Toward Understanding Plant Genome Evolution: Characterizing the Repeatome of genus Cereus (Cereeae, Cactaceae) Using Whole-Genome Resequencing Data and Bioinformatic Tools

• Grant number: 24/08069-4
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: June 01, 2025
• End date: November 30, 2026
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Fernando de Faria Franco
• Grantee: Ahmed Abdelhafiz Alshikh Abdalla
• Host Institution: Centro de Ciências Humanas e Biológicas (CCHB). Universidade Federal de São Carlos (UFSCAR). Sorocaba , SP, Brazil
• Associated research grant: 20/15161-3 - Adaptation during biogeographic transitions from the Cerrado to the Caatinga: evolutionary parallelism and idiosyncrasies in independent clades of genus Cereus (Cactaceae), AP.BTA.R

Abstract

Whole-genome data are a powerful resource for evolutionary studies in model and non-model plant species, shedding light on the processes underlying species diversification and genome organization. These datasets enable diverse analytical approaches using bioinformatics tools, eliminating the need for additional expenses related to data sequencing. The objective of this postdoctoral research project is to reuse existing whole-genome resequencing (WGR) data from the FAPESP 2020/15161-3 project to characterize the repeatome of seven species within the Cereus genus (Cereeae, Cactaceae): C. jamacaru, C. calcirupicola, C. pierrebrauniannus, C. albicaulis, C. mirabella, C. hildmaniannus, and C. fernambucensis. Briefly, the repeatome comprises repetitive DNA sequences, primarily satellite DNAs and transposable elements (TEs), within an organism genome. Understanding the composition and structure of the repeatome is crucial for investigating genome evolution, genetic diversity, and functional genomics. In this study, the postdoctoral researcher will assemble WGR data using the C. jamacaru reference genome. Software such as Repeat Explorer 2 will be utilized for annotating repetitive elements. TEs will be categorized by family, and their composition will be compared across species. Tandemly arranged repetitive elements with a high likelihood of belonging to satellite DNA families will be identified, characterized, and compared among species. There is growing evidence suggesting that environmental conditions influence the amount of repetitive DNA. Therefore, the outcomes of this project will be integrated with other genomic resources and environmental data surveys conducted by our research group to comprehend the selective pressures driving niche evolution during geographic transitions, aligning with the primary objective of the FAPESP 2020/15161-3 project. (AU)