Image credit: Wellcome Sanger Institute

Categories: Sanger Science26 July 2023

Bonailie n farewell to the Berriman group

Nearly twenty three years after first joining the Wellcome Sanger Institute, at the end of July Dr Matt Berriman will complete the move of his research to the University of Glasgow, where he is now Professor of Parasitology.

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Matt joined the Wellcome Sanger Institute as a Senior Computational Biologist in the pathogen genomics unit at the end of 2000. His early work focussed on sequencing and analysing reference genomes of more than 20 eukaryotic pathogens, including globally important Apicomplexan and Kinetoplastid protozoa that cause diseases such as malaria, leishmaniasis and African trypanosomiasis.

In 2008, Matt became a Faculty member and created the parasite genomics group, who studied the parasites that cause malaria and a range of parasitic worms including schistosomes, tapeworms, roundworms, hookworms, threadworms, and whipworms, which cause some of the most neglected diseases and collectively infect more than a billion people.

The Berriman group used comparative genomics to sift through the vast numbers of uncharacterised genes and identify those that are limited to, or evolving more rapidly in, specific groups of parasites. These genes are often involved with pathogenesis processes and interactions between parasites and their hosts.

His group became world renowned for generating complete and highly accurate genomes which the parasitology community have come to rely on to inform their own work. They generated complete genomes from across the Plasmodium genus which they and others have used as the basis to study the organisation and function of the subtelomeric regions of chromosomes. These regions comprise 10-15 per cent of the parasite’s genomes, contain large repertoires of host-interacting genes and play important roles in the establishment and maintenance of infections.

In their 50 Helminth Genomes project, together with collaborators at Washington University and the University of Edinburgh, the Berriman group were major contributors to the sequencing, assembly, and annotation of genomes of many of the most important helminths that infect animals and humans. By generating and comparing new draft helminth genomes to populate the space around high-quality reference genomes, this project provided a broad overview of gene births and expansions relevant to parasitism, such as those involved in manipulating, migrating between or feeding on their hosts. These important genomic resources for most of the major roundworm and flatworm species enable innovation in research and support public health interventions, such as the prioritisation of novel drug targets and compounds that might be used to treat parasitic worm infections.



Scanning electron microscope image of a whipworm parasite. Image credit: Dave Goulding, Wellcome Sanger Institute

Matt was also involved in setting up Sanger’s Tree of Life Programme, and with the initial application for the Darwin Tree of Life Project, which aims to sequence the genomes of all eukaryotic species in Britain and Ireland.

Elsewhere, the group used finer-grained comparisons to drill into the details of parasite evolution within individual clades. They also investigated natural genome variation of other neglected parasites to understand their epidemiology and evolution, and exploited laboratory-models of parasite life-cycles established in-house to create functional genomics datasets that identify genes, and their regulation, involved in host-pathogen interactions or key stages of parasite development.

Throughout his career, Matt has been a unifying figure in the UK parasitology community, with his contributions rightly recognised when he was awarded the C.A. Wright Memorial Medal by the British Society for Parasitology in 2017. Through his collaborative work, he has demonstrated how genomics can be used to tackle a range of complex problems, from understanding anthelminthic drug resistance in gastrointestinal nematodes of small ruminants (BUG Consortium), developing research tools to study echinococcosis and schistosomiasis (FUGI Consortium), to characterising the epidemiological links between canine Guinea worm and “sporadic” human cases.

Alongside their work to create high value datasets, Matt and his group have been heavily involved in developing software (e.g., Artemis, ACT, ABACAS, RATT and REAPR) and community databases such as WormBase ParaSite and GeneDB. These research tools are vitally important to the research community and have had a substantial impact across many domains in genomics and bioinformatics. They have also been at the forefront of setting standards for data sharing and access.

“Matt has been, and will continue to be a brilliant colleague, collaborator and friend. His eye for detail and pioneering research has generated genomic data and tools of truly global importance that have fundamentally changed our understanding of a whole range of neglected tropical diseases, and will continue to inform efforts to tackle these diseases in the decades to come.”

Professor Nick Thomson,
Group Leader and Head of the Parasites and Microbes programme

The Berriman group has been home to large cohort of Master’s and PhD students, postdocs, staff scientists and research associates during his time at Sanger, all of whom have benefited from Matt’s dedication and support to nurturing future generations of researchers. Accordingly, many of those to have gone through his lab have moved on to set up their own research groups and take senior positions in a range of research organizations around the world. Furthermore, work by the Berriman group and their collaborators has resulted in more than 275 publications, which equates roughly to one publication per month, every month since Matt first joined Sanger, a truly staggering achievement.

“Matt has been at the global cutting edge of work on parasite genomics for decades, forging collaborations across continents to build a reference library of sequences for major human and animal parasites that are now openly available for all to use. Importantly, Matt has and is pushing the boundaries of what we can do post-genome: spearheading functional analyses from deep phylogenomics to single cell and population genetics. Matt was a natural and enthusiastic partner from the very start of the Tree of Life programme, and his expertise was valuable as we sought to replicate his success in reference genome generation across the evolutionary tree. We wish Matt and his team all the best as he takes on his new post in Glasgow.”

Professor Mark Blaxter,
Group Leader and Head of the Tree of Life programme

As this ‘cheery parting’ now approaches, all in the Parasites and Microbes programme, Tree of Life programme, and throughout Sanger would like to thank Matt, and the members of his research group past and present, for their immense contributions, and wish them well in the next chapter as they continue the fight against the tropical diseases that most simply ignore.

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