Biology subjects

Irisarri, I.

Publications and source records attributed to Irisarri, I..

16 recordsLinked to original sources

bioRxiv2026

Benchmarking Universal Single-Copy Orthologs for Phylogenomics: The Impact of Paralogy

Universal Single-Copy Orthologs (USCOs) are taxonomically-defined gene sets originally proposed to evaluate completeness in genome assemblies. Due to their single- or low-copy nature, they have also been proposed as ideal markers for phylogenomics. Here, we test this assumption using two vertebrate datasets, mammals and ray-finned fish, and their corresponding USCO reference marker sets, actinopterygii_odb10 and mammalia_odb10. Our results show that although most USCO markers are single-copy, 85% and 91% respectively, empirical analyses using a large number of taxa are able to identify a non-negligible proportion of paralogs in the actinopterygii_odb10 and mammalia_odb10 BUSCO gene sets. Gene phylogenies show that several of these paralogs derive from ancient whole-genome duplication events, particularly the teleost-specific whole-genome duplication, and also more recent duplications such as those in salmonids and cyprinids. Paralogs do not reflect the organismal phylogeny but rather the history of gene duplications, so retaining paralogs in phylogenomic datasets can lead to inaccurate phylogenomic hypotheses. To test the effect of ignoring paralogy in BUSCO gene sets, we analyze the mammal and ray-finned fish datasets using concatenated maximum likelihood and summary coalescent methods by randomly choosing one paralog per locus if these are present. The resulting phylogenomic trees are overall consistent with the reference phylogenies, although small discrepancies were found. Phylogeny-guided paralogy removal also changes the sequences retained for many loci, but whether these changes alter the inferred species trees remains to be tested.

evolutionary biology↗

bioRxiv2026

The structure of a 2-MDa chloroplast RNA polymerase reveals unexpected evolutionary complexity

Transcription in chloroplasts depends on the Plastid-Encoded RNA polymerase (PEP), a bacterial-derived enzyme whose catalytic core remains encoded by the highly reduced genome inherited from the cyanobacterial ancestor. In land plants, PEP has roughly doubled in size, expanding into a [~]1 MDa multisubunit machinery through the acquisition of numerous nuclear-encoded subunits. Based on phylogenetic analyses, this added complexity has been widely attributed to the demands of plant terrestrialization. Contrary to this view, we show that in the unicellular green alga Chlamydomonas reinhardtii, PEP assembles into an even larger [~]2 MDa complex containing twelve previously uncharacterized nuclear-encoded subunits (PEPS1-12), representing an RNA polymerase architecture of unprecedented size. A cryo-EM structure at 2.7 [A] resolution reveals that several of these subunits occupy positions analogous to those in land plant PEP, and that metabolic enzyme folds have been repurposed as structural scaffolds stabilizing the highly expanded plastid-encoded core. Despite this, most of the newly identified PEPS subunits lack detectable sequence or structural similarity to their land plant counterparts. These findings demonstrate that PEP complexity is not a hallmark of land plant evolution and may instead reflect, at least in part, the evolutionary entrenchment of additional subunits around an expanded plastid-encoded core. More broadly, they suggest that essential organellar machines can acquire substantial structural complexity that leaves little trace in sequence-based analyses, a pattern consistent with constructive neutral evolution.

molecular biology↗

bioRxiv2026

Skin microbiome mirrors habitat divergence in amphibious combtooth blenny fish (Teleostei, Blenniidae)

Host-associated microbiomes play vital roles in organismal health, ecological interactions, and evolution, yet little is known about how microbial communities shift during the transition from aquatic to increasingly terrestrial habitats. Here, we characterize the skin microbiomes of three combtooth blenny species (Blenniella paula, Praealticus labrovittatus, and Alticus arnoldorum) that occupy distinct positions along the intertidal gradient in Guam--from fully subtidal (and exclusively aquatic) to intertidal (amphibious) and supratidal environments (exclusively terrestrial). Using 16S rRNA amplicon sequencing, we compared skin-associated bacterial communities with those in surrounding seawater and substrate biofilms to assess habitat influences on microbiome structure. Skin microbiomes were distinct from environmental microbial communities, indicating strong ecological filtering by the host. The divergence between skin and substrate microbiomes in the three species parallels their distribution along progressively higher zones of the intertidal gradient. The most divergent skin microbiome was that of the supratidal fish A. arnoldorum, characterized by higher Gammaproteobacteria abundance and enrichment of epiphytic and mucus-associated taxa. Across all species, we identified 32 microbial orders significantly enriched on the skin relative to environmental samples, including taxa commonly associated with fish mucosa (e.g., Vibrio, Alteromonas, Cetobacterium) and others rarely reported in aquatic marine fish (e.g., Rubritalea, Granulosicoccus). Several rare taxa with potential pathogenicity were also detected at low abundances. Together, these findings suggest that habitat-specific selective pressures strongly shape fish skin microbiomes along subtidal (aquatic) to supratidal (terrestrial) habitats and suggest that microbial symbionts may contribute to the ecological and physiological adaptations enabling amphibious lifestyles. This study provides the first comparative assessment of skin microbiome divergence across amphibious fish species along an intertidal gradient and offers a framework for predicting microbiome responses to environmental change.

