Rizos, I. | Search bioRxiv

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

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↗