Assembly of supernumerary chromosomes and study of their content in the species Prochilodus linetus (Characiformes, Teleostei)

• Grant number: 25/00621-2
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: June 23, 2025
• End date: June 22, 2026
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Fábio Porto-Foresti
• Grantee: Rodrigo Zeni dos Santos
• Supervisor: Klopp Christophe
• Host Institution: Faculdade de Ciências (FC). Universidade Estadual Paulista (UNESP). Campus de Bauru. Bauru , SP, Brazil
• Institution abroad: Centre Inrae Occitanie-Toulouse, Toulouse, France
• Associated to the scholarship: 21/14562-7 - Genomic and evolutionary characterization of B chromosomes in the genus Prochilodus (Teleostei, Characiformes), BP.DR

Abstract

B chromosomes are extra elements to the standard complement of chromosomes A and are present in a wide diversity of organisms. Since they are not essential for the survival of the organisms carrying them, they are also referred to as parasitic chromosomes. Due to its non-essential nature and the fact that this type of chromosome is typically heterochromatic, repetitive sequences tend to cluster in its composition, making the study of its structure even more challenging. These elements were described decades ago in Prochilodus lineatus and recent analyses revealed morphological differentiations among these chromosomes in this species, identifying a total of three B-variants (acrocentric, submetacentric, and metacentric). The repetitive element content of these variants is highly similar, supporting an idea of a common origin for these supernumerary chromosomes. However, the content of single-copy genes has not been assessed to date. The present project aims to assemble a chromosome-level genome of Prochilodus lineatus (one individual bearing three B chromosomes) using PacBio HiFi and Hi-C sequencing. In addition, we will use short-read data from nine individuals carrying only one variant of the B chromosome and two individuals lacking these supernumerary chromosomes to improve the assembly of the micro-B chromosomes in this species. To date, we generated a non-curated primary genome assembly, which yielded 27 chromosomes and candidates scaffolds potentially representing the B chromosome. The primary purpose of this BEPE project is to enhance the continuity and resolution of these scaffolds corresponding to the B chromosome. This will be achieved by using coverage differentiation among short-read libraries and employing bioinformatics tools to decompose these exclusive sequences into k-mers, generating consensus sequences for the different B chromosomes present in the species. Once the B chromosomes are separated and assembled, the genome will be annotated using existing databases and transcriptomic data from male and female Prochilodus lineatus individuals. Professor Christophe Klopp (INRAE, France) has been selected as the supervisor for this project due to his expertise in the field and several recent studies involving RNA-seq analysis, genome annotation in animals, along with the study of complex genome assemblies, including supernumerary or heteromorphic sex chromosomes, and his capacity for training highly qualified bioinformaticians in genomics.