evolutionary biology↗

bioRxiv2026

A deep genetic structure phylogenomically frames the closest algal relatives of land plants

To discern the nature of the closest streptophyte algal relatives of land plants (embryophytes) is a major question in the field of plant evolutionary biology; discerning that nature is essential for our ability to infer the last common ancestor of embryophytes and algae, allowing to retrace the adaptations that ushered in the conquest of land by plants. Albeit initially coming as a surprise, all major phylogenomic efforts have concluded that the Zygnematophyceae are the algal sisters to land plants1-6. The Zygnematophyceae are the streptophyte algal class with the greatest species richness7 and while we now have ample genome information on a few select members of zygnematophytes8-13, our understanding of the genetic and genomic divergence as well as potential is limited by a lack of phylodiverse data that accounts for this diversity and integrates it into a phylogenomic framework. We here sequenced 43 new transcriptome datasets for the Zygnematophyceae and built a phylogenomic tree based on a total of 104 zygnematophyceaen transcriptomes and 2243 loci. We recover a deep genetic structure for the Zygnematophyceae, revealing that this algal class is ancient. Despite the deep split between Spirogyrales and their unicellular sister group Desmidiales, most Spirogyrales emerged after pronounced genetic divergence, accommodating the attainment of multicellularity and divergent traits such as unique cell and plastid division13. Overall, our data capture signatures of massive ancient radiations. Zygnematophyceae are characterized by deep genetic divergences that necessitated a phylodiverse sampling to be revealed, together with their vast evolutionary history, and to illuminate the nature of the algal progenitors of land plants.

evolutionary biology↗

bioRxiv2024

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 combined time-course stress profiling using photophysiology, transcriptomics on 2.7 Tbp of data, and metabolite profiling analyses on more than 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 convergence 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.

evolutionary biology↗

bioRxiv2023

Metabolic rewiring compensates for the loss of glutamate and aspartate biosynthesis in Bacillus subtilis

Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, with excess nitrogen, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle. It will be interesting to investigate whether the B. subtilis strain using the alternative glutamate biosynthesis route can evolve in such a way that it robustly grows during nitrogen limitation and excess.

microbiology↗

bioRxiv2023

Phylogenomic insights into the first multicellular streptophyte

Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants)1-4. 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 habitats5,6. 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 phylogenomic analysis built on 420 loci and sophisticated models, we establish a novel phylogenetic structure, dividing the six distinct genera of Klebsormidiophyceae in a novel four-order-system, with deep divergences more than 898, 765, and 734 million years ago. The reconstruction of ancestral states for habitat suggests an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with Klebsormidiales having conquered land earlier than embryophytes. Focusing on the body plan of the last common ancestor of Klebsormidiophyceae, we postulate it was likely filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. Our data reveal that the first multicellular streptophytes likely lived more than 900 million years ago.

evolutionary biology↗

bioRxiv2023

Efficient hybrid strategies for assembling the plastome, mitochondriome, and large nuclear genome of diploid Ranunculus cassubicifolius (Ranunculaceae)

