Fern genomes elucidate land plant evolution and cyanobacterial symbioses

Sexual reproduction in land plants: an evolutionary perspective

KEY MESSAGE

We link key aspects of land plant reproductive evolution and detail how successive molecular changes leading to novel tissues and organs require co-evolution of communication systems between tissues. The transition of water-dependent reproduction of algae to mechanisms with very limited water dependence in many land plant lineages allowed plants to colonize diverse terrestrial environments, leading to the vast variety of extant plant species. The emergence of modified cell types, novel tissues, and organs enabled this transition; their origin is associated with the co-evolution of novel or adapted molecular communication systems and gene regulatory networks. In the light of an increasing number of genome sequences in combination with the establishment of novel genetic model organisms from diverse green plant lineages, our knowledge and understanding about the origin and evolution of individual traits that arose in a concerted way increases steadily. For example, novel members of gene families in signaling pathways emerged for communication between gametes and gametophytes with additional tissues surrounding the gametes. Here, we provide a comprehensive overview on the origin and evolution of reproductive novelties such as pollen grains, immobile sperms, ovules and seeds, carpels, gamete/gametophytic communication systems, double fertilization, and the molecular mechanisms that have arisen anew or have been co-opted during evolution, including but not limited to the incorporation of phytohormones, reactive oxygen species and redox signaling as well as small RNAs in regulatory modules that contributed to the evolution of land plant sexual reproduction.

The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae

Red algae are an ancient eukaryotic lineage that were among the first to evolve multicellularity. Although they share a common origin with modern-day plants and display complex multicellular development, comprehensive genome data from the most highly evolved red algal groups remain scarce. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a complex red seaweed in the Rhodomelaceae family of the Ceramiales-the largest and most diverse order of red algae. Contrary to the view that red algal genomes are typically small, we report significant genome size expansion in Bostrychia and other Ceramiales, which represents one of at least three independent expansion events in red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole-genome duplications, but in Bostrychia rather stem from the proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with its enlarged genome, Bostrychia has an increased gene content shaped by de novo gene emergence and amplified gene families in common with other Ceramiales, providing insight into the genetic adaptations underpinning this successful and species-rich order. Finally, our sex-specific assemblies resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, each sex chromosome harbors a three amino acid loop extension homeodomain (TALE-HD) transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this red seaweed lineage can provide insight into the evolutionary origins and universal principles underpinning complex multicellularity.

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.

The basal level of salicylic acid represses the PRT6 N-degron pathway to modulate root growth and stress response in rice

Maintaining a stable basal level of salicylic acid (SA) is crucial for plant growth, development, and stress response, although basal levels of SA vary significantly among plant species. However, the molecular mechanisms by which basal SA regulates plant growth and stress response remain to be clarified. In this study, we performed a genetic screen to identify suppressors of the root growth defect in Osaim1, a rice mutant deficient in basal SA biosynthesis. We found that mutation of the E3 ligase OsPRT6, a key component of the Arg/N-degron pathway, can rescue the root growth defect of Osaim1. Further analysis revealed that OsWRKY62 and OsWRKY76 act as substrates of the OsPRT6 N-degron pathway to modulate root growth. We demonstrated that reducing the basal SA level activates the PRT6 N-degron pathway and that basal SA modulates the stress response in part through the PRT6 N-degron pathway. Importantly, the effects of basal SA levels on the PRT6 N-degron pathway are conserved across plant species. Taken together, these findings reveal a novel regulatory mechanism by which basal SA represses the PRT6 N-degron pathway to modulate root growth and abiotic stress response in rice.

Genome-wide identification of five fern bHLH families and functional analysis of bHLHs in lignin biosynthesis in Alsophila spinulosa

BACKGROUND

The basic helix-loop-helix (bHLH) transcription factors are involved in the biosynthesis of various secondary metabolites. However, genome-wide studies on the bHLH gene family in ferns and their role in lignin biosynthesis remain limited. As the second largest group of vascular plants, ferns are of significant interest for understanding plant evolution and secondary metabolism. Among ferns, Alsophila spinulosa stands out as one of the few tree ferns with a distinctive trunk structure. Investigating the genes potentially regulating lignin biosynthesis in A. spinulosa offers valuable insights into the growth and development mechanisms of its trunk, which is pivotal for the overall architecture and function of the plant.

RESULTS

In this study, we conducted a systematic study of bHLH gene families in five ferns, including 186 in A. spinulosa, 130 in A. capillus, 107 in A. filiculoides, 71 in S. cucullata, and 67 in C. richardii. Based on phylogenetic analysis, all bHLH genes were classified into 28 subgroups. The number of bHLH members in different ferns was closely related to their growth patterns and life habits, with the number in tree ferns being much larger than in other ferns. In addition, we identified tandem duplication in C. richardii and A. capillus as a key driver of their bHLH gene diversity, whereas in A. spinulosa, segmental duplication contributed more to gene expansion and evolution. Most of the bHLH genes in ferns are in a state of purifying selection. Additionally, tissue-specific expression patterns of AspbHLH genes suggest diverse functional roles in plant growth, development, and metabolite synthesis. We further focused on three genes, AspbHLH80, AspbHLH120, and AspbHLH185, which are specifically highly expressed in xylem. Results from weighted gene co-expression network analysis (WGCNA) and downstream target gene prediction indicate their potential regulatory roles in lignin biosynthesis.

CONCLUSION

This study presents a comprehensive genomic analysis of the bHLH gene family in five fern species. We found a strong correlation between bHLH gene number and fern growth morphology, with tree ferns exhibiting a significantly higher number of bHLH genes. Tandem duplications were key to bHLH gene diversity in C. richardii, A. capillus, and A. spinulosa, while segmental duplications contributed more to bHLH gene expansion in A. spinulosa. Evolutionary analysis indicated most fern bHLH genes are under purifying selection. Tissue-specific expression patterns of AspbHLH genes suggest roles in growth, development, and secondary metabolism. Furthermore, WGCNA and target gene predictions highlight three genes (AspbHLH80, AspbHLH120, and AspbHLH185) potentially involved in lignin biosynthesis. Overall, this work provides key insights into the mechanisms of wood formation in ferns and advances our understanding of plant secondary metabolism.

