Document Type
Article
Publication Date
2-2020
Publication Title
Journal of Eukaryotic Microbiology
Abstract
Arcella, a diverse understudied genus of testate amoebae is a member of Tubulinea in Amoebozoa group. Transcriptomes are a powerful tool for charac- terization of these organisms as they are an efficient way of characterizing the protein-coding potential of the genome. In this work, we employed both sin- gle-cell and clonal populations transcriptomics to create a reference transcrip- tome for Arcella. We compared our results with annotations of Dictyostelium discoideum, a model Amoebozoan. We assembled a pool of 38 Arcella inter- media 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 anno- tate 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 tran- scriptome 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 dis- covery in Arcella.
Keywords
Gene discovery, next generation sequencing, pathways description
Volume
67
First Page
383
Last Page
392
DOI
10.1111/jeu.12788
Rights
© 2020 International Society of Protistologists
Recommended Citation
Ribeiro, Giulia M.; Porfírio-Sousa, Alfredo L.; Maurer-Alcalá, Xyrus X.; Katz, Laura A.; and Lahr, Daniel J.G., "De novo Sequencing, Assembly, and Annotation of the Transcriptome for the Free-Living Testate Amoeba Arcella intermedia" (2020). Biological Sciences: Faculty Publications, Smith College, Northampton, MA.
https://scholarworks.smith.edu/bio_facpubs/134
Comments
Archived as published.
Open access article.