Biology subjects

Archibald, J. M.

Publications and source records attributed to Archibald, J. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Proteomics reveals conserved features of histone biology in dinoflagellates

Current knowledge of DNA packaging in eukaryotic nuclei largely centers on its basic unit, the nucleosome. Multiple lineages have, however, diverged from this paradigm, most notably dinoflagellates. Among other molecular oddities, these enigmatic protists have enormous genomes, permanently condensed chromosomes and a foreign gene encoding Dinoflagellate Viral Nucleoprotein (DVNP), which is used for packing DNA. Some dinoflagellates also have Histone-like Proteins (HLPs) acquired from bacteria via lateral gene transfer. Dinoflagellates were long thought to lack histones entirely, but canonical histone genes have been identified by transcriptomics. Here, we performed proteomics on purified nuclei and confirmed the presence of all four core histone classes, along with variants, and DVNP in the dinoflagellates Oxyrrhis marina and Amphidinium carterae and HLPs in A. carterae. We also identified putative histone post-translational modifications found in canonical eukaryotes. Comparative genomics of dinoflagellates revealed histone-handling and modification machinery alongside an apparent reduction in, or diversification of, machinery responsible for replication-dependent nucleosome deposition (CAF-1), consistent with a predominantly transcription-associated role for nucleosomes. Furthermore, proteomics revealed modifications of DVNP and HLP, raising the possibility of machinery co-opting. These observations support a new model of a dinoflagellate chromatin that includes the localization of canonical nucleosomes to insulated chromatin territories (INTs).

evolutionary biology↗

bioRxiv2026

Characterization of starch metabolism pathways in dinoflagellates, chromerids and apicomplexans highlights the presence of a starch accumulating symbiont in their common ancestor

Unlike most other heterotrophic protist lineages which synthesize glycogen, alveolates accumulate -glucan storage polysaccharides in the form of starch. Within Alveolata, ciliates do so by using a simple pathway analogous to that used for glycogen metabolism in eukaryotes. However, Myzozoa have evolved five additional enzymatic steps which are common to Dinoflagellata, Chromerids and Apicomplexa. Moreover, dinoflagellates have acquired seven additional enzymes that distinguish them from the Chromerids-Apicompexa lineages, while chromerids possess only a single enzyme not found in dinoflagellates. Such modifications are not found in other eukaryotic lineages save for those resulting directly from primary or secondary plastid endosymbiosis. The many differences affecting the starch pathway of Myzozoa can be explained by a single secondary or tertiary plastid endosymbiosis of a starch-containing alga followed by distinct compartmentalisation outcomes of starch metabolism in Dinoflagellata relative to chromerids and Apicomplexa.

evolutionary biology↗

bioRxiv2026

Skiaviridae: a large DNA virus family that persistently infects thraustochytrid protists

Genomics and metagenomics have transformed our understanding of the diversity of large DNA viruses infecting eukaryotic microorganisms. Using long-read sequencing, we discovered ubiquitous, co-culturing nucleocytoviruses in several thraustochytrid protists. These viruses are closely related to SmDNAV, an 'orphan' virus of the thraustochytrid Sicyoidochytrium minutum. Transcriptomics, proteomics and electron microscopy demonstrate viral gene expression and particle formation in these cultures without obvious defects in culture growth. We also found SmDNAV-type viruses associated with previously sequenced thraustochytrids. Phylogenetic analysis reveals that the SmDNAV and SmDNAV-like genomes belong to a hitherto unrecognized order of Nucleocytoviricota, here named "Skiavirales". All fifteen identified skiavirus genomes lack numerous viral hallmark genes including DNA-dependent RNA polymerase; all but three also lack DNA polymerase family B (PolB). PolB phylogeny suggests a specific relationship between Skiavirales and the recently discovered mirusviruses, which belong to a different viral realm. Gene exchange between skiaviruses, co-occurring mirusviruses, and host nuclear genomes shows that persistent infection by diverse large DNA viruses provides an opportunity for virus-virus and virus-host co-evolution in thraustochytrids and, perhaps, other microbial eukaryotes.

