In project we are interested in detecting centromeric repeats in assembled genomes of songbirds
Avian genomes are considered to be relatively stable in terms of their gene content and chromosomal synteny (Ellegren 2010). However, it remains unknown if the same applies to centromere positions and centromeric repeats. Their high repetitiveness makes centromeres ideal candidates for rapid genomic change (Kapusta & Suh 2017).
Here, we can tackle this lack of knowledge because long-read raw read data and assemblies are now available for a dense taxon sampling of songbirds and outgroups: zebra finch, paradise crow, hooded crow, Hawaiian crow, Japanese quail, and chicken. If time allows, these will be complemented with yet unpublished data from collaborators for purple martin, barn swallow, collared flycatcher, pied flycatcher, Darwin’s finch, duck, emu.
Aim 1: Develop a new pipeline to efficiently characterize potential centromeric satellite repeats from multiple (avian) genomes, combining raw read data and assemblies. This pipeline is planned to be published on GitHub as an easy-to-use tool, with a short methods paper describing it.
Aim 2: Characterize the location of potential centromeres across (song)bird chromosomes and relate these to other genomic features (recombination rate, GC content, transposon density) to reconstruct their evolutionary history (sequence content and chromosomal position). These analyses will be an important contribution to an ongoing effort to characterize how stable or unstable avian genomes are with regards to centromere positions.