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Brockington Group: Defining the evolutionary mechanisms underlying a novel eukaryotic gene cluster


Supervisor: Sam Brockington (Plant Sciences)

Brief summary:

Eukaryotic gene clusters are emerging as a significant phenomenon in plant evolution, with implication for biopharmaceutical discovery, but fundamentally, the evolutionary genomic mechanisms that lead to gene cluster assembly are substantially unknown.

Importance of the area of research concerned:

In prokaryotes over fifty percent of the genes in the genome are organised into operons (e.g. LacZ), whereas in eukaryotic organisms, functionally related genes are commonly dispersed across the genome. Recently it has become increasingly apparent that many eukaryotic plant specialised metabolic pathways are clustered in the genome. Unlike prokaryotic gene operons, specialised metabolism gene clusters have not arisen through horizontal gene transfer. Rather, plant gene clusters are arising though processes of genome duplication, genome rearrangement, and recombination. Remarkably, instances are emerging in which gene clusters controlling the same metabolic pathways have apparently emerged independently, indicating strong selection and common mechanisms of assembly. Eukaryotic genomes are therefore capable of remarkable plasticity, which in turn raises intriguing questions about the molecular mechanisms and evolutionary pressures that have acted to cause these gene clustering arrangements to assemble. An increasing density of genomic resources means we are now able to trace the origin of gene clusters and begin to resolve the mechanisms underlying their assembly.

Project summary:

In this project you will address the origin and assembly of a recently described gene cluster associated with betalain synthesis. Betalains are an unusual class of pigments, that are best known as the colour of beetroot, and are unique to the flowering plant order Caryophyllales. We have recently shown that the betalain biosynthesis pathway has evolved multiple times, underpinning four convergent origins of betalain pigmentation. Two of the inferred origins of betalain synthesis are represented by well assembled and annotated genomes. In one of the origins there is a metabolic gene cluster, but in the other origin there is no cluster. It is not yet clear whether gene clusters are associated with any additional unexplored origins of betalain synthesis. Additionally, the molecular evolutionary mechanisms that underpin the evolution of the betalain gene clusters are unknown.

What will the student do?:

You will establish a comparative genomic framework through de-novo genome sequencing assembly and annotation to obtain a genome representing each origin of betalain pigmentation. You will employ co-expression network analyses to detect the genetic modules associated with betalain metabolism for each genome sequenced taxa representing each origin of betalain pigmentation. You will harness comparative genomic information and synteny to explore the role and characteristics of co-linear genomic gene clusters in the evolution of the betalain networks across multiple origins. Finally, you will interrogate the evolutionary histories of genes within these modules and clusters to understand how betalain biosynthesis pathways and associated gene clusters are assembled. You will combine these approaches to articulate the mechanisms by which clusters form and explore why in some origins of the betalain synthesis pathway they do not seemingly assemble.


  • Brockington SF, Walker RH, Glover BJ, Soltis PS, Soltis DE (2011) Complex evolution of pigmentation in the Caryophyllales. New Phytologist 190: 854–864
  • Sheehan H, Feng T, Walker‐Hale N, Lopez‐Nieves S§, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson, MJ, Cushman, JC, Moore MJ, Smith, SA, Brockington SF (2019) Evolution of L‐DOPA 4,5‐dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales New Phytologist. New Phytologist 227 (3)
  • Ben Field, Anna-Sophie Fiston-Lavier, Ariane Kemen, Katrin Geisler, Hadi Quesneville, Anne E. Osbourn (2011) Formation of plant metabolic gene clusters within dynamic chromosomal regions Proceedings of the National Academy of Sciences Sep 2011, 108 (38) 16116-16121; DOI: 10.1073/pnas.1109273108

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