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

• Published in: The Journal of eukaryotic microbiology Vol. 67; no. 3; pp. 383 - 392
• Main Authors: Ribeiro, Giulia M., Porfírio‐Sousa, Alfredo L., Maurer‐Alcalá, Xyrus X., Katz, Laura A., Lahr, Daniel J.G.
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.05.2020
• Subjects: Gene discovery; Gene expression; Genes; Genomes; next generation sequencing; pathways description; Signal transduction; pathways description; Gene discovery; next generation sequencing
• ISSN: 1066-5234; 1550-7408
• DOI: 10.1111/jeu.12788

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.