Advanced search
Start date
Betweenand
(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

Full text
Author(s):
Ribeiro, Giulia M. [1] ; Porfirio-Sousa, Alfredo L. [1] ; Maurer-Alcala, Xyrus X. [2, 3, 4] ; Katz, Laura A. [2] ; Lahr, Daniel J. G. [1]
Total Authors: 5
Affiliation:
[1] Univ Sao Paulo, Inst Biosci, Dept Zool, Matao St, Travessa 14 Cidade Univ, BR-05508090 Sao Paulo, SP - Brazil
[2] Smith Coll, Dept Biol Sci, 10 Elm St, Northampton, MA 01063 - USA
[3] Univ Massachussetts, Program Organism & Evolutionary Biol, 230 Stockbridge Rd, Amherst, MA 01002 - USA
[4] Univ Bern, Inst Cell Biol, Baltzerstr 4, CH-3012 Bern - Switzerland
Total Affiliations: 4
Document type: Journal article
Source: Journal of Eukaryotic Microbiology; v. 67, n. 3 FEB 2020.
Web of Science Citations: 0
Abstract

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. (AU)

FAPESP's process: 17/16077-3 - Energetic metabolism analysis along culture growth of ARCELLA intermedia
Grantee:Giulia Magri Ribeiro
Support type: Scholarships abroad - Research Internship - Master's degree
FAPESP's process: 16/14317-4 - Identification of genes involved in the test formation in Arcella intermedia leavis through transcriptome
Grantee:Alfredo Leonardo Porfirio de Sousa
Support type: Scholarships in Brazil - Master
FAPESP's process: 16/14402-1 - Analysis of Arcella vulgaris expression profile along your growth curve in laboratory
Grantee:Giulia Magri Ribeiro
Support type: Scholarships in Brazil - Master