Genome assembly of Perophora viridis Verrill, 1871 and characterization of microRNAs in colonial tunicates

• Grant number: 25/13925-0
• Support Opportunities: Scholarships abroad - Research Internship - Master's degree
• Start date: November 10, 2025
• End date: May 09, 2026
• Field of knowledge: Biological Sciences - Zoology - Morphology of Recent Groups
• Principal Investigator: Federico David Brown Almeida
• Grantee: Ivan Andre Morillo Guerrero
• Supervisor: Ivo Ludwig Hofacker
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: University of Vienna, Austria
• Associated to the scholarship: 23/13244-7 - Coloniality and gene expression of stem cell markers during budding of the ascidian Perophora viridis Verril, 1871, BP.MS

Abstract

Perophora viridis is a subtropical colonial tunicate with great potential to be established as an experimental model for the study of circulatory stem cells and regeneration in chordates. The current P. viridis genome assembly is highly fragmented and requires refinement through transcriptome-guided scaffolding approaches, using tools such as L_RNA_scaffolder, SCUBAT, and AGOUTI. An improved version of the genome will allow for comparative studies with other tunicate species, specifically with solitary tunicates, revealing genomic innovations associated with coloniality and unique developmental modes such as stolonial budding.The project also seeks to explore the role of microRNAs (miRNAs) in the regenerative processes of colonial tunicates. Using small RNA libraries from several species (including P. viridis), conserved and novel miRNAs will be identified using a bioinformatic approach (miRNAture and miRDeep2) that will allow me to determine gains and losses of miRNA families throughout chordate evolution. I am particularly interested in miRNAs that control cell proliferation, such as miRNAs that regulate cancer stem cells (oncomiRs), to test whether the presence of these oncomiRs is related to the regenerative capacityand budding of colonial species. Therefore, comparing the miRNA repertoires in colonial and solitary ascidians will contribute to understanding the evolutionary genetic basis of regenerative capacities among chordates.In parallel, I plan to study the evolutionary origin of the lncRNA RMST, an important non-coding RNA involved in neurogenesis and neural stem cell regulation. In vertebrates, RMST has undergone lineage specific diversification. Using structural covariance models and iterative searches with INFERNAL, I will explore the presence and diversification of RMST families in tunicate genomes that are less diversified according to previous studies in our group. These results will allow us to reconstruct their ancestral state and assess whether RMST is a deep regulatory element in the evolutionary history of deuterostomes.This BEPE will be conducted in collaboration with Dr. Cristian A. Velandia (University of Vienna), who has extensive experience in tunicate genomics. The research will strengthen an international network of scientific collaboration and future lines of research, gaining access to new methodologies in genome assembly, ncRNA analysis, and comparative evolution. The results generated here will significantly contribute to the tunicate genomic resources of our laboatory at the USP, and will be complementary to ongoing studies of regeneration, stem cells, and development of Perophora viridis.