Research group

Haerty Group

Exploring how genetic diversity influences health and resilience

Wilfried Haerty

Group activities.

Functional genetic elements, whether encoding proteins or not, represent about 10% of the human genome - at least as we have thus far identified them by their evolutionary footprints. We aim to tackle the evolution of functional elements with a specific focus on those that are non-protein-coding, as there is mounting evidence that these elements are enriched for disease and trait-associated variants.

Our work is primarily computational, focusing on comparative genomics and population genetics as well as data integration approaches to identify putative functional elements, characterise their evolution and assess the potential impact of their disruption.

One part of our work aims at identifying long (>200 nucleotides) non-coding RNAs (lncRNAs) and characterising their potential biological relevance and function, and the impact of mutations within these loci. Tens of thousands of long non-coding RNAs have now been annotated and are in general associated with gene expression regulation. So far the molecular function of a small fraction of these loci have been characterised, and mutations within several of these loci lead to lethal or developmental phenotypic changes at the cellular but also at the organismal level. However the function and the biological relevance of the vast majority of these loci remain to be discovered. As a consequence of the rapid evolution of these non-coding loci, our work primarily focuses on the patterns of sequence and expression variation among populations and closely related species. We are also investigating the impact of induced mutations within selected lncRNAs, aiming to quantify the in-vivo fitness impact of knocking down these loci.

The comparative analysis of Vertebrate genomes is another important focus of our work; improving human genome annotation and allowing the discovery of functional elements within it. However, little has been done towards discovering how these functional elements evolved. We are using comparative genomics to identify not only pan-mammalian conserved functional elements but also lineage and species-specific elements and how they relate to a lineage or species trait.

Projects

Team

Tools and data

Publications

Sarah Cossey

Chief Operating Officer

Biography

Personal Pronouns: She/Her

Contact details:

+44 (0) 1603 450 787

sarah.cossey@earlham.ac.uk

sjc0808

Sarah Cossey

Sarah is a professional accountant and project manager with extensive experience across the public and private sector. Sarah spent nine years in finance and audit within local government and the NHS. She then moved to the Cabinet Office as part of the Senior Management Team of the Office of Public Sector Information (OPSI) in 1998 to lead the finance and business support team.

Prior to joining the Earlham Institute, Sarah spent three years managing a large team within the private sector, in a regional media company, leading a shared finance service through significant change. Sarah is a qualified PRINCE II project manager and has managed projects including the merger of two government departments, the implementation of new IT systems and major organisational change. Sarah has successfully delivered considerable efficiency savings, both within the public and private sectors, and improved service delivery.

Sarah has been at EI since 2011, taking up her current position in 2014. She is a member of the EI Executive Team, and has responsibility for the operational support and oversight of the capabilities at EI. This includes the advanced training, communications and public engagement, knowledge exchange and industrial engagement and corporate services delivery.

Operations Division.

Sarah holds the responsibility for the Operations Division and has led EI through many development projects to improve its infrastructure and facilities. The Operations Division comprises the Communications, Business Development & Impact, Advanced Training, and Business Support teams.

Publications

Awards

Chris Watkins

Project Management Team Leader

Technical Genomics

Biography

Contact details:

+44 (0) 1603 450 076

chris.watkins@earlham.ac.uk

@CJwatkins83

ORCiD

I lead the Project Management Team within the Technical Genomics Group which is primarily responsible for capturing new projects into the high-throughput NGS pipeline including customer prospecting and nurturing, project strategising and pricing, as well as ensuring efficient project delivery. I am a PRINCE2 accredited Project Manager and sit on the EI Quality Assurance (QA) team which works towards maintaining EI's ISO9001 QA accreditation status.

Before joining EI, I completed my PhD in Speech Recognition and Language Modelling at UEA in 2010, before joining the Centre for Visual Computing at the University of Bradford to help grow its research and commercial activity through project management, interactions with local industry, and grant writing.

This led to two successful JISC funded projects worth £850k to digitise human skeletal remains using 3D laser scanning technology in collaboration with the Archaeological Department.

Projects

Publications

Research

Felix Shaw

Research Software Engineer

Papatheodorou Group

Biography

Contact details:

+44 (0) 1603 450 090

felix.shaw@earlham.ac.uk

I'm a researcher working on the COPO (Collaborative Open Plant Omics) platform; a tool for creating, depositing and searching for bundles of research objects.

