De novo assembled single-cell transcriptomes from aquatic phytoflagellates reveal a metabolically distinct cell population

• Single-cell transcriptomics has rapidly become a standard tool for decoding cell identity, fate and interactions in mammalian model organisms. Adopting such techniques to uncover functional dynamics in aquatic single-celled organisms holds huge potential, but evidence of applicability to non-model, poorly understood microeukaryotes remains limited. In the present study, live Ochromonas triangulata cells from fast and slow growth phases were FACS-sorted based on food vacuole staining and chlorophyll fluorescence, and single-cell transcriptomic libraries were prepared following the Smart-seq2 protocol. In total, 744 transcriptomes were Illumina sequenced. Lacking a reference genome, transcriptomes were assembled de novo using Trinity and resulting transcripts were annotated by BLAST using the Swiss-Prot database. Following read mapping, differential gene expression was evaluated using DESeq2 and metabolic maps were generated based on pathways from the KEGG Orthology database. Clustering the read counts revealed the identity of the two expected transcriptional states corresponding to each growth phase as well as a third distinct cluster of cells present in both growth phases. This cryptic group showed extensive downregulation of genes in pathways associated with ribosome-functioning, CO2 fixation and core carbohydrate catabolism such as glycolysis, β oxidation of fatty acids and tricarboxylic acid cycle. Nevertheless, the biological underpinnings of this population, which would have remained unnoticed in an integrated approach, could not be clarified. Additionally, the possibility of using carry-over rRNA reads for taxonomic annotation was tested, verifying the identity of 88% of the O. triangulata cells. In conclusion, we demonstrate the power of single cell transcriptomics for metabolic mapping of microeukaryotes for which reference resources might be limited and thereby highlight its potential as a tool to gain access to microeukaryote dynamics in natural communities.

Ämnesord

NATURVETENSKAP  -- Biologi -- Cellbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Cell Biology (hsv//eng)

NATURVETENSKAP  -- Biologi -- Mikrobiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Microbiology (hsv//eng)

Nyckelord

single-cell trancriptomics

Smart-seq2

Ochromonas triangulata

18S rRNA gene

Publikations- och innehållstyp

vet (ämneskategori)

ovr (ämneskategori)