Genomic study of the red alga Gracilariopsis tenuifrons (Gracilariales, Rhodophyta): an approach involving genome assembly, differential gene expression, and application of CRISPR Cas9

• Grant number: 25/02087-3
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: June 29, 2025
• End date: June 28, 2026
• Field of knowledge: Biological Sciences - Botany - Applied Botany
• Principal Investigator: Mariana Cabral de Oliveira
• Grantee: André Vinicius Fonseca de Faria
• Supervisor: J Mark Cock
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: Station Biologique de Roscoff, France
• Associated to the scholarship: 23/15674-9 - Impacts of marine heatwaves on the red alga Gracilariopsis tenuifrons (Gracilariales, Rhodophyta): from acclimatation to thermal adaptation., BP.PD

Abstract

Studies utilizing omics tools in macroalgae are increasing, demonstrating potential to understand biological processes at the molecular level. Most of this technology has contributed to the evolutionary understanding of algae diversity, the gene expression of possible environmental pressures in a population, and even the modification of specific genome regions using the CRISPR-Cas9 technique. The genome editing system has made significant advances in various vascular plants, but it remains a challenge in macroalgae, especially considering that few well-assembled reference genomes are available. The current project focuses on a species of red macroalga, Gracilariopsis tenuifrons, an agarophyte with economic importance and widely distributed along the Brazilian coast. This study aims to: (i) assemble and annotate the haploid female nuclear genome of G. tenuifrons using long and short reads; (ii) characterize transcribed genes from individuals in different heatwave simulations; and (iii) validate the efficacy of the CRISPR-Cas9-mediated genome editing system in tetraspores. To understand the mechanisms that this macroalga uses to survive under thermal stress, this project will evaluate gene expression in two heatwave scenarios, 31°C and 33°C. We will also assess whether individuals have molecular plasticity to recover after thermal stress at 28°C. Validation of the effectiveness of CRISPR-Cas9 by biolistics and microinjection methods will enhance the utility of G. tenuifrons as a model organism, which is an ecologically and economically important agarophyte in Brazil. Additionally, the developed methodology should be easily applicable to other red algal species.