I hold a First Class Honours degree in Computer Science and gained my PhD from the University of East Anglia in 2015, studying facial animation, computer graphics, signal processing and machine learning.

My current interests are in the fields of data science, open source and how to apply machine learning techniques in these areas to improve the tools available to researchers. I have industry experience working as a web developer in several start-ups and three years experience teaching to undergraduate level.

Projects

Publications

ELIXIR-UK

Coordinating data, tools, training and standards across the UK

Neil Hall

Director

Activities

Group activities.

ELIXIR is a Europe wide data infrastructure for the life sciences. It aims to facilitate sharing of life science data by integrating data sources and tools under a unified set of standards and provide computing infrastructure and the training needed to make these resources accessible to bioinformaticians and life scientists.

EI is the Lead Institute for ELIXIR in the UK. As such it forms the bridge between the UK’s data infrastructure falling under ELIXIR’s platforms (Data, Tools, Compute, Standards and Training) and ELIXIR Hub.

ELIXIR operates a hub and nodes model with the Hub being located at Hinxton. EI hosts the office coordinating the UK Node, bringing UK based resources into the wider project and providing a nucleating centre for UK data, tools, standards and training provision.

EI’s ELIXIR activities are currently headed by Professor Neil Hall, who is supported by Ariadna Miquel Clopés (Research Administrator), Xenia Perez Sitja (Communications and Community Manager) and Nicola Soranzo (Technical Co-ordinator).

ELIXIR-UK is a distributed network co-led by Prof Neil Hall and Prof. Carole Goble at the University of Manchester. ELIXIR-UK is supported by three Research Councils: BBSRC, MRC and NERC. It was funded in 2014 to provide training coordination both across ELIXIR and in the UK.

As well as playing an active leading role in the UK’s ELIXIR contributions, the ELIXIR group at EI also contributes to the development of UK data infrastructure through participation in strategic initiatives and by making contributions in infrastructure development, for example by hosting major activity in BioJS development.

Projects

Team

Tools and data

Publications

Jon Wright

Bioinformatician

Anthony Hall Group

Biography

Personal Pronouns: He/Him

Contact details:

+44 (0) 1603 450 986

jon.wright@earlham.ac.uk

@jonwright99

ORCiD

As a Bioinformatician in Anthony Hall’s group, I’m particularly interested in genome assembly and am currently contributing to the Delivering Sustainable Wheat and Decoding Biodiversity Institute Strategic Programmes.

As part of these programmes, I am assembling the genomes of important UK wheat varieties and historical lines from the Watkins bread wheat landrace collection utilising the latest sequencing technologies available at the Earlham Institute such as PacBio, Nanopore and HiC. These high-quality genomes will allow us to identify structural rearrangements and introgressions that underlie important agronomic traits in these lines, and will also contribute to the wheat pangenome and pangenome-related tools for wheat.

I also collaborate with researchers at Rothamsted Research and the European Reference Genome Atlas (ERGA) to generate a genome assembly of Alopecurus aequalis, a problematic agricultural weed, to understand the genetic basis of weediness.

I joined the Earlham Institute in 2010 to generate assemblies of the 42 chromosome arms of hexaploid wheat for the chromosome-based draft sequence within the International Wheat Genome Sequencing Consortium. Since then, I have been involved in several collaborations to generate genome assemblies for important wheat lines from the UK and around the world using our w2rap pipeline.

My first degree was in Chemistry, after which I completed a MSc in Information Technology before working in the commercial software industry for several years.

I received my PhD in Computational Biology from the John Innes Centre in 2010 where I worked on the model grass Brachypodium distachyon and comparative genomics in the grass family.

Projects

Publications

Tilapia Genomic Resources

Developing genomic resources in wild and farmed tilapia for the benefit of the aquaculture industry globally and in Africa.

Summary

Project Summary.