Functional genomic perspectives on plant terrestrialization

Plant evolutionary research has made leaps in exploring the deep evolutionary roots of embryophytes. A solid phylogenomic framework was established, allowing evolutionary inferences. Comparative genomic approaches revealed that many genes coding for transcription factors, morphogenetic regulators, specialized metabolic enzymes, phytohormone signaling, and more are not innovations of land plants but have a deep streptophyte algal ancestry. Are these just spurious homologs, or do they actualize traits we deem important in embryophytes? Building on streptophyte algae genome data, current endeavors delve into the functional significance of whole cohorts of homologs by leveraging the power of comparative high-throughput approaches. This ushered in the identification of recurrent themes in function, ultimately providing a functional genomic definition for the toolkit of plant terrestrialization.

The Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment

Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome-environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.

The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal

PREMISE

Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.

METHODS

We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.

RESULTS

Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.

CONCLUSIONS

These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.

Time-resolved oxidative signal convergence across the algae-embryophyte divide

The earliest land plants faced a significant challenge in adapting to environmental stressors. Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood. Here, we combine time-course stress profiling using photophysiology, transcriptomics on 2.7 Tbp of data, and metabolite profiling analyses on 270 distinct samples, to study stress kinetics across three 600-million-year-divergent streptophytes. Through co-expression analysis and Granger causal inference we predict a gene regulatory network that retraces a web of ancient signal convergences at ethylene signaling components, osmosensors, and chains of major kinases. These kinase hubs already integrated diverse environmental inputs since before the dawn of plants on land.

Genome-Wide Study of Plant-Specific PLATZ Transcription Factors and Functional Analysis of OsPLATZ1 in Regulating Caryopsis Development of Rice (Oryza sativa L.)

Plant A/T-rich sequence- and zinc-binding protein (PLATZ) is a type of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. This family is essential for plant growth, development, and stress response. In this study, 15 OsPLATZs were identified in the rice genome with complete PLATZ-conserved domains by CD-search, similar to those found in angiosperms. Multi-species phylogenetic analysis showed that PLATZs were conserved in photosynthetic organisms, and an evolutionary branch unique to angiosperms was identified among members of the PLATZ family. Fifteen OsPLATZs were represented by five groups, each with distinct characteristics. An analysis of protein structures and sequence motifs showed that OsPLATZs were similar within groups, but varied between them. The expression profile and qRT-PCR results showed that OsPLATZs had distinct expression patterns in different tissues, with some responding to stress induction. Most of the OsPLATZs localized to the nuclei, and were predicted to bind to DNA sequences by AlphaFold3, suggesting that they likely function as conventional transcription factors. We also identified OsPLATZ1, a caryopsis-specific gene that regulates grain filling and caryopsis development in rice. This research lays the foundation for exploring the structural diversity, evolutionary traits, expression profile, and possible roles of PLATZ transcription factors in rice.

The power of independent generations in plants

This article is a Commentary on Blake‐Mahmud et al. (2025), 245: 885–898.

The rise of CLAVATA: evidence for CLAVATA3 and WOX signaling in the fern gametophyte

CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides are 12-13 amino acid-long peptides that serve as positional signals in plants. The core CLE signaling module consists of a CLE peptide and a leucine-rich repeat receptor-like kinase, but in flowering plants, WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors are also incorporated to form negative feedback loops that regulate stem cell maintenance in the shoot and root. It is not known when WOX genes were co-opted into CLE signaling pathways, only that mosses and liverworts do not require WOX for CLE-regulated stem cell activities. We identified 11 CLE-encoding genes in the Ceratopteris genome, including one (CrCLV3) most similar to shoot meristem CLE peptide CLAVATA3. We performed the first functional characterization of a fern CLE using techniques including RNAi knockdown and synthetic peptide dosage. We found that CrCLV3 promotes cell proliferation and stem cell identity in the gametophyte meristem. Importantly, we provide evidence for CrCLV3 regulation of the WOX gene CrWOXA during the developmental stage when female gametangium formation begins. These discoveries open a new avenue for CLE peptide research in the fern and clarify the evolutionary timeline of CLE-WOX signaling in land plants.

Comparative analysis of Hymenasplenium (Aspleniaceae) chloroplast genomes from China

Hymenasplenium is one of the two genera in the large fern family Aspleniaceae. A previous study explored the molecular phylogeny of this genus using several chloroplast DNA fragments and identified three major clades, one of which is the monophyletic Old World clade with southwestern China as its diversity center. To date, there were only a few studies conducted on chloroplast genomes in Hymenasplenium or Aspleniaceae, limiting the understanding of the plastome features and its role in evolution of this group. Here, we studied the complete chloroplast genomes of 12 Hymenasplenium species covering all four subclades of the Old World clade distributed in China. The length of the Hymenasplenium plastomes ranged from 151,617 to 151,930 bp, and contained 129 genes in total, comprising 87 protein-coding, 34 tRNA, and eight rRNA genes. The GC content ranged from 41.8% to 42.1%. Comparative analyses of the Hymenasplenium chloroplast genomes displayed conserved genomic structure and identical gene arrangement. A total of 1,375 simple sequence repeats and 1,639 large repeats were detected. In addition, we detailed hypervariable regions that can be helpful for further phylogenetic research and species delimitation in Hymenasplenium. Furthermore, we supported phylogenetic relationships among major groups as well as possible cryptic speciation found in previous research in the genus. Our study provides new insights into evolutionary history and basic resources for phylogenetic and taxonomic studies of the genus Hymenasplenium.

Evolution of Plant Genome Size and Composition

The rapid development of sequencing technology has led to an explosion of plant genome data, opening up more opportunities for research in the field of comparative evolutionary analysis of plant genomes. In this review, we focus on changes in plant genome size and composition, examining the effects of polyploidy, whole-genome duplication, and alternations in transposable elements on plant genome architecture and evolution, respectively. In addition, to address gaps in the available information, we also collected and analyzed 234 representative plant genome data as a supplement. We aim to provide a comprehensive, up-to-date summary of information on plant genome architecture and evolution in this review.

