Biology subjects

Not, F.

Publications and source records attributed to Not, F..

17 recordsLinked to original sources

bioRxiv2026

Seasonal patterns in Synechococcus pigment diversity at two temperate sites with contrasting oceanic regimes

Competition for light has driven extensive pigment diversification among phytoplankton species, yet how this diversity shapes their spatiotemporal distribution in the field has been little studied so far. The cyanobacterium Synechococcus is an ideal model for addressing this issue, since this group has colonized most light spectral niches in marine environments. Here, we used an approach based on marker read recruitment from metagenomes to analyze the seasonal succession of Synechococcus pigment types (PTs) at two time-series stations off French coasts exhibiting contrasting oceanic regimes. Marked seasonality was observed at both sites. The shallow, permanently mixed English Channel site SOMLIT-Astan was characterized by an alternation between green-light specialists (PT 3a) peaking in spring, and chromatic acclimaters type A (PT 3dA) accounting for most of the Synechococcus community in winter. In contrast, the pigment diversity was much higher at the deep Mediterranean station BOUSSOLE. In the upper layer, the two main PTs were the blue light specialists (PT 3c), which dominated the community in summer and fall, and PT 3dA cells, which were more abundant in spring. The third most abundant PT was chromatic acclimaters type B (PT 3dB), which accounted for up to 15% of the surface community in late fall. Strikingly, PT 3dA was dominant at depth during most of the year. Multivariate analyses between PT abundances, clade abundances and environmental factors, notably water color indexes, suggested new associations between PTs to specific clades and ecological niches. This study provides novel insights for refining distribution models of Synechococcus PTs and phytoplankton groups in general.

microbiology↗

bioRxiv2025

From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding

In the last decades environmental metabarcoding has revolutionised biodiversity research, particularly for microbial organisms such as protists, enabling large-scale assessments of diversity and ecological patterns across time and space. With the advent of long-read sequencing, Nanopore-based metabarcoding represents a promising alternative to short-read approaches. Due to the limited number of available studies, the effectiveness of Nanopore sequencing - alone or in combination with short-read data - for assessing the biodiversity and ecological patterns of protists in different ecosystems is not yet sufficiently explored. Here we present BaNaNA (Barcoding Nanopore Neat Annotator), a pipeline designed to generate high-quality OTUs and abundance estimates from Nanopore sequencing data. The performance of the pipeline was evaluated using a mock community as well as on marine and freshwater environmental samples to demonstrate its relevance for protist biodiversity and ecological studies. Our results show that BaNaNA generates high-quality full-length 18S rDNA OTUs from Nanopore long reads that are directly comparable to short-read V4-18S rDNA ASVs, supporting their synergistic use in long-term biodiversity studies. While both approaches reveal similar overall community diversity, long-read OTUs provide greater taxonomic resolution, richer phylogenetic information enabling the discovery of new clades, and yield fewer false positives. These advantages make long-read Nanopore metabarcoding not only a powerful complement but also a reliable replacement to short-read methods. By providing a pipeline for processing Nanopore data, BaNaNA paves the way for a broader application of long-read Nanopore sequencing in protist ecology and biodiversity research.

ecology↗

bioRxiv2025

The give and take in photosymbiosis unraveled by metabolomics of Radiolaria

Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments they are among the most important primary producers. Systematic studies of radiolarian biology are limited because Radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis we address here the metabolic contributions of the partners to the performance of the holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic Radiolaria - colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts metabolites by the host. The metabolites identified in both the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in both the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying Radiolaria-microalgae photosymbioses.

microbiology↗

bioRxiv2024

Diversity and evolution of Radiolaria: Beyond the stars of the ocean

Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons have left an extensive fossil record which is extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B and Rad-C. We suggest that most of this undescribed diversity likely comprises skeleton-less life forms or endosymbionts, explaining their elusive nature. Phylogenetic analyses highlight the need for major revision of high-level Radiolaria taxonomy, including placement of the Collodaria within the order Nassellaria. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria [~]760 million years ago (Ma), the development of the skeleton in the early Paleozoic ([~]500 Ma) and the onset of photosymbiotic relationships during the mid to late Mesozoic ([~]140 Ma), related to geological periods of oligotrophy and anoxia. The results presented here provide an extensive and robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.

evolutionary biology↗

bioRxiv2024

Single-cell transcriptomics highlights sexual cues among reproductive life stages of uncultivated Acantharia (Radiolaria)

