Comparative cytogenomics in birds: Extensive genomic reorganization uncovered by in silico analysis.

• Grant number: 25/04254-4
• Support Opportunities: Scholarships abroad - Research Internship - Scientific Initiation
• Start date: August 01, 2025
• End date: September 30, 2025
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Principal Investigator: Marcelo de Bello Cioffi
• Grantee: Guilherme Mota Souza
• Supervisor: Qi Zhou
• Host Institution: Centro de Ciências Biológicas e da Saúde (CCBS). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil
• Institution abroad: Zhejiang University, China
• Associated to the scholarship: 22/14584-3 - Satellite DNAs, and the karyotype and ZZ/ZW sex chromosome differentiation in birds. Part IV. The harpy eagle (Harpia harpyja) as a model., BP.IC

Abstract

While most bird karyotypes are largely conserved, with the majority of species exhibiting a diploid number (2n) between 76 and 80, notable deviations from this ancestral arrangement are evident throughout the phylogeny, as certain species demonstrate significant 2n variations resulting from extensive chromosomal rearrangements. Until recently, comparative cytogenetic analyses in avians predominantly relied on the application of macrochromosome probes in Zoo-FISH experiments. However, in recent years, numerous genomes assembled at the chromosomal level have been created for different bird species, providing substantial insights for genome comparisons within broader evolutionary contexts. This BEPE project intends to conduct comparative cytogenomic investigations in birds, focusing on the detection of highly rearranged regions. For that, we chose three representative bird species as models: the Emu (Dromaius novaehollandiae, with an ancestral 2n = 80); the Harpy Eagle (Harpia harpyja, with a reduced 2n=58); and the Red-legged Seriema (Cariama cristata with an elevated 2n=108). The proposed activities include i) immersive training in bioinformatic analysis for genome assembly and annotation; ii) identifying the ancestral linkage groups (ALGs) that remained unchanged and those that were highly rearranged among species using distinct alignment algorithms; and iii) identifying the translocated regions responsible for the large 2n variation in the Harpy Eagle and Reg-legged Siriema and examining for signs of selection at the rearranged regions. Professor Qi Zhou of Zhejiang University in China was chosen as the student's supervisor due to his extensive knowledge of animal genomics and will update the student with the state-of-the-art genomic methods for comparative genomic tests. This training will have a substantial impact on the student's development and future work in our lab, which is increasingly combining genomic and chromosomal analysis in the new discipline of cytogenomics.