Efficient gene editing of a model fern species through gametophyte-based transformation

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species through gametophytes due to the complex characteristics of fern genomes, genetics, and physiology. Here, we established a protocol for gametophyte-based screening of single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas9-mediated gene knockout in a model fern species, Ceratopteris richardii. We utilized the C. richardii ACTIN promoter to drive sgRNA expression and the enhanced CaMV 35S promoter to drive the expression of Streptococcus pyogenes Cas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes, such as Nucleotidase/phosphatase 1 (CrSAL1) and Phytoene Desaturase (CrPDS), which resulted in an albino phenotype in C. richardii. Knockout of CrSAL1 resulted in significantly (P < 0.05) reduced stomatal conductance (gs), leaf transpiration rate (E), guard cell length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover, CrSAL1 overexpressing plants showed significantly increased net photosynthetic rate (A), gs, and E as well as most of the stomatal traits and ABA-induced ROS production in guard cells compared to the wild-type (WT) plants. Taken together, our optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery, and agricultural applications.

Current and future perspectives for enhancing our understanding of the evolution of plant metabolism

The special issue 'The evolution of plant metabolism' has brought together original research, reviews and opinions that cover various aspects from the full breath of plant metabolism including its interaction with the environment including other species. Here, we briefly summarize these efforts and attempts to extract a consensus opinion of the best manner in which to tackle this subject both now and in the future. This article is part of the theme issue 'The evolution of plant metabolism'.

Conserved carotenoid pigmentation in reproductive organs of Charophyceae

Sexual reproduction in Charophyceae abounds in complex traits. Their gametangia develop as intricate structures, with oogonia spirally surrounded by envelope cells and richly pigmented antheridia. The red-probably protectant-pigmentation of antheridia is conserved across Charophyceae. Chara tomentosa is, however, unique in exhibiting this pigmentation and also in vegetative tissue. Here, we investigated the two sympatric species, C. tomentosa and Chara baltica, and compared their molecular chassis for pigmentation. Using reversed phase C30 high performance liquid chromatography (RP-C30-HPLC), we uncover that the major pigments are β-carotene, δ-carotene and γ-carotene; using headspace solid-phase microextraction coupled to gas chromatography equipped with a mass spectrometer (HS-SPME-GC-MS), we pinpoint that the unusually large carotenoid pool in C. tomentosa gives rise to diverse volatile apocarotenoids, including abundant 6-methyl-5-hepten-2-one. Based on transcriptome analyses, we uncover signatures of the unique biology of Charophycaee and genes for pigment production, including monocyclized carotenoids. The rich carotenoid pool probably serves as a substrate for diverse carotenoid-derived metabolites, signified not only by (i) the volatile apocarotenoids we detected but (ii) the high expression of a gene coding for a cytochrome P450 enzyme related to land plant proteins involved in the biosynthesis of carotenoid-derived hormones. Overall, our data shed light on a key protection strategy of sexual reproduction in the widespread group of macroalgae. The genetic underpinnings of this are shared across hundreds of millions of years of plant and algal evolution. This article is part of the theme issue 'The evolution of plant metabolism'.

Biotic interactions, evolutionary forces and the pan-plant specialized metabolism

Plant specialized metabolism has a complex evolutionary history. Some aspects are conserved across the green lineage, but many metabolites are unique to certain lineages. The network of specialized metabolism continuously diversified, simplified or reshaped during the evolution of streptophytes. Many routes of pan-plant specialized metabolism are involved in plant defence. Biotic interactions are recalled as major drivers of lineage-specific metabolomic diversification. However, the consequences of this diversity of specialized metabolism in the context of plant terrestrialization and land plant diversification into the major lineages of bryophytes, lycophytes, ferns, gymnosperms and angiosperms remain only little explored. Overall, this hampers conclusions on the evolutionary scenarios that shaped specialized metabolism. Recent efforts have brought forth new streptophyte model systems, an increase in genetically accessible species from distinct major plant lineages, and new functional data from a diversity of land plants on specialized metabolic pathways. In this review, we will integrate the recent data on the evolution of the plant immune system with the molecular data of specialized metabolism and its recognition. Based on this we will provide a contextual framework of the pan-plant specialized metabolism, the evolutionary aspects that shape it and the impact on adaptation to the terrestrial environment.This article is part of the theme issue 'The evolution of plant metabolism'.

Bona Fide Plant Steroid Receptors are Innovated in Seed Plants and Angiosperms through Successive Whole-Genome Duplication Events

Whole-genome duplication (WGD) events are widespread in plants and animals, thus their long-term evolutionary contribution has long been speculated, yet a specific contribution is difficult to verify. Here, we show that ɛ-WGD and ζ-WGD contribute to the origin and evolution of bona fide brassinosteroid (BR) signaling through the innovation of active BR biosynthetic enzymes and active BR receptors from their respective ancestors. We found that BR receptors BRI1 (BR INSENSITIVE 1) and BRL1/3 (BRI1-LIKES 1/3) derived by ɛ-WGD and ζ-WGD, which occurred in the common ancestor of angiosperms and seed plants, respectively, while orphan BR receptor BRL2 first appeared in stomatophytes. Additionally, CYP85A enzymes synthesizing the bioactive BRs derived from a common ancestor of seed plants, while its sister enzymes CYP90 synthesizing BR precursors presented in all land plants, implying possible ligand-receptor coevolution. Consistently, the island domains (IDs) responsible for BR perception in BR receptors were most divergent among different receptor branches, supporting ligand-driven evolution. As a result, BRI1 was the most diversified BR receptor in angiosperms. Importantly, relative to the BR biosynthetic DET2 gene presented in all land plants, BRL2, BRL1/3 and BRI1 had high expression in vascular plants ferns, gymnosperms and angiosperms, respectively. Notably, BRI1 is the most diversified BR receptor with the most abundant expression in angiosperms, suggesting potential positive selection. Therefore, WGDs initiate a neofunctionalization process diverged by ligand-perception and transcriptional expression, which might optimize both BR biosynthetic enzymes and BR receptors, likely contributing to the evolution of land plants, especially seed plants and angiosperms.