Currently, it is still a challenge - in terms of laboratory effort and cost, as well as assembly quality - to unravel the sequence of large and complex genomes from non-model plants. This often hampers the study of evolutionarily intricate species groups. The species-rich genus Ranunculus (Ranunculaceae) is an angiosperm model system for the study of polyploidy, apomixis, reticulate evolution, and biogeography. However, neither mitochondrial, nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) or PacBio/HiFi long-read, and hybrid-read assembly strategies. We used the diploid progenitor species R. cassubicifolius (R. auricomus complex), and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome, we favored a PacBio-based assembly three-times polished with filtered reads and subsequently scaffolded into 8 pseudochromosomes by chromatin conformation data (Hi-C) as the representative sequence. We obtained a haploid genome sequence with 2.69 Gbp, 94.5% complete BUSCO embryophyta_odb10 genes found, and 31,322 annotated genes. The genomic information presented here will improve phylogenomic analyses in this species complex, and will enable advanced functional, evolutionary, and biogeographic analyses for the genus and beyond Ranunculaceae in the future. Significance StatementThe genus Ranunculus is a model system in flowering plants for polyploidy, apomixis, evolution, and biogeography research. We present the first nuclear and mitochondrial genome sequence, and the plastid evolution of Ranunculaceae. Using Illumina, ONT, and PacBio data, we developed an efficient assembly strategy that can be applied to other non-model plants. Results presented here are useful for improving population genomic and phylogenomic analyses, and enable better functional analyses at species, genus and family level.

genomics↗

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↗

bioRxiv2022

Environmental gradients reveal stress hubs predating plant terrestrialization

Plant terrestrialization brought forth the land plants (embryophytes). Embryophytes account for most of the biomass on land and evolved from streptophyte algae in a singular event. Recent advances have unraveled the first full genomes of the closest algal relatives of land plants; among the first such species was Mesotaenium endlicherianum. Here, we used fine-combed RNAseq in tandem with photophysiological assessment on Mesotaenium exposed to a continuous range of temperature and light cues. Our data establish a grid of 42 different conditions, resulting in 128 transcriptomes and ~1.5 Tbp (~9.9 billion reads) of data to study combinatory effects of stress response using clustering along gradients. We describe major hubs in genetic networks underpinning stress response and acclimation in the molecular physiology of Mesotaenium. Our data suggest that lipid droplet formation, plastid and cell wall-derived signals denominate molecular programs since more than 600 million years of streptophyte evolution--before plants made their first steps on land.

evolutionary biology↗

bioRxiv2022

A phylogenomically informed five-order system for the closest relatives of land plants

The evolution of streptophytes had a profound impact on life on Earth. They brought forth those photosynthetic eukaryotes that today dominate the macroscopic flora: the land plants (Embryophyta) [1]. There is convincing evidence that the unicellular/filamentous Zygnematophyceae--and not the morphologically more elaborate Coleochaetophyceae or Charophyceae--are the closest algal relatives of land plants [2, 3, 4, 5, 6]. Despite the species richness (>4,000), wide distribution, and key evolutionary position of the zygnematophytes, their internal phylogeny remains largely unresolved [7, 8]. There are also putative zygnematophytes with interesting body plan modifications (e.g., filamentous growth) whose phylogenetic affiliations remain unknown. Here, we studied a filamentous green alga (strain MZCH580) from an Austrian peat bog with central or parietal chloroplasts that lack discernible pyrenoids. It represents Mougeotiopsis calospora PALLA, an enigmatic alga that was described more than 120 years ago [9], but never subjected to molecular analyses. We generated transcriptomic data of M. calospora strain MZCH580, and conducted comprehensive phylogenomic analyses (326 nuclear loci) for 46 taxonomically diverse zygnematophytes. Strain MZCH580 falls in a deep-branching zygnematophycean clade together with some unicellular species, and thus represents a formerly unknown zygnematophycean lineage with filamentous growth. Our well-supported phylogenomic tree lets us propose a new five-order system for the Zygnematophyceae, and provides evidence for at least five independent origins of true filamentous growth in the closest algal relatives of land plants. This phylogeny provides a robust and comprehensive framework for performing comparative analyses and inferring the evolution of cellular traits and body plans in the closest relatives of land plants.

evolutionary biology↗

bioRxiv2021

Underwater CAM photosynthesis elucidated by Isoetes genome

To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigated the underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identified several key differences. Notably, for carboxylation of PEP, Isoetes recruited the lesser-known "bacterial-type" PEPC, along with the "plant-type" exclusively used in other terrestrial CAM and C4 plants. Furthermore, we found that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.

