Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with a broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelp's accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of N. luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80× of coverage, and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Kb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and Macrocystis pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPase enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

Human colonization since the 19th century has resulted in the global spread of pines beyond their original northern boreal distribution. Although the introduction history of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal (ECM) fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, whole genomes of 208 individuals collected across native and introduced ranges were sequenced to reveal the introduction history of pine co-introduced ECM fungi. Population genomics analyses showed that all introductions originated from Europe. With the exception of North America, introduced populations were genetically differentiated from the European population, with varying magnitudes of population expansion in different introduced regions. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial-genetic patterns of native vs exotic habitats. The spread of S. luteus is mediated by human activities accompanying pine introductions, with its demographic history linked to forestry practices. The spatial, temporal, and demographic patterns observed in S. luteus offer insight into the population genetics of a widely introduced ECM fungus and are likely applicable to other pine co-introduced ECM fungi.

Human colonization since the 19 th century has resulted in the global spread of pines across the Southern Hemisphere, well beyond their original northern boreal distribution. Such introductions moved not only the pines but also expanded the distribution of their symbiotic partners. Although the introduction of pines is documented through historical records, little is known about the introduction history of their ectomycorrhizal fungi, which are critical symbionts for the survival and invasion of pines. Using Suillus luteus as an example, population genomic analyses of 208 individuals across both native and introduced ranges showed that all introductions originated from Europe, likely mediated by human activities along with pine introductions. With the exception of North America, introduced populations were genetically differentiated from the Europe population, with varying magnitudes of population expansion in different introduced regions, often linked to forestry practices. Genetic variation within the native European population followed isolation by distance, but not in the introduced range, highlighting the disparity in the spatial genetic patterns of native versus exotic habitats. This study provides insight into the population genetics of a globally introduced ectomycorrhizal fungus whose introduction process is likely applicable to other pine-co-introduced ectomycorrhizal fungi.

Mutations are the ultimate source of genetic diversity on which natural selection and genetic drift act, playing a crucial role in evolution and long-term adaptation. At the molecular level, the spontaneous mutation rate (µ), defined as the number of mutations per base per generation, thus determines the adaptive potential of a species. Through a mutation accumulation experiment, we estimate the mutation rate and spectrum in Prasinoderma coloniale, a phytoplankton species from an early-branching lineage within the Archaeplastida, characterized by an unusually high genomic guanine-cytosine (GC) content (69.8%). We find that P. coloniale has a very low total mutation rate of µ = 2.00 × 10-10. The insertion-deletion mutation rate is almost 5 times lesser than the single nucleotide mutation rate with µID = 3.40 × 10-11 and µSNM = 1.62 × 10-10. Prasinoderma coloniale also exhibits an atypical mutational spectrum: While essentially all other eukaryotes show a bias toward GC to AT mutations, no evidence of this AT-bias is observed in P. coloniale. Since cytosine methylation is known to be mutagenic, we hypothesized that this may result from an absence of C-methylation. Surprisingly, we found high levels of C-methylation (14% in 5mC, 25% in 5mCG contexts). Methylated cytosines did not show increased mutation rates compared with unmethylated ones, not supporting the prevailing notion that C-methylation universally leads to higher mutation rates. Overall, P. coloniale combines a GC-rich genome with a low mutation rate and original mutation spectrum, suggesting the almost universal AT-bias may not have been present in the ancestor of the green lineage.

Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.

Many macrofungi are impractical or impossible to culture. Consequently, DNA for long-read sequencing required for the assembly of high-quality genomes must be isolated from samples taken from the environment. Collection is often in remote locations, limiting the options for stabilising samples to methods that do not require refrigeration. Fungi contain species-specific arrays of metabolites that may complicate purification techniques and call for judgement to be made to apply appropriate modifications to the DNA extraction protocol in specific cases. The protocols and commentary we describe are informed by the preparation of DNA from a range of Australasian ectomycorrhizal and saprotrophic macrofungi. We collect samples into isopropanol at ambient temperature and employ a strategy of chromatin isolation followed by the sequential removal of unwanted molecular components to purify DNA.

Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.

Mushroom-forming fungi (Agaricomycetes) are emerging as pivotal players in several fields of science and industry. Genomic data for Agaricomycetes are accumulating rapidly; however, this is not paralleled by improvements of gene annotations, which leave gene function notoriously poorly understood. We set out to improve our functional understanding of the model mushroom Coprinopsis cinerea by integrating a new, chromosome-level assembly, high-quality gene predictions, and functional information derived from broad gene-expression profiling data. The new annotation includes 5' and 3' untranslated regions (UTRs), polyadenylation sites (PASs), upstream open reading frames (uORFs), splicing isoforms, and microexons, as well as core gene sets corresponding to carbon starvation, light response, and hyphal differentiation. As a result, the genome of C. cinerea has now become the most comprehensively annotated genome among mushroom-forming fungi, which will contribute to multiple rapidly expanding fields, including research on their life history, light and stress responses, as well as multicellular development.

Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ectomycorrhiza (ECM) first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de novo tree and fungal transcriptional datasets. We identified co-expressed genes enabling ECM symbiosis at early and mature stages of the interaction. These sets of genes can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defenses and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases, and the downregulation of plant cell wall remodeling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene regulation, but also its temporal scale and dynamics seem to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway and nutrient transporters was also studied, revealing constitutive levels of expression and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility, and serve as a data-rich transcriptomic resource to open new research questions in the field.

Bretziella fagacearum is a destructive vascular wilt fungal pathogen affecting oaks in the United States and Canada. The epidemiology of oak wilt varies across different geographical locations, indicating the need to investigate the population dynamics of B. fagacearum to discern potential differences in its genotypes using genomic tools. A good-quality genome of B. fagacearum is crucial as a reference for population genetics studies. Here, we report a high-quality genome of B. fagacearum isolate C519. The genome assembly consists of nine scaffolds, corresponding to the nine chromosomes, totaling 27,072,536 bp with a GC content of 47.29%. It is predicted to encode 7,554 proteins, which are annotated using RNA sequencing data from the same isolate. The circular mitochondrial genome consists of a chromosome of 174,403 bp with a GC content of 28.59% and contains 54 open reading frames, including 14 core genes, 28 tRNAs, 4 rRNAs, and 8 hypothetical proteins. The reference genome can enhance the understanding of molecular epidemiology and biology of B. fagacearum, aiding in identifying genetic variations and pathogen-host interactions and developing diagnostic tools and disease management strategies.The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Despite large omics datasets, the prediction of eukaryotic genes is still challenging. We have developed a new method to improve the prediction of eukaryotic genes and demonstrate its utility using the genome of the fungal wheat pathogen Zymoseptoria tritici. From 10,933 to 13,260 genes were predicted by four previous annotations, but only one third were identical. A novel bioinformatics suite, InGenAnnot, was developed to improve Z. tritici gene annotation using Iso-Seq full-length transcript sequences. The best gene models were selected among different ab initio gene predictions, according to transcript and protein evidence. Overall, 13,414 reannotated gene models (RGMs) were predicted, improving previous annotations. Iso-Seq transcripts outlined 5' and 3' untranslated regions for 73% of the RGMs and alternative transcripts mainly due to intron retention. Our results showed that the combination of different ab initio gene predictions and evidence-driven curation improved gene annotation of a eukaryotic genome. It also provided new insights into the transcriptional landscape of this fungus. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

