Biology subjects

Jamy, M.

Publications and source records attributed to Jamy, M..

10 recordsLinked to original sources

bioRxiv2026

The Leray-XT COI primer pair is not suitable for observing ciliates and radiolarians

The Leray-XT primer pair has been widely used to amplify the mitochondrial cytochrome c oxidase subunit I (COI) gene from animals. In some marine metabarcoding studies, protists have also been amplified and sequenced using these primers. Here, we ask if the Leray-XT COI primer pair is suitable for observing ciliates and radiolarians, which are numerically and ecologically important components of marine protistan communities. We show that while there are sufficient COI reference sequences for ciliates in NCBI for taxonomic assignments, there are currently only two COI reference sequences for radiolarians. Using in-silico analyses, we additionally show that while the reverse primer Leray-XT primer can bind and potentially amplify both ciliates and radiolarians, the forward primer cannot bind to either taxon. These results show that the Leray-XT primer pair is not suitable for observing ciliates and radiolarians, although it may be useful for observing other marine protistan taxa.

microbiology↗

bioRxiv2025

New deep-branching environmental plastid genomes on the algal tree of life

Marine algae support the entire ocean ecosystem and beyond. Algae in culture poorly represents their large environmental diversity, and we still have a limited understanding of their convoluted evolution by endosymbiosis. Here, we performed a phylogeny-guided plastid genome-resolved metagenomic survey of Tara Oceans expeditions. We present a curated resource of 660 new non-redundant plastid genomes of environmental pelagic algae. This catalogue vastly expands the plastid genome diversity within major algal groups, often corresponding to algae without closely related reference genomes. Notably, we recovered four plastid genomes, including one near complete, forming a deep-branching plastid lineage of nano-size algae that we informally named leptophytes. This group is globally distributed and generally rare, although it can reach relatively high abundance at least in the Arctic. A mitochondrial contig including 62 genes showing strong read coverage correlation with leptophytes was also recovered from these Arctic samples and assigned to this group. Leptophytes encompass the enigmatic marine plastid group DPL2, one of the very few known plastid groups not clearly belonging to any major algal groups and for which only 16S rDNA amplicon data is available. Extensive gene content comparison and organellar phylogenomics support the view that leptophytes are sister to haptophytes, and raise the intriguing possibility that cryptophytes acquired their plastids from haptophytes. Collectively, our study demonstrates that metagenomics can reveal currently hidden diversity of organellar genomes, and shows the importance of including this diversity to improve models for plastid evolution.

evolutionary biology↗

bioRxiv2023

nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

1 AbstractMetagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases. This, however, is a very time-consuming task when performed manually - particularly when combined with the appropriate preprocessing of sequencing reads before the classification. Here we present nf-core/taxprofiler, a highly parallelised read-processing and taxonomic classification pipeline. It is designed for the automated and simultaneous classification and/or profiling of both short- and long-read metagenomic sequencing libraries against a 11 taxonomic classifiers and profilers as well as databases within a single pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the pipeline benefits from high levels of scalability and portability, accommodating from small to extremely large projects on a wide range of computing infrastructure. It has been developed following best-practise software development practises and community support to ensure longevity and adaptability of the pipeline, to help keep it up to date with the field of metagenomics.

genomics↗

bioRxiv2023

Identification of a new gregarine parasite in mass mortality events of freshwater pearl mussels (Margaritifera margaritifera) in Sweden

Freshwater bivalves play key ecological roles in lakes and rivers, largely contributing to healthy ecosystems. The freshwater pearl mussel, Margaritifera margaritifera, is found in Europe and on the East coast of North America. Once common in oxygenated streams, M. margaritifera is rapidly declining, and consequently assessed as a threatened species worldwide. Deterioration of water quality has been considered the main factors for the mass mortality events affecting this species. Yet, the role of parasitic infections has not been investigated. Here, we report the discovery of three novel protist lineages found in Swedish populations of M. margaritifera belonging to one of the terrestrial groups of gregarines (Eugregarinorida, Apicomplexa). These lineages are closely related-but clearly separated- from the tadpole parasite Nematopsis temporariae. In one lineage, which is specifically associated with mortality events of M. margaritifera, we found using microscopy and in situ hybridization cysts in the gills and other organs of diseased individual, containing single vermiform zoites. This represents the first report of a parasitic infection in M. margaritifera that may be linked to the decline of this mussel species. We propose a tentative life cycle with distribution of different developmental forms and potential exit from the host into the environment.

