite putative ACR3 genes being present in the genomes of bryophytes, whether they have the same relevance also in this lineage is currently unknown. In this study, we characterized the MpACR3 gene from the bryophyte Marchantia polymorpha L. through a multiplicity of functional approaches ranging from phylogenetic reconstruction, expression analysis, loss- and gain-of-function as well as genetic complementation with an MpACR3 gene tagged with a fluorescent protein. Genetic complementation demonstrates that MpACR3 plays a pivotal role in As tolerance in M. polymorpha, with loss-of-function Mpacr3 mutants being hypersensitive and MpACR3 overexpressors more tolerant to As. Additionally, MpACR3 activity regulates intracellular As concentration, affects its speciation and controls the levels of intracellular oxidative stress. The MpACR3::3xCitrine appears to localize at the plasma membrane and possibly in other endomembrane systems. Taken together, these results demonstrate the pivotal function of ACR3 detoxification in both sister lineages of land plants, indicating that it was present in the common ancestor to all embryophytes. We propose that Mpacr3 mutants could be used in developing countries as low-cost and low-technology visual bioindicators to detect As pollution in water.

Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land

Land plants are celebrated as one of the three great instances of complex multicellularity, but new phylogenomic and phenotypic analyses are revealing deep evolutionary roots of multicellularity among algal relatives, prompting questions about the causal basis of this major evolutionary transition.

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation

BACKGROUND

Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing notably to the Amazonian bioeconomy. The seed pulp is utilized in desserts and beverages, and its seed butter is used in cosmetics. Here, we present the sequenced telomere-to-telomere genome of cupuassu, disclosing its genomic structure, evolutionary features, and phylogenetic relationships within the Malvaceae family.

FINDINGS

The cupuassu genome spans 423 Mb, encodes 31,381 genes distributed in 10 chromosomes, and exhibits approximately 65% gene synteny with the Theobroma cacao genome, reflecting a conserved evolutionary history, albeit punctuated with unique genomic variations. The main changes are pronounced by bursts of long-terminal repeat retrotransposons at postspecies divergence, retrocopied and singleton genes, and gene families displaying distinctive patterns of expansion and contraction. Furthermore, positively selected genes are evident, particularly among retained and dispersed tandem and proximal duplicated genes associated with general fruit and seed traits and defense mechanisms, supporting the hypothesis of potential episodes of subfunctionalization and neofunctionalization following duplication, as well as impact from distinct domestication process. These genomic variations may underpin the differences observed in fruit and seed morphology, ripening, and disease resistance between cupuassu and the other Malvaceae species.

CONCLUSIONS

The cupuassu genome offers a foundational resource for both breeding improvement and conservation biology, yielding insights into the evolution and diversity within the genus Theobroma.