De novo Sequencing, Assembly, and Annotation of the Transcriptome for the Free-Living Testate Amoeba Arcella...

Arcella, a diverse understudied genus of testate amoebae is a member of Tubulinea in Amoebozoa group. Transcriptomes are a powerful tool for characterization of these organisms as they are an efficient way of characterizing the protein-coding potential of the genome. In this work, we employed both single-cell and clonal populations transcriptomics to create a reference transcriptome for Arcella. We compared our results with annotations of Dictyostelium discoideum, a model Amoebozoan. We assembled a pool of 38 Arcella intermedia transcriptomes, which after filtering are composed of a total of 14,712 translated proteins. There are GO categories enriched in Arcella including mainly intracellular signal transduction pathways; we also used KEGG to annotate 11,546 contigs, which also have similar distribution to Dictyostelium. A large portion of data is still impossible to assign to a gene family, probably due to a combination of lineage-specific genes, incomplete sequences in the transcriptome and rapidly evolved genes. Some absences in pathways could also be related to low expression of these genes. We provide a reference database for Arcella, and we highlight the emergence of the need for further gene discovery in Arcella.