Biosynthesis and differential spatial distribution of the 3-deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant-cyanobacteria symbiosis exposed to cold

Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2 in their leaf cavities, Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanidin (DA) accumulation, rare in angiosperms and of unknown function. To understand DA accumulation upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a new Azolla filiculoides genome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses. Azolla sp. Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation and Nostoc azollae transcript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery. The high transcript accumulation upon cold acclimation of AfDFR1 encoding a flavanone 4-reductase active in vitro suggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation.

An efficient and effective RNA extraction protocol for ferns

Premise

The extraction of high-quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial.

Methods

We developed a cetyltrimethylammonium bromide (CTAB)-based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns-a lineage of plants high in secondary compounds-and in an array of tissue types. Two alternative options (precipitation vs. clean-up without intermediate precipitation) are presented, both of which yield high-quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9-2.1 and OD 260/230 > 1.6, and RNA integrity numbers >7.

Conclusions

This study presents an efficient protocol for the extraction of high-quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap.

Identification of a novel gene, Bryophyte Co-retained Gene 1, that has a positive role in desiccation tolerance in the moss Physcomitrium patens

The moss Physcomitrium patens is a model system for the evolutionary study of land plants, and as such, it may contain as yet unannotated genes with functions related to the adaptation to water deficiency that was required during the water-to-land transition. In this study, we identified a novel gene, Bryophyte Co-retained Gene 1 (BCG1), in P. patens that is responsive to dehydration and rehydration. Under de- and rehydration treatments, BCG1 was significantly co-expressed with DHNA, which encodes a dehydrin (DHN). Examination of previous microarray data revealed that BCG1 is highly expressed in spores, archegonia (female reproductive organ), and mature sporophytes. In addition, the bcg1 mutant showed reduced dehydration tolerance, and this was accompanied by a relatively low level of chlorophyll content during recovery. Comprehensive transcriptomics uncovered a detailed set of regulatory processes that were affected by the disruption to BCG1. Experimental evidence showed that BCG1 might function in antioxidant activity, the abscisic acid pathway, and in intracellular Ca2+ homeostasis to resist desiccation. Overall, our results provide insights into the role of a bryophyte co-retained gene in desiccation tolerance.

The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes

A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.

Discovery of bifunctional diterpene cyclases/synthases in bacteria supports a bacterial origin for the plant terpene synthase gene family

Land plants are well-known producers of terpenoids that play diverse roles in plant-environment interactions. The vast chemical diversity of terpenoids is initiated by terpene synthases. Plants contain a distinct mid-sized terpene synthase gene family termed TPS, which appears to have an ancient origin in a fused bacterial Class I (di)terpene synthase (TS) and Class II diterpene cyclase (DTC), corresponding to the catalytically relevant α-domain and βγ-didomains, respectively. However, while such fused tridomain bifunctional (Class I/II) diterpene cyclases/synthases (DCSs) have been found in plants (and fungi), no examples have been reported from bacteria, leaving the origin of the fusion event initiating the TPS gene family opaque. Here, the discovery of such tridomain bifunctional DCSs in bacteria is reported. Extensive genome mining unearthed five putative bacterial DCSs, with biochemical characterization revealing the expected bifunctional activity for three. The most intriguing was CseDCS from Candidatus sericytochromatia bacterium, which produces ent-kaurene, an intermediate in plant hormone biosynthesis, as this is the hypothesized activity for the ancestral TPS. Unlike the extant functionally equivalent TPSs, it was possible to split CseDCS into separate, independently acting DTC and TS, with the first producing the expected ent-copalyl diphosphate (CPP), serving as a CPP synthase (CPS), while the second converts this to ent-kaurene, serving as a kaurene synthase (KS). Nevertheless, sequence alignment and mutation analysis revealed intriguing similarities between this cyanobacterial fused CPS-KS and functionally equivalent TPSs. Regardless of the exact relationship, the discovery of fused bifunctional DCSs in bacteria supports the hypothesized origin of the plant TPS family from such a bacterial gene.

Large-scale analysis of the PAC domain structure of arogenate dehydratases reveals their evolutionary patterns in angiosperms

Arogenate dehydratase (ADT) is the key limiting enzyme of plant phenylalanine biosynthesis, but some ADTs display a prephenate decarboxylase/dehydratase activity-conferring (PAC) domain. The genome resources of 70 species were employed to identify genes and outline their characteristics, especially the number and type of PAC domain structures. We obtained 522 ADTs, and their size, exon number, amino acid number and putative protein isoelectric point greatly varied from 306 to 2520 bp, 1 to 15, 101 to 839 and 4.37 to 11.18, respectively. We classified the ADTs into Class α (without a PAC domain) (115, 22.0 %), β (with a type I PAC domain) (244, 46.7 %) and γ (with a type II PAC domain) (163, 31.2 %), and their distribution frequencies exhibited large differences among various branches of angiosperms. We found that Class γ members are more conserved than Class β members, although they commonly experienced multiple duplication events and strong purifying selection, which resulted in a small number, and the putative origin order was from Class α to β and then to γ. In addition, the co-occurrence of both Class β and γ members could ensure the survival of angiosperms, while their optimized composition and strategically intertwined regulation may facilitate core eudicot success.

Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha

Chloroplasts develop from undifferentiated plastids in response to light. In angiosperms, after the perception of light, the Elongated Hypocotyl 5 (HY5) transcription factor initiates photomorphogenesis, and two families of transcription factors known as GOLDEN2-LIKE (GLK) and GATA are considered master regulators of chloroplast development. In addition, the MIR171-targeted SCARECROW-LIKE GRAS transcription factors also impact chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Using the model liverwort Marchantia polymorpha, we show that GLK controls chloroplast biogenesis, and HY5 shows a small conditional effect on chlorophyll content. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that MpGLK has a broader set of targets than has been reported in angiosperms. We also identified a functional GLK homolog in green algae. In summary, our data support the hypothesis that GLK carries out a conserved role relating to chloroplast biogenesis in land plants and green algae.

