Comparative analysis of the molecular composition of the nucleolus organizer regions in the Physalaemus cuvieri - Physalaemus ephippifer species complex

• Grant number: 25/07768-9
• Support Opportunities: Scholarships in Brazil - Master
• Start date: July 01, 2025
• End date: March 31, 2027
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Luciana Bolsoni Lourenço
• Grantee: Helena Mattiazzo Milanez
• Host Institution: Instituto de Biologia (IB). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 24/00073-2 - Chromosomal variations in two species complexes of Anura: simple polymorphisms or elements with important roles in the speciation process?, AP.R

Abstract

The Physalaemus cuvieri - Physalaemus ephippifer species complex harbors expressive karyotypic diversity, an the NORs represent the main diagnostic chromosome marker of the distinct genetic lineages from this group. In addition, the heteromorphic sex chromosomes found in P. ephippifer and their homologous chromosomes from L1 were previously described and are NOR-bearing. The association of the NORs to satellite DNAs (satDNAs) was inferred through the genomic analysis of repetitive sequences from P. ephippifer and corroborated in FISH essays. However, the molecular composition of the NORs characteristic of the other lineages and the role of the association of these repetitive sequences in their evolutionary dynamic remain unelucidated. In this context, we aim to investigate the presence of repetitive elements in association to nucleolar ribosomal genes in the different taxa from the species complex P. cuvieri - P. ephippifer. Special attention will be given to lineages L1, in which the NORs are found in chromosomes 8 and 9, and, in the last, are coincident to heterochromatic bands; and L3, which is characterized by expressive polymorphism regarding this genomic element. In order to study the repetitive fraction of the different genomes, short read libraries obtained through Illumina sequencing will be analyzed with RepeatExplorer, RepeatModeler, RepearMasker, Dfam and tRNAscan-SE. Clusters of the rDNA 40S will be de novo-assembled with NOVOPlasty, using a partial sequence of the rRNA 18S or 28S genes as seed. FISH essays will be developed in order to map all repetitive sequences grouped with the rDNA 40S within superclusters in metaphasic chromosomes and in chromatin fibers (Fiber-FISH). Moreover, epigenetic marks (such as 5mC, H3K27me3 and H3K9me3) will be explored and silver-impregnation will be conducted to study the potential implications of the association to repetitive elements in the NOR activity. The obtained results from different lineages will be compared. (AU)