plant biology↗

bioRxiv2021

The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families

Land plants constantly respond to fluctuations in their environment. Part of their response is the production of a diverse repertoire of specialized metabolites. One of the foremost sources for metabolites relevant to environmental responses is the phenylpropanoid pathway, which was long thought to be a land plant-specific adaptation shaped by selective forces in the terrestrial habitat. Recent data have however revealed that streptophyte algae, the algal relatives of land plants, have candidates for the genetic toolkit for phenylpropanoid biosynthesis and produce phenylpropanoid-derived metabolites. Using phylogenetic and sequence analyses, we here show that the enzyme families that orchestrate pivotal steps in phenylpropanoid biosynthesis have independently undergone pronounced radiations and divergence in multiple lineages of major groups of land plants; sister to many of these radiated gene families are streptophyte algal candidates for these enzymes. These radiations suggest a high evolutionary versatility in the enzyme families involved in the phenylpropanoid-derived metabolism across embryophytes. We suggest that this versatility likely translates into functional divergence and may explain the key to one of the defining traits of embryophytes: a rich specialized metabolism.

plant biology↗

bioRxiv2020

A molecular timescale for the origin of red algal-derived plastids

In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. These lineages and countless others representing a huge diversity of forms and lifestyles all belong to four algal groups: cryptophytes, ochrophytes, haptophytes, and myzozoans. Despite the ecological importance of these groups, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. Over the last years, new hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we have established a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using a taxon- and gene-rich phylogenomic dataset combined to Bayesian molecular clock analyses. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlapped in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which has profoundly altered the global geochemical and ecological conditions of the Earth.

evolutionary biology↗

bioRxiv2020

Phylogenomic Insights into the Origin of Primary Plastids

The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and a cyanobacterium, presumably in a common ancestor of all primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, the monophyly of both plastid and host (nuclear) genomes is required to support a single ancestral endosymbiosis, whereas non-monophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the Archaeplastida host monophyly in four available phylogenomic datasets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes loci were investigated. Our analyses revealed a general lack of support for host monophyly in the shorter individual datasets. However, when analyzed together under rigorous data curation and complex mixture evolutionary models, the combined dataset consistently recovered the monophyly of Archaeplastida hosts. This study represents an important step towards better understanding the eukaryotic evolution and the origin of plastids.

evolutionary biology↗

bioRxiv2019

Abiotic environmental adaptation in vertebrates is characterized by functional genomic constraint

Understanding the genomic basis of adaptation to different abiotic environments is important for understanding organismal responses to current short-term environmental fluctuations. Using functional and comparative genomics approaches, we here investigated whether genomic adaptation to a set of environmental parameters is contingent across vertebrate genomes or, alternatively, contains an element of evolutionary constraint that would be evident through recurrent involvement of specific subsets of genes and functions in adaptation to similar environments. We first identified 200 genes with signatures of selection from transcriptomes of 24 species of lacertid lizards with known adaptations in preferred temperature, correlated with thermal environment experienced by these lizards in their range. In order to discern genes adapting to climate from other selective factors, we then performed a meta-analysis of 1100 genes with signatures of selection obtained from-omics studies in vertebrate species adapted to different abiotic environments. We found that this gene set formed a tightly connected interactome which was to 23% enriched in predicted functions of adaptation to climate and to 18% involved in organismal stress response. We found a much higher degree of recurrent use of identical genes (43.6%) and functional similarity than expected by chance, and no clear division between genes used in ectotherm and endotherm physiological strategies. 171 out of 200 genes of Lacertidae were part of this network, indicating that a comparative genomic approach can help to disentangle genes functionally related to adaptation to different abiotic environments from other selective factors. These results furthermore highlight an important role of genomic constraint in adaptation to the abiotic environment, and narrows the set of candidate markers to be used in future research on environmental adaptability related to climate change.\n\nSignificance Statement / Nontechnical summaryWhile the convergent evolution of phenotypes in similar environments is a well-studied phenomenon, the genomic basis of such common phenotypes and physiologies is still enigmatic. The prevalent notion is that re-use of the same genes to adapt to similar environments in different species is about as likely as winning the lottery - but organismal systems are also, to some extent, comparable between different species such as man and fruit fly through shared genes and gene functions. In this paper, we test whether constraint or contingency is more prevalent in genomic adaptation of vertebrates to aspects of their abiotic environment. We find evidence for strong functional constraint and stress responsiveness of the genes involved, which might help understand how currently experienced stress under changing climates may result in future adaptation.

evolutionary biology↗