Previous Funders:

UKRI Natural Environment Research Council (NERC)
UKRI Biotechnology and Biological Sciences Research Council (BBSRC) GCRF Data and Resources

Current Funders:

UKRI Biotechnology and Biological Sciences Research Council (BBSRC)
EU Development Fund

Most of the world's fisheries are overexploited and it seems inevitable that fish-farming will largely replace fishing, just as livestock farming has replaced hunting as the main source of food from land animals. Unfortunately, many farmed fish, such as salmon, are themselves predators and need to be fed on fish meal.

Global tilapia production hit 6 million tonnes for the first time in 2020 and is now a $7.6 billion dollar industry, highlighting the huge growth in the freshwater aquaculture industry. However, that growth is threatened by a number of factors - including disease and arising pathogens, unwanted hybridization with wild fish, and climate change.

Most tilapia production is based on a handful of strains, but there are more than 50 wild species throughout Africa which could harbour valuable genes for growth, disease resistance, temperature & salt tolerance etc. Many tilapia will hybridize readily, so that the natural genetic traits could easily be bred into farmed strains without the need for GM technology. However, this feature also renders them vulnerable to genetic swamping by stocking with alien farmed strains into natural water bodies, a practice now widespread in Africa..

In this project we are establishing the needed genomic resources to enable the study of genomic diversity of wild tilapia populations, including past and ongoing gene flow between populations and across species. These species present different degrees of environmental adaptation for salinity, temperature, oxygen content. Using comparative genomics and system biology approaches we aim to investigate, characterise, and understand the genomic bases associated with those traits of interest. In close collaboration with WorldFish, we are generating similar high quality genomic resources for elite farmed strains of Nile tilapia with the aim of enabling future selective breeding for traits such as pathogen and environmental resilience.

Image above courtesy of WorldFish.

Detail

Details.

Genetic diversity of wild populations in Tanzania (BBSRC, NERC)

In this project, we are surveying the natural tilapia diversity of Tanzania, a particular hotspot for wild tilapia strains. We applied coverage low genome sequencing of nearly 600 tilapia sampled across water bodies in Tanzania. We are investigating population structure including past and contemporary gene flow between populations and species taking into account water basins.

We have developed quick molecular diagnostic tests of hybridization for the benefit of fishery managers in other locations, and use these to calibrate simple visual methods to identify hybrids in the field.

The genome sequence information of all of these tilapia strains will be deposited in online public databases, where it will provide a major resource for future studies in tilapia strain development.

Genetic diversity of tilapia stocks in Lake Victoria Basin (EU Development Fund, WoldFish)

Supported by a EU Development Fund project (TrueFish), in close collaboration with WorldFish, the Lake Victoria Fisheries Organization (LVFO), the Kenya Marine and Fisheries Research Institute (KMFRI), the Uganda National Fisheries Resources Research Institute (NaFIRRI), and the Tanzania Fisheries Research Institute (TAFIRI), we are investigating the genetic diversity of tilapia stocks in the water bodies constituting the Lake Victoria Basin. We aim to apply low coverage genome sequencing to assess the quality of the stocks to enable information based policy for the preservation and exploitation of these populations. In close collaboration with our partners we will deliver active training to local staff and students

High quality genomic resources for strain improvement (BBSRC, WorldFish)

The success of tilapia aquaculture is associated with the development of elite strains, often selected for improved growth rate. Because of the origin of those strains current reference genomes are not adequate to enable genomic selection. In close collaboration with WorldFish we are producing high quality genome resources for two of those strains through the application of long read technologies to deliver chromosome scale genome references and associated high quality annotations.

Publications

Technology

Collaborators

Impact statement.

Tilapia are now the third most important freshwater species in aquaculture. Our work in close collaboration with National Fisheries organisations in Uganda, Kenya, and Tanzania aims at identifying the genetics status of existing stocks in water bodies of East Africa countries.

We will disseminate our research and deliver relevant bioinformatics training for local staff and research students through our partners in Uganda, Kenya, and Tanzania. Our work in close collaboration with WorldFish will lead to enhanced genomic resources for elite strains enabling further selective breeding.

Our activities will lead to improved research and monitoring and ultimately to enhancement of the aquaculture industry. We believe that this research will be of great interest to students and the general public in the UK and internationally and we will carry out a variety of dissemination activities through a range of media. Furthermore, the genome sequence information will be publicly available to future researchers, benefiting the wider academic community interested in research themes as diverse as selective breeding, fish health, and evolutionary biology.

