Nanopore sequencing reveals the DNA replication timing programme of the malaria parasite Plasmodium falciparum

Abstract

The DNA replication timing programme, defined as the temporal order in which genomic loci replicate, is of fundamental importance to maintaining genome stability. In human cells, replication timing is routinely measured using Repli-seq which reveals that the human genome is divided into replication timing domains that replicate in early or late S-phase. These timing domains are associated with gene expression, chromatin compaction, and three-dimensional genome organisation. In particular, late-replicating domains can be hotspots of genomic instability under replication stress. Because of the parasite's unusual cell cycle, Repli-seq cannot be used in the malaria parasite Plasmodium falciparum, leaving the open question as to whether its genome is divided into replication timing domains and how this might impact evolution of the parasite. Here, we leverage the power of Oxford Nanopore Technologies long-read DNA sequencing together with DNAscent to determine, for the first time, the replication timing programme of P. falciparum. We show how it relates to elevated rates of DNA breaking and replication fork stalling, and predict that these stalls are predominantly transient.