Investigating genetic and epigenetic landscapes with long-read sequencing
Event overview
The Arabidopsis thaliana genome was first sequenced in 2000, yet not one chromosome has been finished end to end. These unresolved regions have persisted as gaps in the assembly due to the high repetition and similarity of the DNA sequence. Recent developments in long-read sequencing technologies have allowed these regions to be resolved for the first time. During this talk, Matthew presented his team’s ongoing project to utilise these sequencing technologies to generate a de novo genome assembly of Arabidopsis thaliana that fully resolves all five centromeres, allowing the genetic and epigenetic landscape to be investigated for the first time.
In eukaryotes, centromere formation is vital to allow faithful segregation of the genetic material during cell division. However, despite this vital and conserved role, centromeres been reported to show paradoxically rapid evolution in both the underlying DNA sequences and in many of the core protein components. We find the centromeres in Arabidopsis consist of megabase-scale tandemly repeated satellite arrays, with repeat variants that are private to each chromosome. Beyond simple DNA sequencing, we are now able to use these sequencing technologies to reveal the epigenetic landscape on which these centromeres are built. These results demonstrate that it is now possible to finish entire chromosomes without gaps, and our future work will focus on identifying factors influencing centromeric recombination and evolution.
Topics covered
- Long-read sequencing
- De novo genome assembly and validation
- The genetic and epigenetic landscape of Arabidopsis centromeres
Meet the speaker
Dr. Matthew Naish completed his undergraduate in Natural Sciences, Plant Sciences at Cambridge University. He then joined the lab of Prof. Jose Gutierrez-marcos in Warwick University where he completed a Ph.D., working on developmental reprogramming of Arabidopsis. Dr. Naish then joined Ian Henderson’s lab at Cambridge in 2019 to work on Arabidopsis centromeres.