De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis

Abstract

Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.

Changes in Gravitaxis and Gene-Expression in an Euglena gracilis Culture over Time

“…On day 11, changes in photosynthetic and chromosomal genes were observed additionally, to set the number of differentially expressed genes in perspective to the whole genome. GO terms were retrieved from Ebenezer et al [ 8 ] and Cordoba et al [ 7 ]. However, in the recent database of Cordoba for most GO terms far more transcripts were found, provided in Table 2 for comparison (Data of Ebenezer and Cordoba with respect to observed changes are provided in Supplementary S4 ).…”

“…The number of DEG of a same GO term was correlated with the total number of genes classified to the same GO term. The published databases provided in Ebenezer et al 2018 ( Supplementary S2 “proteome”) [ 8 ] and Cordoba et al 2021 ( Supplementary S2 ) [ 7 ] served as references.…”

Taxonomic and morphofunctional phytoplankton response to environmental variability in rivers from different hydrographic basins in Southern Brazil

“…Euglenophyceae have high metabolic flexibility and, exploiting diverse organic carbon sources under different conditions, (Cordoba et al, 2021). This adaptation confers an advantage in oligotrophic or organic matter-rich water bodies, strongly light-limited (Bicudo & Menezes, 2017).…”

Molecular Toxicity Mechanism Induced by the Antibacterial Agent Triclosan in Freshwater Euglena gracilis Based on the Transcriptome

“…Euglena gracilis , a secondary green alga that mostly lives in fresh water, has the dual characteristics of flora and fauna [ 37 ]. Meanwhile, due to its lack of cell wall and sensitivity to environmental pressure, it is often used as a model organism to evaluate the ecotoxicity of various chemicals [ 38 , 39 , 40 ].…”