evolutionary biology↗

bioRxiv2026

Multiple origins of endogenous virophage and polinton-like virus in the halophilic protist Halocafeteria seosinensis

Virophages and Polinton-like Viruses (PLVs) are related viral elements classified within the supergroup Polisuviricotina. While virophages typically depend on large dsDNA viruses (Nucleocytoviricota) for replication in eukaryotic hosts, the replication strategies of most PLVs are unknown. While both virophages and PLVs can exist as stand-alone entities or be integrated into host genomes, their co-occurrence within a single eukaryotic genome is rare. We investigated the chromosome-scale nuclear genome assembly of the halophilic protist Halocafeteria seosinensis and discovered 41 endogenous PLVs and 36 virophage sequences, most of which are full-length elements; together they comprise 6.2% of the genome. These viral elements belong to six PLV and seven virophage subtypes. Notably, we found genes shared between H. seosinensis PLVs and virophages, suggesting active genetic exchange between them. We also observed supraparasitism, with MULE DNA transposons and LINE retrotransposons frequently embedded within the viral genomes. Our study reveals dynamic interactions between viral elements and host mobile DNA in a halophilic protist, expanding our understanding of viral diversity in extreme environments. SIGNIFICANCEVirophages and polinton-like viruses (PLVs) are enigmatic viral elements found in many aquatic habitats. Our understanding of their diversity stems mainly from analysis of environmental sequence data, but they have also been found integrated into the genomes of cultured protists. The evolutionary impacts of such integrations are poorly understood. In this study, we reveal the co-occurrence of multiple PLV and virophage subtypes that together constitute a substantial fraction of the genome of the halophilic protist Halocafeteria seosinensis. These distantly related viral lineages coexist within the same genome and share a common gene pool, forming chimeric arrangements with host transposons and with one another. The H. seosinensis genome thus serves as a dynamic arena for viral gene exchange and genome remodelling, reshaping host genome architecture and potentially conferring immunity to giant viruses.

genomics↗

bioRxiv2026

CRISPR/Cas9 gene editing in the heterotrophic protist Acanthamoeba castellanii

Members of the amoebozoan genus Acanthamoeba are unicellular heterotrophic protists that inhabit a wide range of terrestrial and aquatic environments. They are opportunistic pathogens known to host disease-causing bacteria as well large DNA viruses. While Acanthamoeba is commonly used to study cellular locomotion, phagocytosis, and disease, genetic tools for precise editing of the Acanthamoeba genome are still in their infancy. Here we have developed CRISPR/Cas9 tools for genetically engineering the model acanthamoebid Acanthamoeba castellanii strain Neff. In proof-of-principle experiments, we targeted the myosin-II heavy chain gene. Evidence for editing was found using reverse transcriptase PCR, microscopy, and DNA sequencing, which also identified unique alleles for the target locus. Collectively, we demonstrate that CRISPR can be employed to edit Acanthamoeba genes using a knock-in approach. This work serves as a foundation to further develop A. castellanii as a model system with which to study diverse questions in cell and molecular biology, biochemistry and evolution.

molecular biology↗

bioRxiv2026

Spliceosome loss in the red tide ciliate Mesodinium rubrum presents a symbiotic cul-de-sac

Mesodinium rubrum, a marine microbial eukaryote associated with some of the largest red tides on Earth, has the remarkable ability to commandeer the plastids, mitochondria and nuclei from the alga Teleaulax amphioxeia for photosynthesis. Here we report analyses of assemblies of M. rubrums two nuclear genomes. Unexpectedly, M. rubrum appears to have completely lost its spliceosomal introns, most spliceosomal molecules, and the key genes for an intron splicing-associated process, Nonsense-mediated mRNA Decay (NMD). In contrast, non-spliceosomal tRNA introns have been retained, as have thousands of intron analogs spliced out of DNA during ciliate somatic genome development (internal eliminated sequences - IESs). Intron-containing genes, especially from intron-rich species like T. amphioxeia, would likely be defunct if horizontally transferred to a host without a spliceosome like M. rubrum, and thus we propose that introns can be a roadblock to progressive endosymbiotic genomic integration.