As an innate property of life, the ability to reproduce is a key process for the perpetuation of organisms. Along the evolution of protist reproductive strategies, the molecular machinery of sexual recombination is estimated to have been inherited from the last eukaryotic common ancestor (LECA). Nevertheless, unraveling the sexual cycles of extant free-living protist lineages remains challenging, given the enigmatic roles of many uncultivated life stages. Among the uncultivated planktonic group of Acantharia (Radiolaria), a hypothetical sexual cycle has been proposed since the late 19th century, including the existence of a gamete-like life stage of undetermined ploidy, referred to as swarmers. In order to investigate the sexual nature of acantharian reproductive stages, we conducted single-cell transcriptomic analysis across various acantharian life stages. Our results show distinct functional profiles for reproductive and vegetative life stages, while revealing the expression of the reference eukaryotic genes involved in gamete fusion, HAP2/GCS1 and GEX1-KAR5, in swarmers and pre-swarmer stages. Annotation of differentially expressed life stage-specific genes, also highlights putative meiosis-related functions among swarmers, while suggesting the existence of a potential swarmer/vegetative intermediate stage expressing putative growth-related genes. This original life stage-specific genetic data is coherent with morphological evidence supporting the existence of an acantharian sexual cycle, with swarmers acting as gametes. Moreover, it paves the way for a deeper understanding of radiolarian cell biology and ecology at a single-cell scale. HighlightsO_LIAcantharia demonstrate both morphological and genetic evidence of a sexual cycle C_LIO_LIAcantharian reproductive stages are enriched in functions related to cell division C_LIO_LINuclear fusion gene family GEX1-KAR5 is up-regulated in putative acantharian gametes C_LIO_LIMost expressed genes specific to acantharian reproductive stages are unassigned C_LIO_LIReproduction-specific unassigned genes include putative sex-related functions C_LI

microbiology↗

bioRxiv2022

Global observation of plankton communities from space

Satellite remote sensing from space is a powerful way to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here we present an approach to identify representative communities from a global plankton network that included both zooplankton and phytoplankton and using global satellite observations to predict their biogeography. Six representative plankton communities were identified from a global co-occurrence network inferred using a novel rDNA 18S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to train a model that predicted these representative communities from satellite data. The model showed an overall 67% accuracy in the prediction of the representative communities. The prediction based on 17 satellite-derived parameters showed better performance than based only on temperature and/or the concentration of chlorophyll a. The trained model allowed to predict the global spatiotemporal distribution of communities over 19-years. Our model exhibited strong seasonal changes in the community compositions in the subarctic-subtropical boundary regions, which were consistent with previous field observations. This network-oriented approach can easily be extended to more comprehensive models including prokaryotes as well as viruses.

ecology↗

bioRxiv2022

Beyond the limits of the unassigned protist microbiome: inferring large-scale spatio-temporal patterns of marine parasites

Marine protists are major components of the oceanic microbiome that remain largely unrepresented in culture collections and genomic reference databases. The exploration of this uncharted protist diversity in oceanic communities relies essentially on studying genetic markers from the environment as taxonomic barcodes. Here we report that across 6 large scale spatio-temporal planktonic surveys, half of the genetic barcodes remain taxonomically unassigned at the genus level, preventing a fine ecological understanding for numerous protist lineages. Among them, parasitic Syndiniales (Dinoflagellata) appear as the least described protist group. We have developed a computational workflow, integrating diverse 18S rDNA gene metabarcoding datasets, in order to infer large-scale ecological patterns at 100% similarity of the genetic marker, overcoming the limitation of taxonomic assignment. From a spatial perspective, we identified 2 171 unassigned clusters exclusively shared between the Tropical/Subtropical Ocean and the Mediterranean Sea among all Syndiniales orders and 25 ubiquitous clusters shared within all the studied marine regions. From a temporal perspective, over 3 time-series, we highlighted 38 unassigned clusters that follow rhythmic patterns of recurrence and are the best indicators of parasite communitys variation. These clusters withhold potential as ecosystem change indicators, mirroring their associated host community responses. Our results underline the importance of Syndiniales in structuring planktonic communities through space and time, raising questions regarding host-parasite association specificity and the trophic mode of persistent Syndiniales, while providing an innovative framework for prioritizing unassigned protist taxa for further description.

genomics↗

bioRxiv2021

Intra-genomic rDNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

Ribosomal DNA (rDNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large scale exploration of environmental microbial diversity through metabarcoding approaches have been focused mainly on the V4 and V9 regions of the 18S rDNA gene. The accurate interpretation of such environmental surveys is hampered by technical (e.g., PCR and sequencing errors) and biological biases (e.g., intra-genomic variability). Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra-genomic variability of Nassellaria and Spumellaria is generally low, yet some Spumellaria specimens showed two different copies of the V4 with <97% similarity. From the different sequencing methods, Illumina showed the highest number of contaminations (i.e., environmental DNA, cross-contamination, tag-jumping), revealed by its high sequencing depth; and MinION showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results highlight the requirement for a careful interpretation of Illumina based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full environmental rDNA metabarcoding surveys.

