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

Autor(es)

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]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: Journal of Eukaryotic Microbiology; v. 67, n. 3 FEB 2020.
• Citações Web of Science: 0

Resumo

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)

• Processo FAPESP: 17/16077-3 - Análise de componentes do metabolismo energético ao longo do crescimento em cultura de Arcella intermedia
• Beneficiário: Giulia Magri Ribeiro
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Mestrado
• Processo FAPESP: 16/14317-4 - Identificação de genes envolvidos na formação da teca em Arcella intermedia leavis através de transcriptomas
• Beneficiário: Alfredo Leonardo Porfirio de Sousa
• Modalidade de apoio: Bolsas no Brasil - Mestrado
• Processo FAPESP: 16/14402-1 - Análise do perfil de expressão gênica de Arcella vulgaris ao longo de sua curva de crescimento em laboratório
• Beneficiário: Giulia Magri Ribeiro
• Modalidade de apoio: Bolsas no Brasil - Mestrado