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School of Biological and Chemical Sciences

Josiah Seaman

PhD student



Project title: Repeated Patterns of Gene Loss After an Ancient Whole Genome Duplication in Ash Trees

Summary: My research interests are focused on what we can learn from the large scale layout of chromosomes: gene clusters and synteny.  I build visualization tools to help researchers more easily sanity check large data sets.

  • What genes cluster together on a chromosome?
  • How much does gene copy number vary between closely related species?
  • Studying the interplay between synteny and transposable elements
  • Visualizing genome assemblies

My thesis is an investigation of the evolutionary history of gene duplication and loss in 31 species of of Ash trees (genus Fraxinus).  The recent explosion of genome sequence data suggest that flowering plant genome evolution has been punctuated by whole genome duplications (WGD) followed by diploidization (gene copy loss after a WGD), leading to large families of genes and duplicated syntenic regions. Genus Fraxinus provides an ideal opportunity to examine diploidization, as the genus appears to have shared a WGD event with genus Olea approximately 21 mya (Sollars et al. 2017).

I am seeking to answer the questions:

  1. Does diploidization follow repeatable patterns?
  2. Can retention of gene duplicates be predicted by protein function?
  3. To what extent can stoichiometric sensitivity explain duplicate retention?