Topic title: The “black holes” of plant chromosomes: centromere structure and evolution
Supervisor: prof. Martin Lysak (email@example.com)
Centromeres are crucial for the division of eukaryotic cells, because they are required for attachment to spindle microtubules during the segregation of monocentric chromosomes. Though the role of centromeres is conserved across eukaryotes, they exhibit surprising diversity in sequence, structure, and size within and between species. Until recently, megabase-long arrays of repetitive sequences frequently precluded assembly and detailed comparative analysis of centromeres. Now, improvements in long read sequencing approaches and advances in read alignment and genome assembly enabled telomere-to-telomere (T2T) genome assemblies, and thus, detailed characterization of centromere structure. This PhD project will focus on analysis of centromere structure, interphase organization and evolution in crucifer species (Brassicaceae, the mustard family) on sequence and epigenetic level. Comparisons will include all available T2T assemblies with the aim to identify shared vs specific features of crucifer (peri)centromeres and elucidate drivers and trends of their evolution.
Naish M et al. (2022) The genetic and epigenetic landscape of the Arabidopsis centromeres. Science 374: eabi7489. doi: 10.1126/science.abi7489.
Wlodzimierz P et al. (2023) Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature 618: 557-565. doi: 10.1038/s41586-023-06062-z.
Requirements on candidates:
The ideal candidate will have experience analyzing and interpreting whole-genome sequence data. S/he should have good analytical and programming skills.
comparative plant genomics, plant paleogenomics, epigenetics, bioinformatics, centromere, DNA repeats, chromosome and karyotype evolution, genome assembly, whole-genome duplications