genomics↗

bioRxiv2026

Sequencing, Chromosome-scale Assembly, and Annotation of the Genome of the Halophilic Nanoflagellate Halocafeteria seosinensis

Compared with bacterial and archaeal extremophiles, single-celled eukaryotes living in extreme habitats are understudied and underrepresented in genomic databases. An exception is the obligately halophilic stramenopile Halocafeteria seosinensis strain EHF34. A transcriptome-focused analysis of this extremophilic protists revealed the importance of organic osmolyte regulation and transport in its adaptation to hypersaline environments. However, genomic resources for H. seosinensis are currently limited to a highly fragmented assembly generated by short-read sequencing, which has hindered further investigation of the genome biology and evolution of this fascinating organism. Here, we used long-read Oxford Nanopore sequencing to generate a highly contiguous, chromosome-scale genome assembly for H. seosinensis. The assembly is 38.8 megabase pairs (Mbp) in size and contains 60 nuclear contigs, making it the most contiguous genome for a member of the order Bicosoecida. Approximately 19% of the genome is comprised of transposable elements. Of the 11,684 predicted protein-coding genes, many appear to be associated with DNA mobility-related functions, and several may be linked to adaptation to a hypersaline environment. Analysis of the H. seosinensis long-read genome assembly presented herein will facilitate our understanding of the ways in which protists have adapted to extreme environments. SignificanceHalocafeteria seosinensis is an extremophilic protist adapted to hypersaline environments. Previous analyses of a transcriptome and short-read draft genome assembly for this organism provided insights into the molecular mechanisms underlying osmotic regulation, which facilitate its adaptation to high-salt conditions. However, the lack of contiguity and quality of the draft assembly prevented the characterization of complex genomic regions, including transposable elements and viral insertions, as well as genomic comparisons with related species. Here we present a highly contiguous, chromosome-scale genome assembly for H. seosinensis that enables accurate gene prediction, detailed analysis of repeat content, and comparative genomic analysis. This long-read genome assembly will serve as a valuable resource for studying one of the few tractable halophilic protists sequenced to date.

genomics↗

bioRxiv2026

Full-length 16S ribosomal RNA gene sequencing reveals dynamics of tick-adapted and environmentally derived bacteria in the microbiome of the black-legged tick, Ixodes scapularis in Nova Scotia, Canada

Lyme disease is a tick-borne illness caused by the spirochaete bacterium Borrelia (Borreliella) burgdorferi. The black-legged tick Ixodes scapularis, which transmits B. burgdorferi and several other human pathogens, is endemic to the eastern United States and, due to climate change, is rapidly expanding into central and eastern Canada. Amplification and sequencing of bacterial DNA from I. scapularis is increasingly used to monitor the presence and abundance of B. burgdorferi and associated bacteria. However, variation in the nature of molecular data collected across studies presents challenges for analysis and interpretation. Here we use full-length Oxford Nanopore 16S ribosomal RNA gene amplicon sequencing to characterize the microbiome of I. scapularis, with an explicit focus on distinguishing between tick-adapted bacteria (endosymbionts and pathogens) and environmentally acquired bacteria (external sources, including soil, vegetation or vertebrate hosts). We show that environmental dominance strength differs between these two ecological classes of bacteria, and that environmental dominance does not appear to represent stochastic background alone; environmentally derived bacterial taxa detected in tick microbiomes are not mere contaminants. Paired soil microbiome profiling from tick collection sites will be required to test whether environmental dominance and associated co-occurrence structure track with seasonal changes in exposure and environmental microbial populations.

microbiology↗

bioRxiv2026

A billion-year-old bacterial machinery replicates plastid DNA and supports kleptoplastidy