People working on the project.

EI Lead

Wilfried Haerty

Group Leader

Graham Etherington

Senior computational biologist

Sam Speak

Postdoctoral Research Scientist

Haerty Group

Wilfried Haerty

Group activities.

Projects.

Tilapia Genomic Resources

Earth Biogenome Project

Population Genomics of Pollinating Insects

Alternative splicing in health and disease

Data Science for Cellular Genomics

Somatic variation in healthy organisms

Cell expression heterogeneity impact on environmental response

Methods to detect hidden diversity

Characterising gene function, biosynthetic pathways, and variation in agri/aquacultural traits

Team members.

Graham Etherington

Wilfried Haerty

Yuxuan Lan

David Wright

Jessica Peers

Rebecca Shaw

Sofia Kudasheva

Zhengao Di

Francisco Cervilla Martinez

Sam Speak

William Lloyd

Josie Dix

Edward Holtom

Gurpinder Singh Sidhu

Tina Asgari

Tools.

Plant Rgenes

Publications.

Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution

Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity

De novo annotation reveals transcriptomic complexity across the hexaploid wheat pan-genome

Human-specific tandem repeat in CACNA1C modulates responses to neuronal stimulation

Characterizing the Genome of the Bumblebee Bombus haematurus – A Range-Expanding Pollinator

Characterisation of the Historic Demographic Decline of the British European Polecat Population

A comparison of long-read single-cell transcriptomic approaches

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly

RNA-Seq analysis reveals the long noncoding RNAs associated with immunity in wild Myotis myotis bats

High-quality genome assembly for the genetically improved Abbassa Nile tilapia enables the reconstruction of X and Y haplotypes

Correction: The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity

Gene pseudogenization in fertility-associated genes in cheetah ( Acinonyx jubatus ), a species with long-term low effective population size

Autoactive CNGC15 enhances root endosymbiosis in legume and wheat

Spatial Transcriptomics Reveals Expression Gradients in Developing Wheat Inflorescences at Cellular Resolution

Identification and characterization of human KALRN mRNA and Kalirin protein isoforms

A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell

Characterisation of the historic demographic decline of the British European polecat population

Low protein diet protects the liver from Salmonella Typhimurium-mediated injury by modulating the mTOR/autophagy axis in macrophages

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion

Sonification of Genomic Data to Represent Genetic Load in Zoo Populations

Socially plastic responses in females are robust to evolutionary manipulations of adult sex ratio and adult nutrition

Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes

U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs

Single cell RNA-sequencing and RNA-tomography of the avian embryo extending body axis

Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons

Tools for pathogen genetic surveillance: Lessons from the ash dieback invasion of Europe

Genomics‐informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations

Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size

The genome sequence of the Violet Carpenter Bee, Xylocopa violacea (Linnaeus, 1785): a hymenopteran species undergoing range expansion.

Low protein diet protects liver function upon Salmonella infection by metabolic reprogramming of macrophages

Telomere‐to‐telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

Single-cell and spatial transcriptomics of the avian embryo tailbud

De novo annotation of the wheat pan-genome reveals complexity and diversity of the hexaploid wheat pan-transcriptome

Schizosaccharomyces versatilis represents a distinct evolutionary lineage of fission yeast

Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals

Socially plastic responses in females are robust to evolutionary manipulations of adult sex ratio and adult nutrition

Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations

U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing ofC. elegansmRNAs

Telomere-to-telomereSchizosaccharomyces japonicusgenome assembly reveals hitherto unknown genome features

Schizosaccharomyces versatilisrepresents a distinct evolutionary lineage

Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons

Conservation and divergence of regulatory architecture in nitrate-responsive plant gene circuits

Chromatin accessibility in gill tissue identifies candidate genes and loci associated with aquaculture relevant traits in tilapia

Panhematopoietic RNA barcoding enables kinetic measurements of nucleate and anucleate lineages and the activation of myeloid clones following acute platelet depletion

Single-cell gene and isoform expression analysis reveals signatures of ageing in haematopoietic stem and progenitor cells

Ancient and ongoing hybridization in theOreochromiscichlid fishes

Endophytic fungi related to the ash dieback causal agent encode signatures of pathogenicity on European ash