molecular biology↗

bioRxiv2021

Seasonal temporal dynamics of marine protists communities in tidally mixed coastal waters

Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes determining marine species and community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts and ribosomal DNA metabarcoding from plankton samples collected biweekly over 8 years (2009-2016) at the SOMLIT-Astan station (Roscoff, Western English Channel). Considering the temporal structure of community dynamics (creating temporal correlation), we elucidated the recurrent seasonal pattern of the dominant species and OTUs (rDNA-derived taxa) that drive annual plankton successions. The use of morphological and molecular analyses in combination allowed us to assess absolute species abundance while improving taxonomic resolution, and revealed a greater diversity. Overall, our results underpinned a protist community characterised by a seasonal structure, which is supported by the dominant OTUs. We detected that some were partly benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. While the occurrence of these microorganisms is driven by the physical and biogeochemical conditions of the environment, internal community processes, such as the complex network of biotic interactions, also play a key role in shaping protist communities.

ecology↗

bioRxiv2021

Planktonic protist diversity across contrasting Subtropical and Subantarctic waters of the southwest Pacific

Planktonic protists are an essential component of marine pelagic ecosystems where they mediate important trophic and biogeochemical functions. Although these functions are largely influenced by their taxonomic affiliation, the composition and spatial variability of planktonic protist communities remain poorly characterized in vast areas of the ocean. Here, we investigated the diversity of these communities in contrasting oceanographic conditions of the southwest Pacific sector (33-58{degrees}S) using DNA metabarcoding of the 18S rRNA gene. Seawater samples collected during twelve cruises (n = 482, 0-2000 m) conducted east of New Zealand were used to characterize protist communities in Subtropical (STW) and Subantarctic (SAW) water masses and the Subtropical Front (STF) that separates them. Diversity decreased with latitude and temperature but tended to be lowest in the STF. Sample ordination resulting from the abundance of amplicon single variants (ASVs) corresponded to the different water masses. Overall, Dinophyceae (34% of standardized total number of reads) and Chlorophyta (27%) co-dominated the euphotic zone, but their relative abundance and composition at class and lower taxonomic levels varied consistently between water masses. Among Chlorophyta, several picoplanktonic algae species of the Mamiellophyceae class including Ostreococcus lucimarinus dominated in STW, while the Chloropicophyceae species Chloroparvula pacifica was most abundant in SAW. Bacillariophyta (7%), Prymnesiophyceae (5%), and Pelagophyceae (3%) classes were less abundant but showed analogous water mass specificity at class and finer taxonomic levels. Protist community composition in the STF had mixed characteristics and showed regional differences with the southern STF (50{degrees}S) having more resemblance with subantarctic communities than the STF over the Chatham Rise region (42-44{degrees}S). Below the euphotic zone, Radiolaria sequences dominated the dataset (52%) followed by Dinophyceae (27%) and other heterotrophic groups like Marine Stramenopiles and ciliates (3%). Among Radiolaria, several unidentified ASVs assigned to Spumellarida were most abundant, but showed significantly different distribution between STW and SAW highlighting the need to further investigate the taxonomy and ecology of this group. This study represents a significant step forward towards characterizing protistan communities composition in relation to major water masses and fronts in the South Pacific providing new insights about the biogeography and ecological preferences of different taxa from class to species and genotypic level. HighlightsO_LIWater-mass preference of different taxa emerged at class, species and genotypic level. C_LIO_LIMamiellophyceae green algae dominated in subtropical waters. C_LIO_LIDinophyceae and Chloropicophyceae green algae dominated in subantarctic waters. C_LIO_LIA diverse assemblage of Radiolaria dominated the mesopelagic zone. C_LIO_LISmall rather than large taxa dominated phytoplankton blooms in subtropical waters. C_LI

ecology↗

bioRxiv2020

Morpho-molecular diversity and evolutionary analyses suggest hidden life styles in Spumellaria (Radiolaria)