White-rot and brown-rot fungi (WRF and BRF, respectively) decompose lignocellulose, the main structural component of plant biomass, through distinct mechanisms. This study examines the transcriptomic responses of three WRF species (Pleurotus ostreatus, Phanerochaete chrysosporium, and Heterobasidion irregulare) and two BRF species (Fomitopsis schrenkii and Rhodonia placenta) grown on poplar wood (W) and glucose (G) as sole carbon sources. RNA-seq analysis revealed upregulation of carbohydrate-active enzymes (CAZymes) linked to lignocellulose degradation. WRF displayed a broader enzymatic repertoire, whereas BRF employed a more selective approach. Among these responses, GH16 glycoside hydrolases were consistently upregulated across all species, including BRF. Since GH16 enzymes are involved in both plant hemicellulose modification and cell wall remodeling, their wood-induced expression may reflect multiple processes rather than a single conserved wood-decay mechanism. Structural and phylogenetic analyses revealed species-specific divergence, consistent with potential functional specialization. These findings broaden our understanding of fungal enzymatic strategies and highlight GH16 enzymes as candidates for further study. Beyond the immediate context of wood decay, this work has broader implications for fungal ecology, evolutionary biology, and biotechnological applications such as biomass conversion and sustainable bioenergy.

Diatoms are a class of algae that play an essential role in global ecology and produce valuable chemicals. They are known for forming intricate nanostructured silica cell walls (frustules). The introduction of non-siliceous elements like aluminum into diatoms induces properties such as a lower dissolution rate of the frustule, increasing the specific surface area of the frustule and enhancing metabolism. Previous studies have focused primarily on characterizing physiological impacts, leaving the genetic response(s) to non-siliceous elements largely unexplored. This study investigates the transcriptional response of the pennate diatom, Entomoneis vertebralis to dissolved aluminum. Our findings reveal that in the presence of added 10 µM aluminum, biogenic silica content of the cell wall increases approximately twofold along with significant changes to core metabolism. An increase in transcription of genes encoding nitrate transporters has been observed despite the apparent downregulation of nitrogen assimilation pathways. Additionally, increased transcription of genes involved in carbon fixation were noted. Amino acid and protein motif analyses identified proteins that were differentially regulated shared amino acid compositions and motifs characteristic to silicification-associated genes. A unique structure-based analysis pipeline revealed that some of these proteins have a conserved structural core while being diverse in sequence, which could be features associated with biosilicification. Differential expression transcriptomics has provided insight into diatom metabolism when exposed to aluminum, highlighting potential targets for metabolic engineering. Furthermore, we identified potential silicification-associated genes using tools based on structure and amino acid composition, advancing our understanding of diatom silicification.

Industrial cash crop tea is a cherished drink for its bioactive components like terpenoids and flavonoids shaping its flavor and health benefits. Trichoderma species are potent biocontrol agents and plant growth regulators, with unexplored potential in modulation of C. sinensis terpenoid biosynthesis. Genome sequencing of a tea root-associated Trichoderma sp. strain AM6 revealed a genome size of 39.91 Mbp, comprising 446 contigs organized into 406 scaffolds, with 98.8 % completeness. Single scaffold mitochondrial genome assembly of 34,430 bp in length with a GC content of 28.03 % encodes a total of 49 genes including 27 tRNA, 2 rRNA, and 20 protein-coding genes. Metabolic pathway analysis indicates exclusive reliance on the mevalonate pathway for terpenoid biosynthesis in Trichoderma, unlike C. sinensis, which utilizes both the mevalonate and non-mevalonate (MEP/DOXP) pathways. Untargeted LC-ESI-MS/MS analysis of Trichoderma identified 11,841 secondary metabolites, including 34 monoterpenoids, 72-diterpenoids, and 76-sesquiterpenoids, emphasizing its metabolic diversity. Comparative phylogenomic study positioned it as a phylogenetically distinct species with unique adaptive traits. Untargeted GC-MS shows high volatile abundance from microbial consortia (T5) followed by only Trichoderma treatment (T2) compared to control (T1). Terpenoid transcripts of C. sinensis from the plant-microbe consortium assembly sets illuminate upregulation of genes assigned to 3-hydroxy-3-methylglutaryl-Co-A reductase (HMGCR) and downregulation of genes assigned to 1-Deoxy-D-xylulose-5-phosphate (DXS), indicating metabolic shift towards more mevalonate pathway activity influenced by this novel Trichoderma strain itself and in combination with other tea root-associated microbes.