MYB-related transcription factors control chloroplast biogenesis

Chloroplast biogenesis is dependent on master regulators from the GOLDEN2-LIKE (GLK) family of transcription factors. However, glk mutants contain residual chlorophyll, indicating that other proteins must be involved. Here, we identify MYB-related transcription factors as regulators of chloroplast biogenesis in the liverwort Marchantia polymorpha and angiosperm Arabidopsis thaliana. In both species, double-mutant alleles in MYB-related genes show very limited chloroplast development, and photosynthesis gene expression is perturbed to a greater extent than in GLK mutants. Genes encoding enzymes of chlorophyll biosynthesis are controlled by MYB-related and GLK proteins, whereas those allowing CO2 fixation, photorespiration, and photosystem assembly and repair require MYB-related proteins. Regulation between the MYB-related and GLK transcription factors appears more extensive in A. thaliana than in M. polymorpha. Thus, MYB-related and GLK genes have overlapping as well as distinct targets. We conclude that MYB-related and GLK transcription factors orchestrate chloroplast development in land plants.

Evaluation of arsenic phytoremediation potential in Azolla filiculoides Lam. plants under low pH stress conditions

The Azolla filiculoides plants were challenged with different arsenic (As) concentration under low pH stress conditions. The growth rate and doubling time of the plants were severely affected by higher As treatments at pH 5.00 when compared with stress pH 4.75 treatments. Hence, pH 5.00 was considered for further studies. In 10-30 μM As treated cultures, after 6 days, the relative growth rate (RGR) of Azolla plants was significantly reduced and in higher concentration of As, the RGR was negatively regulated. The root trait parameters were also significantly affected by increasing concentrations of As. Further, photosynthetic performance indicators also show significant decline with increasing As stress. Overall, the plants treated with 40 and 50 μM of As displayed stress phenotypes like negative RGR, reduced doubling time and root growth, browning of leaves and root withering. The total proline, H2O2, POD and Catalase activities were significantly affected by As treatments. Meantime, 30 μM of As treated cultures displayed 15 μg/g/Fw As accumulation and moderate growth rate. Thus, the Azolla plants are suitable for the phytoremediation of As (up to 30 μM concentration) in the aquatic environment under low pH conditions (5.00). Furthermore, the transcriptome studies on revealed that the importance of positively regulated transporters like ACR3, AceTr family, ABC transporter super family in As (10 μM) stress tolerance, uptake and accumulation. The transporters like CPA1, sugar transporters, PiT were highly down-regulated. Further, expression analysis showed that the MATE1, CIP31, HAC1 and ACR3 were highly altered during the As stress conditions.

A conserved GRAS-domain transcriptional regulator links meristem indeterminacy to sex determination in Ceratopteris gametophytes

Most land plants alternate between generations of sexual gametophytes and asexual sporophytes. Unlike seed plants, fern gametophytes are free living and grow independently of their sporophytes. In homosporous ferns such as Ceratopteris, gametophytes derived from genetically identical spores exhibit sexual dimorphism, developing as either males or hermaphrodites. Males lack meristems and promote cell differentiation into sperm-producing antheridia. In contrast, hermaphrodites initiate multicellular meristems that stay undifferentiated, sustain cell division and prothallus expansion, and drive the formation of egg-producing archegonia. Once initiating the meristem, hermaphrodites secrete the pheromone antheridiogen, which triggers neighboring slower-growing gametophytes to develop as males, while the hermaphrodites themselves remain insensitive to antheridiogen. This strategy promotes outcrossing and prevents all individuals in the colony from becoming males. This study reveals that an evolutionarily conserved GRAS-domain transcriptional regulator (CrHAM), directly repressed by Ceratopteris microRNA171 (CrmiR171), promotes meristem development in Ceratopteris gametophytes and determines the male-to-hermaphrodite ratio in the colony. CrHAM preferentially accumulates within the meristems of hermaphrodites but is excluded from differentiated antheridia. CrHAM sustains meristem proliferation and cell division through conserved hormone pathways. In the meantime, CrHAM inhibits the antheridiogen-induced conversion of hermaphrodites to males by suppressing the male program expression and preventing meristem cells from differentiating into sperm-producing antheridia. This finding establishes a connection between meristem indeterminacy and sex determination in ferns, suggesting both conserved and diversified roles of meristem regulators in land plants.

Asgard archaea defense systems and their roles in the origin of eukaryotic immunity

Dozens of new antiviral systems have been recently characterized in bacteria. Some of these systems are present in eukaryotes and appear to have originated in prokaryotes, but little is known about these defense mechanisms in archaea. Here, we explore the diversity and distribution of defense systems in archaea and identify 2610 complete systems in Asgardarchaeota, a group of archaea related to eukaryotes. The Asgard defense systems comprise 89 unique systems, including argonaute, NLR, Mokosh, viperin, Lassamu, and CBASS. Asgard viperin and argonaute proteins have structural homology to eukaryotic proteins, and phylogenetic analyses suggest that eukaryotic viperin proteins were derived from Asgard viperins. We show that Asgard viperins display anti-phage activity when heterologously expressed in bacteria. Eukaryotic and bacterial argonaute proteins appear to have originated in Asgardarchaeota, and Asgard argonaute proteins have argonaute-PIWI domains, key components of eukaryotic RNA interference systems. Our results support that Asgardarchaeota played important roles in the origin of antiviral defense systems in eukaryotes.

