A 160 Gbp fork fern genome shatters size record for eukaryotes

Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold

Nearly 10,000 plant species are represented by RNA-seq datasets in the NCBI sequence read archive, which are difficult to search in unassembled format due to database size. Here, we optimize RNA-seq assembly to transform most of this public RNA-seq data to a searchable database for biosynthetic gene discovery. We test our transcriptome mining pipeline towards the diversification of moroidins, which are plant ribosomally-synthesized and posttranslationally-modified peptides (RiPPs) biosynthesized from copper-dependent peptide cyclases. Moroidins are bicyclic compounds with a conserved stephanotic acid scaffold, which becomes cytotoxic to non-small cell lung adenocarcinoma cells with an additional C-terminal macrocycle. We discover moroidin analogs with second ring structures diversified at the crosslink and the non-crosslinked residues including a moroidin analog from water chickweed, which exhibits higher cytotoxicity against lung adenocarcinoma cells than moroidin. Our study expands stephanotic acid-type peptides to grasses, Lowiaceae, mints, pinks, and spurges while demonstrating that large-scale transcriptome mining can broaden the medicinal chemistry toolbox for chemical and biological exploration of eukaryotic RiPP lead structures.

Progressive evolution of plants: A critical review

A comprehensive review of the evolutionary mechanisms in plants has been performed. This review examines fundamental questions regarding plant evolution, including the development of sexes, convergent characteristics, and neutral effects in plant ecosystems. The available evidence suggests that plant evolution is not a random process, as previously hypothesized. Instead, a substantial body of evidence points to the existence of directed and predictable patterns in plant evolution, applicable not only to plants but also to other organisms. The concept of directed evolution is explored in the context of plant biology.

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.

Dynamic changes in chromatin structure and transcriptional activity in the generative cells of Lilium longiflorum

Pollen is required for fertilization and the associated production of seeds and fruits, which are important for human nutrition. Research on the tricellular pollen of Arabidopsis thaliana revealed that chromatin is highly condensed and transcriptional activity is suppressed in sperm cells. However, comprehensive structural investigations involving generative cells of bicellular pollen have not been conducted. In this study, we provide relevant insights into other angiosperms that produce bicellular pollen. Lilium longiflorum, which has large and easily observable nuclei, was used for a detailed analysis of the chromatin structure and transcriptionally active regions in pollen and pollen tubes. Chromatin was condensed, resulting in a ribbon-like structure that was clearly visible in mature generative cell nuclei. Additionally, transcriptionally active regions were restricted to the intersections of chromatin as pollen desiccated. Although de novo transcription was revealed to be unnecessary for pollen tube growth, transcriptional activity temporarily resumed before generative cell division during pollen tube growth. Moreover, the inhibition of de novo transcription influenced changes in nuclear morphology. In this study, the distinctive chromatin structures and transcriptional activity states in generative cell nuclei of bicellular pollen were elucidated, with the generated data contributing to a deeper understanding of transcription and other regulatory mechanisms involved in pollen maturation and pollen tube growth.

Mosses Reveal a Universal Genome-Cell Size Relationship Across Land Plants Shaped by Shared Evolutionary Pressures

The relationship between genome size and cell size is present in all land plants including mosses, and is stronger in smaller cells. This relationship depends on environmental pressures, and affects plants differently depending on their dominant photosynthetic phase.

Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis). First, we used RepeatExplorer2 to calculate the genome proportion (GP) of all repeat types and compared the GP of long terminal repeat (LTR) retroelements against annotated complete and incomplete LTR retroelements (Ty1/copia and Ty3/gypsy) identified by DANTE in a whole genome assembly. We show that DANTE-identified LTR retroelements can comprise ∼0.75% of the inflorescence poly-A transcriptome and ∼0.24% of the stem ribo-depleted transcriptome. In the RNA libraries from inflorescence tissue, both LTR retroelements and DNA transposons identified by RepeatExplorer2 were highly abundant, where they may be taking advantage of the reduced epigenetic silencing in the germ line to amplify. Typically, there was a higher representation of DANTE-identified LTR retroelements in the transcriptome than RepeatExplorer2-identified LTR retroelements, potentially reflecting the transcription of elements that have insufficient genomic copy numbers to be detected by RepeatExplorer2. In contrast, for ribo-depleted libraries of stem tissues, the reverse was observed, with a higher transcriptome representation of RepeatExplorer2-identified LTR retroelements. For RepeatExplorer2-identified repeats, we show that the GP of most Ty1/copia and Ty3/gypsy families were positively correlated with their transcript proportion. In addition, guanine- and cytosine-rich repeats with high sequence similarity were also the most abundant in the transcriptome, and these likely represent young elements that are most capable of amplification due to their ability to evade epigenetic silencing.