The endosymbiotic evolution of plastids and mitochondria was central to the origin and success of eukaryotes. One of the most prominent molecular machineries thought to have disappeared early in eukaryote evolution is the multi-subunit bacterial DNA polymerase III (DNApol-III), which is the principal enzyme complex supporting DNA replication in bacteria. Here, we combined worldwide metagenomics and cultivation to characterise the mosaic genomic landscape of abundant phytoplankton lineages of Teleaulax (Cryptophyceae), which contain an endosymbiotically-derived nucleomorph genome. Unexpectedly, the nuclear, plastid and nucleomorph genomes of Teleaulax contain ubiquitously expressed genes for plastid-targeted DNApol-III subunits. These genes shed light on the functioning of Teleaulax genomes when sequestered by the ciliate Mesodinium during its kleptoplastidic photosynthetic activity1-3. In particular, the alpha subunit gene (encoding the polymerase activity), which resides in the nucleomorph genome, is continuously expressed in Mesodinium in controlled laboratory experiments. This provides a mechanistic explanation for the replication of Teleaulax plastid genomes weeks after the nuclear genome is lost4. Beyond Teleaulax and close relatives, we also identified genes encoding plastid-targeted DNApol-III subunits (including alpha) in nuclear genomes of unicellular and multicellular lineages of Archaeplastida that form, along with those of Cryptophyceae, monophyletic clades firmly positioned within Cyanobacteria. Together, our results reveal a previously overlooked retention of bacterial DNA replication machinery from plastid primary endosymbiosis in Archaeplastida, its acquisition by Cryptophyceae during secondary endosymbiosis, and its direct role in contemporary plankton as a facilitator of kleptoplastidic photosynthetic activity by heterotrophic ciliates.

microbiology↗

bioRxiv2026

Phylogeny and morphology of novel Labyrinthulomycetes in Nova Scotia, Canada

Labyrinthulomycetes are ubiquitous marine decomposers and include the thraustochytrids, a lineage known for their extensive production of polyunsaturated fatty acids and biotechnology applications. Despite historical taxonomic confusion, environmental surveys have begun to expand the known diversity within labyrinthulomycetes. Here we present 18S ribosomal DNA (rDNA) sequences from 17 novel labyrinthulomycetes strains established as axenic cultures from natural samples taken from three locations in Nova Scotia, Canada. We also present light and transmission electron microscopic analysis for three of these isolates. The combination of phylogenetic and morphological analysis suggests that these isolates belong to three different genera, Thraustochytrium, Ulkenia and Oblongichytrium. Our results expand the known genetic diversity of labyrinthulomycetes in Atlantic Canadian waters, contributing new strains to understudied genera for future comparative genomic investigations, including Ulkenia and Oblongichytrium for which very few genomic resources are available.

evolutionary biology↗

bioRxiv2025

Single nucleotide polymorphisms and structural variants reveal complex and variable ploidy in the amoebozoan Acanthamoeba castellanii

Acanthamoeba castellanii is a free-living amoeba that is emerging as a model organism for the study of eukaryotic microbiology. It is one of the most widely studied members of the Amoebozoa, and is both an important grazer in soil communities and an opportunistic human pathogen; A. castellanii is thus of evolutionary, ecological, and biomedical significance. Despite its potential as a lab workhorse, the genome biology of A. castellanii is complex and poorly understood. Polyploidy is a common feature of many amoebozoan genomes, and members of the genus Acanthamoeba are no exception; they appear to be not only polyploid, where genome copy number is inflated beyond the conventional haploid and diploid states, but also aneuploid, i.e., with inter-chromosomal copy number variation. To better understand aneuploidy in A. castellanii and how it may vary over time and between closely related strains, we analyzed nanopore and Illumina sequence datasets from several wild-type and mutant A. castellanii lines, with a focus on quantifying single nucleotide polymorphism (SNP) and structural variant allele frequencies across chromosome-scale scaffolds. Our findings suggest that intragenomic chromosome copy number is highly variable in Acanthamoeba and can change dynamically even over laboratory time scales. Significance StatementAcanthamoeba castellanii is becoming an important model organism for basic and applied research. However, its apparent polyploidy and aneuploidy has the potential to complicate the interpretation of results that depend on knowledge of gene copy number. In this study, we reveal the complex nature of ploidy in this organism by analyzing long- and short-read sequence data. Our results provide a reference point against which genomic and experimental data from A. castellanii can be interpreted, and guide future efforts aimed at more precisely characterizing how the organism regulates its genome and chromosome copy number.