Origin and Evolution of the Azolla Superorganism

Azolla is the only plant with a co-evolving nitrogen-fixing (diazotrophic) cyanobacterial symbiont (cyanobiont), Nostoc azollae, resulting from whole-genome duplication (WGD) 80 million years ago in Azolla's ancestor. Additional genes from the WGD resulted in genetic, biochemical, and morphological changes in the plant that enabled the transmission of the cyanobiont to successive generations via its megaspores. The resulting permanent symbiosis and co-evolution led to the loss, downregulation, or conversion of non-essential genes to pseudogenes in the cyanobiont, changing it from a free-living organism to an obligate symbiont. The upregulation of other genes in the cyanobiont increased its atmospheric dinitrogen fixation and the provision of nitrogen-based products to the plant. As a result, Azolla can double its biomass in less than two days free-floating on fresh water and sequester large amounts of atmospheric CO2, giving it the potential to mitigate anthropogenic climate change through carbon capture and storage. Azolla's biomass can also provide local, low-cost food, biofertiliser, feed, and biofuel that are urgently needed as our population increases by a billion every twelve years. This paper integrates data from biology, genetics, geology, and palaeontology to identify the location, timing and mechanism for the acquisition of a co-evolving diazotrophic cyanobiont by Azolla's ancestor in the Late Cretaceous (Campanian) of North America.

The crane fly glycosylated triketide δ-lactone cornicinine elicits akinete differentiation of the cyanobiont in aquatic Azolla fern symbioses

The restriction of plant-symbiont dinitrogen fixation by an insect semiochemical had not been previously described. Here we report on a glycosylated triketide δ-lactone from Nephrotoma cornicina crane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genus Azolla. Only the glycosylated trans-A form of chemically synthesized cornicinine was active: 500 nM cornicinine in the growth medium turned all cyanobacterial filaments from Nostoc azollae inside the host leaf-cavities into akinetes typically secreting CTB-bacteriocins. Cornicinine further inhibited akinete germination in Azolla sporelings, precluding re-establishment of the symbiosis during sexual reproduction. It did not impact development of the plant Arabidopsis thaliana or several free-living cyanobacteria from the genera Anabaena or Nostoc but affected the fern host without cyanobiont. Fern-host mRNA sequencing from isolated leaf cavities confirmed high NH4-assimilation and proanthocyanidin biosynthesis in this trichome-rich tissue. After cornicinine treatment, it revealed activation of Cullin-RING ubiquitin-ligase-pathways, known to mediate metabolite signaling and plant elicitation consistent with the chlorosis phenotype, and increased JA-oxidase, sulfate transport and exosome formation. The work begins to uncover molecular mechanisms of cyanobiont differentiation in a seed-free plant symbiosis important for wetland ecology or circular crop-production today, that once caused massive CO2 draw-down during the Eocene geological past.

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.

Novel Types of Phyllobilins in a Fern - Molecular Reporters of the Evolution of Chlorophyll Breakdown in the Paleozoic Era

Breakdown of chlorophyll (Chl), as studied in angiosperms, follows the pheophorbide a oxygenase/phyllobilin (PaO/PB) pathway, furnishing linear tetrapyrroles, named phyllobilins (PBs). In an investigation with fern leaves we have discovered iso-phyllobilanones (iPBs) with an intriguingly rearranged and oxidized carbon skeleton. We report here a key second group of iPBs from the fern and on their structure analysis. Previously, these additional Chl-catabolites escaped their characterization, since they exist in aqueous media as mixtures of equilibrating isomers. However, their chemical dehydration furnished stable iPB-derivatives that allowed the delineation of the enigmatic structures and chemistry of the original natural catabolites. The structures of all fern-iPBs reflect the early core steps of a PaO/PB-type pathway and the PB-to-iPB carbon skeleton rearrangement. A striking further degradative chemical ring-cleavage was observed, proposed to consume singlet molecular oxygen (1O2). Hence, Chl-catabolites may play a novel active role in detoxifying cellular 1O2. The critical deviations from the PaO/PB pathway, found in the fern, reflect evolutionary developments of Chl-breakdown in the green plants in the Paleozoic era.

Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae

Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.

Control of leaf development in the water fern Ceratopteris richardii by the auxin efflux transporter CrPINMa in the CRISPR/Cas9 analysis

BACKGROUND

PIN-FORMED genes (PINs) are crucial in plant development as they determine the directionality of auxin flow. They are present in almost all land plants and even in green algae. However, their role in fern development has not yet been determined. This study aims to investigate the function of CrPINMa in the quasi-model water fern Ceratopteris richardii.

RESULTS

CrPINMa possessed a long central hydrophilic loop and characteristic motifs within it, which indicated that it belonged to the canonical rather than the non-canonical PINs. CrPINMa was positioned in the lineage leading to Arabidopsis PIN6 but not that to its PIN1, and it had undergone numerous gene duplications. CRISPR/Cas9 genome editing had been performed in ferns for the first time, producing diverse mutations including local frameshifts for CrPINMa. Plants possessing disrupted CrPINMa exhibited retarded leaf emergence and reduced leaf size though they could survive and reproduce at the same time. CrPINMa transcripts were distributed in the shoot apical meristem, leaf primordia and their vasculature. Finally, CrPINMa proteins were localized to the plasma membrane rather than other cell parts.

CONCLUSIONS

CRISPR/Cas9 genome editing is feasible in ferns, and that PINs can play a role in fern leaf development.

Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii

BACKGROUND AND AIMS

In flowering plants, regeneration can be achieved by a variety of approaches, and different sets of transcriptional factors are involved in these processes. However, regeneration in taxa other than flowering plants remains a mystery. Ceratopteris richardii is a representative fern capable of both direct and indirect organogenesis, and we aimed to investigate the genetics underlying the transition from callus proliferation to differentiation.

METHODS

Morphological and histological analyses were used to determine the type of regeneration involved. RNA sequencing and differential gene expression were used to investigate how the callus switches from proliferation to differentiation. Phylogenetic analysis and RNA in situ hybridization were used to understand whether transcriptional factors are involved in this transition.

KEY RESULTS

The callus formed on nascent leaves and subsequently developed the shoot pro-meristem and shoot meristem, thus completing indirect de novo shoot organogenesis in C. richardii. Genes were differentially expressed during the callus transition from proliferation to differentiation, indicating a role for photosynthesis, stimulus response and transmembrane signalling in this transition and the involvement of almost all cell layers that make up the callus. Transcriptional factors were either downregulated or upregulated, which were generally in many-to-many orthology with genes known to be involved in callus development in flowering plants, suggesting that the genetics of fern callus development are both conserved and divergent. Among them, an STM-like, a PLT-like and an ethylene- and salt-inducible ERF gene3-like gene were expressed simultaneously in the vasculature but not in the other parts of the callus, indicating that the vasculature played a role in the callus transition from proliferation to differentiation.