The genus Paris: a fascinating resource for medicinal and botanical studies

The genus Paris, comprising a series of distinctive medicinal plants, has been utilized globally for its therapeutic properties over centuries. Modern pharmacological studies have demonstrated that secondary metabolites from Paris species exhibit significant pharmacological activities, including anticancer, hemostatic, anti-inflammatory, antimicrobial, and other effects. Additionally, the unique morphological traits and large genome size of Paris species have continuously captured the interest of botanists and horticulturalists. Nonetheless, the conservation of wild Paris populations is threatened due to the lengthy reproductive cycle and overexploitation, posing considerable challenges to their development and sustainable use. This review provides a comprehensive overview of the botanical characteristics, historical medicinal uses, pharmacological effects, and toxicity evaluation of secondary metabolites in Paris species. It also covers the molecular biological research conducted on the genus Paris and proposes key research questions and important directions for future solutions. We advocate the expansion and implementation of multi-omics approaches, as well as molecular and genetic technologies recently advanced in model plant research, to intensively study Paris species. This will facilitate the comprehensive understanding of gene function and molecular mechanisms underlying specialized metabolite formation in Paris.

Influence of Ty3/gypsy and Ty1/copia LTR-retrotransposons on the large genomes of Alstroemeriaceae: genome landscape of Bomarea edulis (Tussac) Herb

Repetitive elements are the main components of many plant genomes and play a crucial role in the variation of genome size and structure, ultimately impacting species diversification and adaptation. Alstroemeriaceae exhibits species with large genomes, not attributed to polyploidy. In this study, we analysed the repetitive fraction of the genome of Bomarea edulis through low-coverage sequencing and in silico characterization, and compared it to the repeats of Alstroemeria longistaminea, a species from a sister genus that has been previously characterized. LTR-retrotransposons were identified as the most abundant elements in the B. edulis genome (50.22%), with significant variations in abundance for specific lineages between the two species. The expansion of the B. edulis genome was likely due to three main lineages of LTR retrotransposons, Ty3/gypsy Tekay and Retand and Ty1/copia SIRE, all represented by truncated elements which were probably active in the past. Furthermore, the proportion of satDNA (~ 7%) was six times higher in B. edulis compared to A. longistaminea, with most families exhibiting a dispersed, uniform distribution in the genome. SatDNAs, thus, contributed to some extent to genome obesity. Despite diverging around 29 Mya, both species still share some satDNA families and retrotransposons. However, differences in repeat abundances and sequence variants led to genome differentiation despite their similar sizes and structure.

Plant synthetic genomics: Big lessons from the little yeast

Yeast has been extensively studied and engineered due to its genetic amenability. Projects like Sc2.0 and Sc3.0 have demonstrated the feasibility of constructing synthetic yeast genomes, yielding promising results in both research and industrial applications. In contrast, plant synthetic genomics has faced challenges due to the complexity of plant genomes. However, recent advancements of the project SynMoss, utilizing the model moss plant Physcomitrium patens, offer opportunities for plant synthetic genomics. The shared characteristics between P. patens and yeast, such as high homologous recombination rates and dominant haploid life cycle, enable researchers to manipulate P. patens genomes similarly, opening promising avenues for research and application in plant synthetic biology. In conclusion, harnessing insights from yeast synthetic genomics and applying them to plants, with P. patens as a breakthrough, shows great potential for revolutionizing plant synthetic genomics.

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.