microbiology↗

bioRxiv2023

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes

The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operons clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing techniques (PacBio HiFi, and Nanopore UMI with/without clonal pre-amplification) and three tools for resolving amplicons sequence variants (ASVs) (Uchime3, Unoise3, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essential error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples.

microbiology↗

bioRxiv2022

metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists.

In recent years, metabarcoding has become the method of choice for investigating the composition and assembly of microbial eukaryotic communities, and an increasing number of environmental datasets are being published. Although unprocessed sequence files are often publicly available, processed data, i.e. sequences clustered as operational taxonomic units (OTUs) or amplicon sequence variants (ASVs) are rarely at hand in a comparable format. This hampers comparative studies between different environments and datasets, for example examining the biogeographical patterns of specific groups/species, as well analysing the micro-genetic diversity within these groups. Here, we present a newly-assembled database of processed 18S rRNA metabarcodes that are annotated with the PR2 reference sequence database. This database, called metaPR2, contains 41 datasets corresponding to more than 4,000 samples and 73,000 ASVs. The database is accessible through both a web-based interface (https://shiny.metapr2.org) and as an R package, and should prove very useful to all researchers working on protist diversity in a variety of systems.

ecology↗

bioRxiv2021

Global patterns and rates of habitat transitions across the eukaryotic tree of life

The successful colonisation of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and terrestrial (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine-terrestrial transitions, but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich environmental phylogenies inferred from a combination of long-read and short-read metabarcoding data spanning the ribosomal DNA operon. Our results show that overall marine and terrestrial microbial communities are phylogenetically distinct, but transitions have occurred in both directions in almost all major eukaryotic lineages, with at least 350 transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has most likely been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-saline habitats, and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that crossing the salt barrier has played an important role in eukaryotic evolution by providing new ecological niches to fill.

evolutionary biology↗

bioRxiv2019

Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. However, new long-read sequencing technologies such as the Pacific Biosciences platform may provide sufficiently large sequence lengths to overcome the poor phylogenetic resolution of short amplicons. To test this idea, we amplified soil DNA and used PacBio Circular Consensus Sequencing (CCS) to obtain a ~4500 bp region of the eukaryotic rDNA operon spanning most of the small (18S) and large subunit (28S) ribosomal RNA genes. The CCS reads were first treated with a novel curation workflow that generated 650 high-quality OTUs containing the physically linked 18S and 28S regions of the long amplicons. In order to assign taxonomy to these OTUs, we developed a phylogeny-aware approach based on the 18S region that showed greater accuracy and sensitivity than similarity-based and phylogenetic placement-based methods using shorter reads. The taxonomically-annotated OTUs were then combined with available 18S and 28S reference sequences to infer a well-resolved phylogeny spanning all major groups of eukaryotes, allowing to accurately derive the evolutionary origin of environmental diversity. A total of 1019 sequences were included, of which a majority (58%) corresponded to the new long environmental CCS reads. Comparisons to the 18S-only region of our amplicons revealed that the combined 18S-28S genes globally increased the phylogenetic resolution, recovering specific groupings otherwise missing. The long-reads also allowed to directly investigate the relationships among environmental sequences themselves, which represents a key advantage over the placement of short reads on a reference phylogeny. Altogether, our results show that long amplicons can be treated in a full phylogenetic framework to provide greater taxonomic resolution and a robust evolutionary perspective to environmental DNA.

microbiology↗

bioRxiv2018

New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these orphan groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome datasets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker TSAR to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

evolutionary biology↗

bioRxiv2017

RNA sequencing of Stentor cell fragments reveals key processes underlying cellular regeneration

While ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 up-regulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many up-regulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes such as dual-specific tyrosine-(Y)-phosphorylation regulated kinases and MORN domain containing proteins that seemingly act as key-regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies, our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities.

genomics↗