CONCLUSIONS

Indirect de novo shoot organogenesis could occur in ferns, and the callus transition from proliferation to differentiation required physiological changes, differential expression of transcriptional factors and involvement of the vasculature.

Adaptive evolution of chloroplast division mechanisms during plant terrestrialization

Despite extensive research, the origin and evolution of the chloroplast division machinery remain unclear. Here, we employ recently sequenced genomes and transcriptomes of Archaeplastida clades to identify the core components of chloroplast division and reconstruct their evolutionary histories, respectively. Our findings show that complete division ring structures emerged in Charophytes. We find that Glaucophytes experienced strong selection pressure, generating diverse variants adapted to the changing terrestrial environments. By integrating the functions of chloroplast division genes (CDGs) annotated in a workflow developed using large-scale multi-omics data, we further show that dispersed duplications acquire more species-specific functions under stronger selection pressures. Notably, PARC6, a dispersed duplicate CDG, regulates leaf color and plant growth in Solanum lycopersicum, demonstrating neofunctionalization. Our findings provide an integrated perspective on the functional evolution of chloroplast division machinery and highlight the potential of dispersed duplicate genes as the primary source of adaptive evolution of chloroplast division.

Sequence similarity networks bear out hierarchical relationships of green cytochrome P450

Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes. Here, we focused on land plants and algae to study the role of CYP diversification. CYPs, acting as monooxygenases, catalyze hydroxylation reactions crucial for specialized plant metabolic pathways, including detoxification and phytohormone production; the CYPome consists of one enormous superfamily that is divided into clans and families. Their evolutionary history speaks of high substrate promiscuity; radiation and functional diversification have yielded numerous CYP families. To understand the evolutionary relationships within the CYPs, we employed sequence similarity network analyses. We recovered distinct clusters representing different CYP families, reflecting their diversified sequences that we link to the prediction of functionalities. Hierarchical clustering and phylogenetic analysis further elucidated relationships between CYP clans, uncovering their shared deep evolutionary history. We explored the distribution and diversification of CYP subfamilies across plant and algal lineages, uncovering novel candidates and providing insights into the evolution of these enzyme families. This identified unexpected relationships between CYP families, such as the link between CYP82 and CYP74, shedding light on their roles in plant defense signaling pathways. Our approach provides a methodology that brings insights into the emergence of new functions within the CYP450 family, contributing to the evolutionary history of plants and algae. These insights can be further validated and implemented via experimental setups under various external conditions.

Proteome plasticity during Physcomitrium patens spore germination - from the desiccated phase to heterotrophic growth and reconstitution of photoautotrophy

The establishment of moss spores is considered a milestone in plant evolution. They harbor protein networks underpinning desiccation tolerance and accumulation of storage compounds that can be found already in algae and that are also utilized in seeds and pollen. Furthermore, germinating spores must produce proteins that drive the transition through heterotrophic growth to the autotrophic plant. To get insight into the plasticity of this proteome, we investigated it at five timepoints of moss (Physcomitrium patens) spore germination and in protonemata and gametophores. The comparison to previously published Arabidopsis proteome data of seedling establishment showed that not only the proteomes of spores and seeds are functionally related, but also the proteomes of germinating spores and young seedlings. We observed similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and β-oxidation and the glyoxylate cycle. However, there were also striking differences. For example, spores lacked any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis seeds, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss. The comparison of spores to Nicotiana tabacum pollen indicated similarities for example in regards to resistance to desiccation and hypoxia, but the overall developmental pattern did not align as in the case of seedling establishment and spore germination.

Phylogenomic insights into the first multicellular streptophyte

Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1,2,3,4 Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats.5,6 Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.

Shared infection strategy of a fungal pathogen across diverse lineages of land plants, the Fusarium example

Plants engage with a wide variety of microorganisms either in parasitic or mutualistic relationships, which have helped them to adapt to terrestrial ecosystems. Microbial interactions have driven plant evolution and led to the emergence of complex interaction outcomes via suppression of host defenses by evolving pathogens. The evolution of plant-microbe interactions is shaped by conserved host and pathogen gene modules and fast-paced lineage-specific adaptability which determines the interaction outcome. Recent findings from different microbes ranging from bacteria, oomycetes, and fungi suggest recurrent concepts in establishing interactions with evolutionarily distant plant hosts, but also clade-specific adaptation that ultimately contributes to pathogenicity. Here, we revisit some of the latest features that illustrate shared colonization strategies of the fungal pathogen Fusarium oxysporum on distant plant lineages and lineage-specific adaptability of mini-chromosomal units encoding effectors, for shaping host-specific pathogenicity in angiosperms.

The Mutational Road not Taken: Using Ancestral Sequence Resurrection to Evaluate the Evolution of Plant Enzyme Substrate Preferences

We investigated the flowering plant salicylic acid methyl transferase (SAMT) enzyme lineage to understand the evolution of substrate preference change. Previous studies indicated that a single amino acid replacement to the SAMT active site (H150M) was sufficient to change ancestral enzyme substrate preference from benzoic acid to the structurally similar substrate, salicylic acid (SA). Yet, subsequent studies have shown that the H150M function-changing replacement did not likely occur during the historical episode of enzymatic divergence studied. Therefore, we reinvestigated the origin of SA methylation preference here and additionally assessed the extent to which epistasis may act to limit mutational paths. We found that the SAMT lineage of enzymes acquired preference to methylate SA from an ancestor that preferred to methylate benzoic acid as previously reported. In contrast, we found that a different amino acid replacement, Y267Q, was sufficient to change substrate preference with others providing small positive-magnitude epistatic improvements. We show that the kinetic basis for the ancestral enzymatic change in substate preference by Y267Q appears to be due to both a reduced specificity constant, kcat/KM, for benzoic acid and an improvement in KM for SA. Therefore, this lineage of enzymes appears to have had multiple mutational paths available to achieve the same evolutionary divergence. While the reasons remain unclear for why one path was taken, and the other was not, the mutational distance between ancestral and descendant codons may be a factor.

Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns

BACKGROUND

Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events.

RESULTS

In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species.

CONCLUSIONS

Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research.

Extraordinary preservation of gene collinearity over three hundred million years revealed in homosporous lycophytes

Homosporous lycophytes (Lycopodiaceae) are a deeply diverged lineage in the plant tree of life, having split from heterosporous lycophytes (Selaginella and Isoetes) ~400 Mya. Compared to the heterosporous lineage, Lycopodiaceae has markedly larger genome sizes and remains the last major plant clade for which no chromosome-level assembly has been available. Here, we present chromosomal genome assemblies for two homosporous lycophyte species, the allotetraploid Huperzia asiatica and the diploid Diphasiastrum complanatum. Remarkably, despite that the two species diverged ~350 Mya, around 30% of the genes are still in syntenic blocks. Furthermore, both genomes had undergone independent whole genome duplications, and the resulting intragenomic syntenies have likewise been preserved relatively well. Such slow genome evolution over deep time is in stark contrast to heterosporous lycophytes and is correlated with a decelerated rate of nucleotide substitution. Together, the genomes of H. asiatica and D. complanatum not only fill a crucial gap in the plant genomic landscape but also highlight a potentially meaningful genomic contrast between homosporous and heterosporous species.

Genome-wide molecular evolution analysis of the GRF and GIF gene families in Plantae (Archaeplastida)

BACKGROUND

Plant growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) interact with each other and collectively have important regulatory roles in plant growth, development, and stress responses. Therefore, it is of great significance to explore the systematic evolution of GRF and GIF gene families. However, our knowledge and understanding of the role of GRF and GIF genes during plant evolution has been fragmentary.

RESULTS

In this study, a large number of genomic and transcriptomic datasets of algae, mosses, ferns, gymnosperms and angiosperms were used to systematically analyze the evolution of GRF and GIF genes during the evolution of plants. The results showed that GRF gene first appeared in the charophyte Klebsormidium nitens, whereas the GIF genes originated relatively early, and these two gene families were mainly expanded by segmental duplication events after plant terrestrialization. During the process of evolution, the protein sequences and functions of GRF and GIF family genes are relatively conservative. As cooperative partner, GRF and GIF genes contain the similar types of cis-acting elements in their promoter regions, which enables them to have similar transcriptional response patterns, and both show higher levels of expression in reproductive organs and tissues and organs with strong capacity for cell division. Based on protein-protein interaction analysis and verification, we found that the GRF-GIF protein partnership began to be established in pteridophytes and is highly conserved across different terrestrial plants.

CONCLUSIONS

These results provide a foundation for further exploration of the molecular evolution and biological functions of GRF and GIF genes.

Organellar phylogenomics of Ophioglossaceae fern genera

Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.

A mysterious cloak: the peptidoglycan layer of algal and plant plastids

The plastids of algae and plants originated on a single occasion from an endosymbiotic cyanobacterium at least a billion years ago. Despite the divergent evolution that characterizes the plastids of different lineages, many traits such as membrane organization and means of fission are universal-they pay tribute to the cyanobacterial origin of the organelle. For one such trait, the peptidoglycan (PG) layer, the situation is more complicated. Our view on its distribution keeps on changing and little is known regarding its molecular relevance, especially for land plants. Here, we investigate the extent of PG presence across the Chloroplastida using a phylogenomic approach. Our data support the view of a PG layer being present in the last common ancestor of land plants and its remarkable conservation across bryophytes that are otherwise characterized by gene loss. In embryophytes, the occurrence of the PG layer biosynthetic toolkit becomes patchier and the availability of novel genome data questions previous predictions regarding a functional coevolution of the PG layer and the plastid division machinery-associated gene FtsZ3. Furthermore, our data confirm the presence of penicillin-binding protein (PBP) orthologs in seed plants, which were previously thought to be absent from this clade. The 5-7 nm thick, and seemingly unchanged, PG layer armoring the plastids of glaucophyte algae might still provide the original function of structural support, but the same can likely not be said about the only recently identified PG layer of bryophyte and tracheophyte plastids. There are several issues to be explored regarding the composition, exact function, and biosynthesis of the PG layer in land plants. These issues arise from the fact that land plants seemingly lack certain genes that are believed to be crucial for PG layer production, even though they probably synthesize a PG layer.

Widespread horizontal gene transfer between plants and bacteria

Plants host a large array of commensal bacteria that interact with the host. The growth of both bacteria and plants is often dependent on nutrients derived from the cognate partners, and the bacteria fine-tune host immunity against pathogens. This ancient interaction is common in all studied land plants and is critical for proper plant health and development. We hypothesized that the spatial vicinity and the long-term relationships between plants and their microbiota may promote cross-kingdom horizontal gene transfer (HGT), a phenomenon that is relatively rare in nature. To test this hypothesis, we analyzed the Arabidopsis thaliana genome and its extensively sequenced microbiome to detect events of horizontal transfer of full-length genes that transferred between plants and bacteria. Interestingly, we detected 75 unique genes that were horizontally transferred between plants and bacteria. Plants and bacteria exchange in both directions genes that are enriched in carbohydrate metabolism functions, and bacteria transferred to plants genes that are enriched in auxin biosynthesis genes. Next, we provided a proof of concept for the functional similarity between a horizontally transferred bacterial gene and its Arabidopsis homologue in planta. The Arabidopsis DET2 gene is essential for biosynthesis of the brassinosteroid phytohormones, and loss of function of the gene leads to dwarfism. We found that expression of the DET2 homologue from Leifsonia bacteria of the Actinobacteria phylum in the Arabidopsis det2 background complements the mutant and leads to normal plant growth. Together, these data suggest that cross-kingdom HGT events shape the metabolic capabilities and interactions between plants and bacteria.

Immunobiodiversity: Conserved and specific immunity across land plants and beyond

Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.