NERC Environmental Omics Facility (NEOF)
Lead Research Organisation:
University of Liverpool
Department Name: Institute of Integrative Biology
Abstract
New 'omic' technologies have transformed biology by allowing scientists to read genomes (genomics) and to measure the amount of proteins (proteomics) or other chemicals (metabolomics) within living cells and organisms. Tiny amounts of DNA can be collected from the environment (environmental DNA, eDNA) to measure biodiversity and monitor the health of our soils, rivers and seas. This creates a tremendous opportunity to understand the diversity of different individuals and species within the natural environment, their evolution, and the diversity of different characters and forms that allow them to live within their environment. Understanding biodiversity is more pressing than ever, given the rate at which it is being lost from the planet and the central role that it plays in allowing species and ecosystems to respond to, and survive, climate change.
Scientists wanting to use omic technologies in their research face significant hurdles: the equipment required costs millions of pounds and few labs can afford it; the expertise to apply these techniques is rare, particularly to species from the natural environment; and there is a lack of the specialist skills present within the environmental science community to design studies using omic technology and to then analyse the resulting data. To overcome these hurdles and equip scientists with the tools and skills they need to address their research questions using omics, we will provide the NERC Environmental Omics Facility (NEOF). NEOF will be a unique capability within the UK that has the expertise and equipment to train scientists in omic methods, help them to understand the potential of the technology and design studies to use it, provide the means to test adventurous ideas, and to support larger-scale NERC research projects. NEOF will be run by a team of scientists who are world-leading experts and are able to cover a broad range of omics methods, with experience of applying these to questions in environmental sciences. We will use this expertise to train early-stage scientists and to upskill scientists at any stage of their career. We will empower the community of NERC scientists to engage with new technologies and approaches and to then use them to address questions using omics that were previously impossible to answer in environmental science. We also have extensive equipment and space that we will use to support omic analysis for NERC scientists.
NEOF will be excellent value for NERC. We are able to provide £20m of existing equipment and >£2m of previous refurbishment so that NERC does not need to buy this for us. Our Universities will provide further refurbishment, space and support towards this proposal. Our team has >10 years' experience of delivering a highly effective facility to NERC, with a host of processes in place to ensure that projects are managed quickly and to budget. Because of this, we will be able to hit the ground running and provide this facility immediately to NERC scientists.
Scientists wanting to use omic technologies in their research face significant hurdles: the equipment required costs millions of pounds and few labs can afford it; the expertise to apply these techniques is rare, particularly to species from the natural environment; and there is a lack of the specialist skills present within the environmental science community to design studies using omic technology and to then analyse the resulting data. To overcome these hurdles and equip scientists with the tools and skills they need to address their research questions using omics, we will provide the NERC Environmental Omics Facility (NEOF). NEOF will be a unique capability within the UK that has the expertise and equipment to train scientists in omic methods, help them to understand the potential of the technology and design studies to use it, provide the means to test adventurous ideas, and to support larger-scale NERC research projects. NEOF will be run by a team of scientists who are world-leading experts and are able to cover a broad range of omics methods, with experience of applying these to questions in environmental sciences. We will use this expertise to train early-stage scientists and to upskill scientists at any stage of their career. We will empower the community of NERC scientists to engage with new technologies and approaches and to then use them to address questions using omics that were previously impossible to answer in environmental science. We also have extensive equipment and space that we will use to support omic analysis for NERC scientists.
NEOF will be excellent value for NERC. We are able to provide £20m of existing equipment and >£2m of previous refurbishment so that NERC does not need to buy this for us. Our Universities will provide further refurbishment, space and support towards this proposal. Our team has >10 years' experience of delivering a highly effective facility to NERC, with a host of processes in place to ensure that projects are managed quickly and to budget. Because of this, we will be able to hit the ground running and provide this facility immediately to NERC scientists.