genomics↗

bioRxiv2024

Pangenome biology and evolution in harmful algal-bloom-forming pelagophyte algae

In prokaryotes lateral gene transfer (LGT) is a key mechanism leading to intra-species variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens - a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Aureococcus anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase-pairs; Mbp), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain level genetic variation in Ac. anophagefferens with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis. 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.

evolutionary biology↗

bioRxiv2024

Epigenetic silencing and host genome evolution determine fate of viral insertions in Acanthamoeba

Acanthamoeba is a cosmopolitan freshwater amoebae known for its association with Nucleocytoplasmic Large DNA Viruses (NCLDVs). Previous studies have shown that Acanthamoeba spp. undergo lateral gene transfer (LGT) with NCLDVs. Here we have leveraged chromosome-scale assemblies of two strains of Acanthamoeba castellanii, Neff and C3, to investigate the occurrence and genomic context of viral LGT in Acanthamoeba. We show that the viral footprints in the C3 and Neff genomes are largely non-overlapping and that viral genes in Neff are found disproportionately in large sub-telomeric insertions. Multiple partial copies of these insertions are found throughout the Neff genome, but they are not expressed and do not encode functions for their own mobility. Viral regions are hyper-methylated and highly condensed, suggesting that the expression of recently acquired viral DNA is suppressed in heterochromatic regions. We propose a three-step model for the origin and fate of viral sequences in Acanthamoeba: (i) integration of DNA from giant viruses, (ii) epigenetic suppression of the viral DNAs, which allows them to persist in the genome, and (iii) deterioration of viral genomes by point mutation and intra- and inter-chromosomal recombination. Viral integrations in Acanthamoeba spp. are transient and may not have long-lasting effects on the fitness of the host amoeba. Our work strengthens a growing body of work showing widespread but transient integration of viral DNA in protists and extends the relevance of epigenetic silencing mechanisms to the evolution of Amoebozoa. We highlight the importance of host genome dynamics for understanding the evolution of endogenized viral elements.

genomics↗

bioRxiv2024

The fate of artificial transgenes in Acanthamoeba castellanii

In this study, artificial transformation experiments were performed to investigate how the A. castellanii genome responds to foreign DNA presented in both circular and linear plasmid form. Nanopore sequencing was used as a high throughput method to screen for transgene DNA in the resulting transformant cultures, and candidate transgene integrations were identified. Molecular biology experiments were performed to validate the sequence data and provide additional context on the fate of transgenes. A method was devised to estimate the rate of read chimerism in nanopore sequencing runs and accurately account for the effects of read chimerism in identifying putative transgene integrations. Based on the experimental data in hand, a potential mechanism for transgene maintenance in A. castellanii is proposed, one in which incoming foreign DNA is tandemly duplicated and telomeres are added to the ends. This nascent linear molecule is maintained as a transgene-bearing minichromosome, while also allowing for chromosomal integration.

molecular biology↗

bioRxiv2024

Targeted metagenomics reveals pangenomic diversity of the nitroplast (UCYN-A) and its algal host plastid

UCYN-A (Cand. Atelocyanobacterium thalassa) has recently been recognized as a globally-distributed, early stage, nitrogen-fixing organelle (the nitroplast) of cyanobacterial origin present in select species of haptophyte algae (e.g., Braarudosphaera bigelowii). Although the nitroplast was recognized as the UCYN-A2 sublineage, it is yet to be confirmed in other sublineages of the algal/UCYN-A complex. We used water samples collected from Halifax Harbour (Bedford Basin, Nova Scotia, Canada) and the offshore Scotian Shelf to further our understanding of B. bigelowii and UCYN-A in the coastal Northwest Atlantic. Sequencing data revealed UCYN-A-associated haptophyte signatures and yielded near-complete metagenome-assembled genomes (MAGs) for UCYN-A1, UCYN-A4, and the plastid of the A4-associated haptophyte. Comparative genomics provided new insights into the pangenome of UCYN-A. The UCYN-A4 MAG is the first genome sequenced from this sublineage and shares [~]85% identity with the UCYN-A2 nitroplast. Genes missing in the reduced genome of the nitroplast were also missing in the A4 MAG supporting its likely classification as a nitroplast as well. The UCYN-A1 MAG was found to be nearly 100% identical to the reference genome despite coming from different ocean basins. Time-series data paired with the recurrence of specific microbes in enrichment cultures gave insight into the microbes that frequently co-occur with the algal/UCYN-A complex (e.g., Pelagibacter ubique). Overall, our study expands knowledge of UCYN-A and its host across major ocean basins and investigates their co-occurring microbes in the coastal Northwest Atlantic (NWA), thereby facilitating future studies on the underpinnings of haptophyte-associated diazotrophy in the sea.