Spumellaria (Radiolaria, Rhizaria) are holoplanktonic amoeboid protists, ubiquitous and abundant in the global ocean. Their silicified skeleton preserves very well in sediments displaying an excellent fossil record, from the early middle Cambrian (ca. 509-521 Ma), extremely valuable for paleo-environmental reconstruction studies. Spumellaria are tedious to maintain in laboratory conditions preventing an accurate perception of their extant diversity and ecology in today’s oceans, most of which being inferred from sediment records. This study represents an integrated and comprehensive classification of Spumellaria based on the combination of ribosomal taxonomic marker genes (rDNA) and morphological characteristics. In contrast to established taxonomic knowledge, we demonstrate that symmetry of the skeleton takes more importance than internal structures at high taxonomic rank classification. Such reconsideration allows gathering different morphologies with concentric structure and a spherical or radial symmetry believed to belong to other Radiolaria orders from the fossil record, as for some Entactinaria families. Results obtained in this study suggest the existence of new Spumellaria diversity at early diverging positions, in which a non-bearing skeleton organism lives within shelled ones. Using fossil calibrated molecular clock we estimated the origin of Spumellaria in the middle Cambrian (ca. 515 Ma), in agreement with the appearance of the first radiolarian representatives in the fossil record. The morpho-molecular and evolutionary framework established herein allows a direct connection between living specimens and fossil morphologies from the Cambrian, bringing both a standpoint for future molecular environmental surveys and a better understanding for paleo-environmental reconstruction studies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

molecular biology↗

bioRxiv2020

No evidence of phago-mixotropy in Micromonas polaris, the dominant picophytoplankton species in the Arctic

In the Arctic Ocean, the small green alga Micromonas polaris dominates pico-phytoplankton during the summer months. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analysed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean. Using both fluorescent beads and fluorescently labelled bacteria as prey, we found no evidence of phago-mixotrophy in any M. polaris strain by flow cytometric measurement of prey ingestion. In addition, in silico predictions reveal that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.

ecology↗

bioRxiv2019

Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing

Photosynthetic picoeukaryotes (PPE) are key components of primary production in marine and freshwater ecosystems. In contrast with those of marine environments, freshwater PPE groups have received little attention. In this work, we used flow cytometry cell sorting, microscopy and metabarcoding to investigate the composition of small photosynthetic eukaryote communities from six eutrophic shallow lakes in South America, Argentina. We compared the total molecular diversity obtained from PPE sorted populations as well as from filtered total plankton samples (FTP). Most reads obtained from sorted populations belonged to the classes: Trebouxiophyceae, Chlorophyceae and Bacillariophyceae. We retrieved sequences from non-photosynthetic groups, such as Chytridiomycetes and Ichthyosporea which contain a number of described parasites, indicating that these organisms were probably in association with the autotrophic cells sorted. Dominant groups among sorted PPEs were poorly represented in FTP and their richness was on average lower than in the sorted samples. A significant number of operational taxonomic units (OTUs) were exclusively found in sorting samples, emphasizing that sequences from FTP underestimate the diversity of PPE. Moreover, 22% of the OTUs found among the dominant groups had a low similarity (<95%) with reported sequences in public databases, demonstrating a high potential for novel diversity in these lakes.

ecology↗

bioRxiv2018

Time calibrated morpho-molecular classification of Nassellaria (Radiolaria)

Nassellaria are marine radiolarian protists belonging to the Rhizaria lineage. Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians.

molecular biology↗

bioRxiv2018

Chloroplasts of symbiotic microalgae remain active during bleaching induced by thermal stress in Collodaria (Radiolaria)

Collodaria (Radiolaria) are important contributors to planktonic communities and biogeochemical processes (e.g. the biologic pump) in oligotrophic oceans. Similarly to corals, Collodaria live in symbiosis with dinoflagellate algae, a relationship that is thought to explain partly their ecological success. In the context of global change, the robustness of the symbiotic interaction and potential subsequent bleaching events are worth consideration. In the present study, we compared the ultrastructure morphology, symbiont density, photosynthetic capacities and respiration rates of colonial Collodaria exposed to a range of temperatures corresponding to natural conditions (21{degrees}C), moderate (25{degrees}C) and high (28{degrees}C) thermal stress. We showed that symbiont density immediately decreased when temperature rises to 25{degrees}C and the collodaria holobiont metabolic activity increased. When temperature reached 28{degrees}C, the collodarian host arrived at a tolerance threshold with a respiration nearly stopped and largely damaged morphological structures. Over the course of the experiment the photosynthetic capacities of remaining symbionts were stable, chloroplasts being the last degraded organelles from the microalgae. These results contribute to a better characterization and understanding of temperature-induced bleaching processes in planktonic photosymbiosis.

physiology↗

bioRxiv2017

A de novo approach to disentangle partner identity and function in holobiont systems

BackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.\n\nResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partners transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. Conclusions\n\nIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.

genomics↗

bioRxiv2017

Analysis Of The Genomic Basis Of Functional Diversity In Dinoflagellates Using A Transcriptome-Based Sequence Similarity Network

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.

genomics↗