Organisations
Publications
Recknagel H
(2024)
Genetic basis and expression of ventral colour in polymorphic common lizards.
in Molecular ecology
Recknagel H
(2023)
Common lizard microhabitat selection varies by sex, parity mode, and colouration.
in BMC ecology and evolution
Recknagel H
(2021)
The functional genetic architecture of egg-laying and live-bearing reproduction in common lizards.
in Nature ecology & evolution
Ridgway AM
(2024)
Sox21b underlies the rapid diversification of a novel male genital structure between Drosophila species.
in Current biology : CB
Rogers TF
(2021)
Multi-Copy Gene Family Evolution on the Avian W Chromosome.
in The Journal of heredity
Rogers Thea Frances
(2021)
The role of sex-specific selection in genome evolution
Roper M
(2022)
Individual variation explains ageing patterns in a cooperatively breeding bird, the long-tailed tit Aegithalos caudatus.
in The Journal of animal ecology
Sales N
(2020)
Fishing for mammals: Landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from riverine systems
in Journal of Applied Ecology
San-Jose LM
(2023)
Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics.
in Molecular ecology
Sendell-Price Ashley
(2020)
The genomics of diversification in South Pacific Silvereyes (Zosterops lateralis)
Description | Work has been used to monitor SARS-CoV2 variants in wastewater in support of the pandemic resonse. |
First Year Of Impact | 2020 |
Sector | Healthcare |
Description | Genomics of Host-Parasite Coevolution: A Test of Arms Race and Red Queen Dynamics in a Wild Insect System |
Amount | £395,422 (GBP) |
Funding ID | NE/W001616/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 08/2022 |
End | 01/2025 |
Description | Genomics of Host-Parasite Coevolution: A Test of Arms Race and Red Queen Dynamics in a Wild Insect System |
Amount | £153,085 (GBP) |
Funding ID | NE/W001519/1 |
Organisation | United Kingdom Research and Innovation |
Sector | Public |
Country | United Kingdom |
Start | 01/2022 |
End | 01/2025 |
Description | Identifying the genetic targets of sexual selection |
Amount | £497,744 (GBP) |
Funding ID | NE/V001566/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 11/2020 |
End | 10/2024 |
Description | Revealing the interplay of genetics and biomechanics underlying butterfly scale morphogenesis |
Amount | £0 (GBP) |
Organisation | Human Frontier Science Program (HFSP) |
Sector | Charity/Non Profit |
Country | France |
Start | 01/2021 |
End | 12/2021 |
Title | Costs of reproduction and their effect on age-related gene expression in Bombus terrestris queens |
Description | We used mRNA-seq to identify the RNA profiles in three tissue types (brain, fat body and ovary) in two time points (after 10% cohort death (TP1) and 60% cohort death (TP2)) for two treatments (egg removal (R) and egg removal and replacement (C)), with up to six biological replicates per tissue/time point/treatment combination. Each sample was sequenced on two lanes (L1 and L2) of the sequencing machine in order to generate sufficient numbers of reads while controlling for between lane variability. Illumina TruSeq stranded mRNA-seq libraries were constructed (from submitted RNA) and sequenced by Edinburgh Genomics (Edinburgh, UK) using 100 base pair paired-end reads. Quality of raw reads was assessed using FastQC v0.11.9 and aligning/pseudoaligning the reads to the Bombus terrestris genome/transcriptome (Bombus_terrestris.Bter_1.0.dna.toplevel.fa/ Bombus_terrestris.Bter_1.0.cdna.all.fa) using HISAT2 v2.1.0 and Kallisto v0.46.1, respectively. Bombus GEO dataset; accession number GSE172422 NBAF1153 outputs (from NERC project NE/R000875/1) |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | No |
Impact | None to date. |
Title | The effect of larval diet on the fecundity-longevity relationship and age-related gene expression in Drosophila melanogaster |
Description | We used mRNA-seq to identify the RNA profiles in three tissue types (fat body, head and ovary) in two time points (after 10% cohort death (RNA-1) and 60% cohort death (RNA-2)) for two treatments (medium-quality larval diet (M) and high-quality larval diet (H)), with three biological replicates per tissue/time point/treatment combination. Illumina TruSeq stranded mRNA-seq libraries were constructed (from submitted RNA) and sequenced by Edinburgh Genomics (Edinburgh, UK) using 100 base pair paired-end reads. Quality of raw reads was assessed using FastQC v0.11.9 and aligning/pseudoaligning the reads to the Drosophila melanogaster genome/transcriptome (Drosophila_melanogaster.BDGP6.22.dna.toplevel.fa / Drosophila_melanogaster.BDGP6.22.cdna.all.fa) using HISAT2 v2.1.0 and Kallisto v0.46.1, respectively. Drosophila GEO dataset: accession number GSE175623 NBAF1153 outputs (from NERC project NE/R000875/1) |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | No |
Impact | None to date. |