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Updated: Apr 30, 2026

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
Published on: March 22, 2018
Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication
Jolien J E van Hooff1, Berend Snel, Michael F Seidl
1Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, The Netherlands.
Abstract:
Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny-compelling evidence for a WGD-has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.
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