Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology

Abstract

Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.

Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans

“…(LFNC01000001.1) and Phytomonas serpens (AIHY00000000.1) were accessed from GenBank [ 56 , 57 ]. Raw reads were accessed (last time on 05/05/21) for Euglena viridis (SRR14099996) [ 58 ], Rhabdomonas costata [ 59 ], B. saltans (ERR036178) [ 60 ], Papus ankaliazontas (SRR13394431), Ankaliazontas spiralis and Procryptobia sorokini (cocultured, SRR13394430) [ 61 ]. These were processed in the same way as diplonemid assemblies.…”

Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis

“…We classified 166 of these as class I proteins with bipartite signal sequences and 73 as class II proteins with only a signal peptide ( Dataset S1 and SI Appendix , section 1.5 ); we also annotated 35 proteins as transporters, constituting integral membrane proteins of the chloroplast envelope ( Dataset S1 ). To validate the specificity of our approach on a negative control, we performed the same analysis on the predicted proteome of heterotrophic euglenid, Rhabdomonas costata, previously suggested to ancestrally lack chloroplasts ( 23 ). Here we predicted 2,082 candidates with putative bipartite signals, which we then checked for contaminations, transmembrane domains and annotated their functions yielding 63 proteins ( Dataset S2 ).…”

Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis

“…We classified 166 of these as class I proteins with bipartite signal sequences and 73 as class II proteins with only a signal peptide (Table S2; SI Text , Section 1.5); we also annotated 35 proteins as transporters, constituting integral membrane proteins of the chloroplast envelope (Table S2). To validate the specificity of our approach on a negative control, we performed the same analysis on the predicted proteome of heterotrophic euglenid, Rhabdomonas costata , previously suggested to ancestrally lack chloroplasts (23). Here we predicted 2082 candidates with putative bipartite signals, which we then checked for contaminations, transmembrane domains and annotated their functions yielding 63 proteins (Table S3).…”