Kretzschmaria zonata is an ascomycete fungus known as a significant plant pathogen that causes serious damage to teak plantations, but little is known about its genomic and metabolic features. Studies suggest this fungus is an interesting source of cell wall degrading enzymes. This study evaluated the genome and the diversity of genes encoding carbohydrate-active enzymes (CAZymes) of Kretzschmaria zonata GFP 132. The fungal ability to grow on different carbohydrates and its sugar metabolic network were also investigated. The findings were compared with other fungi, taxonomically close, phytopathogens or fungi known as good producers of plant cell wall degrading enzymes (CWDE). The assembled genome corresponding to 30.15 Mbp and 12,135 protein-coding genes, had approximately 5% of total protein-coding genes as putative CAZymes. In general, the closely related fungi, K. deusta, Hypoxylon submonticulosum, and Xylaria cf. heliscus exhibited a similar CAZymes profile. When compared with other phytopathogenic fungi, the variation in the CAZyme profile suggests that it does not accompany the similar species' lifestyle. Curiously, the repertoire of genes encoding CDWE was similar to Aspergillus niger, an Eurotiomycete, and different from Trichoderma reesei which is Sordariomycete like K. zonata. Based on genome, K. zonata possesses a complete sugar metabolic network, except for an absent gene in the galacturonic acid metabolic pathway. This is consistent with the inability of the fungus to grow in galacturonic acid as the sole carbon source. Finally, K. zonata was able to assimilate a wide range of mono and polysaccharides as carbon source, which opens perspectives for new studies to obtain new enzymes required to increase the efficiency of existing biotechnological industrial processes.

Haematococcus lacustris is a ubiquitous unicellular green alga with industrial bioproduct applications, namely, as feedstock for natural astaxanthin. We report the annotated 291.5 Mbp genome for H. lacustris Liv1 to support future algal research in the areas of carotenoid biosynthesis and crop protection.

The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.

Microplastics cause negative environmental consequences such as the release of toxic additive leachates, increased greenhouse gas emissions during degradation, and threaten food chains. Microplastic particles are known to serve as a vector for the transport of microbes (fungi and bacteria) to new environments, threatening biodiversity. Robust biofilm formation makes fungi candidates for collecting and remediating environmental microplastics. However, fungal-microplastic colonization mechanisms have not yet been explored. In this work, we aim to understand which fungal molecules mediate microplastic binding. We examine the common fungal genus Aspergillus, which we found binds microplastics tightly, removing particles from suspension. Upon inoculation of Aspergilli with microplastic particles, up to 3.85 ± 1.48 g of microplastics were flocculated per gram of dry fungal biomass; this phenomenon was observed across various plastics ranging in size from 0.05 to 5 mm. Gene knockouts revealed that hydrophobins drive microplastic-fungi binding, evidenced by a decrease in flocculation relative to that of wild-type Aspergillus fumigatus. Moreover, purified hydrophobins flocculated microplastics independently of the fungus, validating their ability to bind to microplastics. Our work elucidates a role for hydrophobins in fungal colonization of microplastics and highlights a target for mitigating the harm of microplastics through engineered fungal-microplastic interactions.

Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ECM first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de-novo tree and fungal transcriptional datasets. We identified core plant regulons enabling ECM symbiosis at early and mature stages of the interaction. These regulons can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defences and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases and the downregulation of plant cell-wall remodelling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene-regulation, but also its temporal scale and dynamics seems to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway was also studied, revealing constitutive levels of expression of a part of the pathway and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility and serve as a data-rich transcriptomic resource to open new research questions in the field. Significance statement Ectomycorrhizal symbiosis is essential for forest ecosystems, but the genetic determinants of host and fungal compatibility remain underexplored. Employing comparative transcriptomics, we identified plant general and ECM-specific gene regulons, outlining the expression profile of Common Symbiosis Pathway genes in multiple ECM interactions and highlighting fungal and plant genes associated to interkingdom crosstalk and cell wall remodelling. These findings help us gain insights into the molecular events determining mycorrhiza compatibility. ### Competing Interest Statement The authors have declared no competing interest.