microbiology↗

bioRxiv2023

Herpes-like viral elements and universal subtelomeric ribosomal RNA genes in a chromosome-scale thraustochytrid genome assembly

We used long-read sequencing to produce a telomere-to-telomere genome assembly for the heterotrophic stramenopile protist Aurantiochytrium limacinum MYA-1381. Its [~]62 Mbp nuclear genome comprises 26 linear chromosomes with a novel configuration: subtelomeric rDNAs are interspersed with long repeated sequence elements denoted as LOng REpeated - TElomere And Rdna Spacers (LORE-TEARS). These repeats may play a role in chromosome end maintenance. A [~]300 Kbp circular herpesvirus-like genomic element is present at a high copy number. A 269 Kbp related virus-like element was found to reside between two complete sets of rRNA and LORE-TEAR sequences on one end of chromosome 15, indicating recent recombination between the viral and nuclear genome. Our data reveal new types of giant endogenous viral elements originating from herpes-like viruses and existing as either stand-alone or integrated elements.

genomics↗

bioRxiv2023

A unique symbiosome in an anaerobic single-celled eukaryote

Symbiotic relationships drive evolutionary change and are important sources of novelty. Here we demonstrate a highly structured syntrophic symbiosis between species of the anaerobic protist Anaeramoeba (Anaeramoebae, Metamonada) and bacterial ectosymbionts. We dissected this symbiosis with long-read metagenomics, transcriptomics of host and symbiont cells coupled with fluorescent in situ hybridization (FISH), and microscopy. Genome sequencing, phylogenomic analyses and FISH show that the symbionts belong to the Desulfobacteraceae and were acquired independently in two different Anaeramoeba species. We show that ectosymbionts likely reside deep within cell surface invaginations in a symbiosomal membrane network that is tightly associated with cytoplasmic hydrogenosomes. Metabolic reconstructions based on the genomes and transcriptomes of the symbionts suggest a highly evolved syntrophic interaction. Host hydrogenosomes likely produce hydrogen, acetate, and propionate that are consumed by the symbionts dissimilatory sulfate reduction, Wood-Ljungdahl and methylmalonyl pathways, respectively. Because the host genome sequences encode several vitamin B12-dependent enzymes but appear to lack the ability to biosynthesize this vitamin, we hypothesize that the symbionts supply their hosts with B12. We detected numerous lateral gene transfers from diverse bacteria to Anaeramoeba, including genes involved in oxygen defense and anaerobic metabolism. Gene families encoding membrane-trafficking components that regulate the phagosomal maturation machinery are notably expanded in Anaeramoeba spp. and may be involved in organizing and/or stabilizing the symbiosomal membrane system. Overall, the Anaeramoebae have evolved a dynamic symbiosome comprised of a vacuolar system that facilitates positioning and maintenance of sulfate-reducing bacterial ectosymbionts.

evolutionary biology↗

bioRxiv2023

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution. HIGHLIGHTSO_LIGenomes of four filamentous algae (Zygnema) sisters to land plants C_LIO_LIZygnema are rich in genes for multicellular growth and environmental acclimation: signaling, lipid modification, and transport C_LIO_LICell wall innovations: diversification of hexameric rosette cellulose synthase in Zygnematophyceae C_LIO_LICo-expression networks reveal conserved modules for balancing growth and acclimation C_LI

evolutionary biology↗