Project proposal and aims:
In multicellular organisms, all cells of an individual normally contain the same genetic information and cell differentiation is controlled by turning on or turning off different combinations of genes. An alternative but rare way to change the developmental fate of cells is the loss of specific DNA sequences. A striking example of such programmed DNA elimination occurs in birds, where a whole chromosome is eliminated from somatic cells during early embryogenesis and is maintained only in the germline. Although the existence of this germline restricted chromosome (GRC) has been known for more than two decades from zebra finch (Taeniopygia guttata), only recently it has been demonstrated that this chromosome is very likely present in all songbirds, the largest and most diverse group of birds, comprising more than 5000 species, making them the largest taxonomic group with obligatory programmed DNA elimination. The function and evolutionary significance of this enigmatic chromosome is, however, still unknown. 

The songbird GRC is an unusual chromosome in many respects. In male germ cells, it normally occurs as a single copy, while females contain two GRC copies, although many exceptions have been observed. Although the GRC has long been believed to only be maternally inherited, recent findings suggest that paternal inheritance can also occasionally occur. These observations indicate that the GRC often shows unstable meiotic and mitotic inheritance, similar to what has been observed in parasitic B chromosomes. And yet its presence in all songbird species analyzed so far indicates that it has not been lost from the genome for over 30 million years of songbird evolution. This suggests that, unlike B chromosomes, it has some essential function preventing its loss, which is, however, still unknown. In stark contrast to the evolutionarily stable chromosomes of birds, the GRC shows extremely dynamic evolution manifested by unusually large variation in its size as well as gene content among species and sometimes even within species. This suggests an intriguing possibility that the GRC could contribute to the relatively rapid radiation of songbirds compared to other bird lineages. 

The aim of this project will be to determine the essential function of the GRC for songbirds and study its potential role in speciation in two model systems: (i) two closely related species of nightingales (Luscinia sp.) and (ii) multiple estrildid finches of the genus Lonchura. The selected candidate can utilize whole-chromosome GRC assemblies for these species, which we have generated during our ongoing research on the GRC. In addition, we will generate single-cell transcriptomic data from embryotic tissues and gonads to study the GRC gene expression during ontogeny. 

The project will be realized at the Department of Zoology, Faculty of Science, Charles University in the lab of Population and speciation genetics under the supervision of Radka Reifová ( Furthermore, the project will be realized in close collaboration with the group of Alexander Suh, (University of East Anglia, Norwich, UK). The ideal candidate should have experience with bioinformatic analyses of genomic and transcriptomic data.

Our recent publications on this topic:
Schlebusch SA et al. (2022). Rapid gene content turnover on the germline-restricted chromosome in songbirds. Nature Communications (in revision). 
Sotelo-Muñoz M, et al. (2022). Germline-restricted chromosome shows remarkable variation in size among closely related passerine species. Chromosoma 131(1-2):77-86. 
Borodin P et al. (2022): Mendelian nightmares: The germline-restricted chromosome of songbirds. Chromosome Research. In press. 
Johnson Pokorná M and Reifová R (2021). Evolution of B chromosomes: from dispensable parasitic chromosomes to essential genomic players. Frontiers in Genetics 12:727570. 

I declare that:
● co-founding 1000 EUR/month is ensured
● project is approved by head of corresponding department

Co-founding resources:
The causes and evolutionary consequences of programmed DNA elimination in songbirds. (23-07287S, GAČR project proposal, 2023-2025). 
Internal resources of the Department of Zoology if the GAČR project is not successful. 

Contact details:
RNDr. Radka Reifová, Ph.D.
Department of Zoology
telephone number: +420-221951852

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