Sequencing a Soil Sentinel (SeqaWorm)
Lead Research Organisation:
University of Edinburgh
Department Name: Inst of Evolutionary Biology
Abstract
Efforts to assess ecosystem health by monitoring performance indicators in free-living receptor organisms using contemporary ecotoxicogenomic technologies (transcriptomics, proteomics, and metabolomics) is striving in at least two fundamental ways to emulate the principles of molecular diagnostics in human medicine. First, there is increasing emphasis on describing in molecular terms the mechanisms of chemical toxicosis leading to disruptions in physiological processes, from development, survival, and growth, to reproduction. Second, technology is being harnessed to progressively dismantle the traditional 'gene for' approach in favour of a systems perspective that encompasses complex, modular, gene-protein networks. Environmental diagnostics is undoubtedly approaching an exciting phase in its evolution into a robust, predictive, science. However, in order to extract the maximum benefit from available technological platforms it is clear that the paucity of fully annotated sequence data in non-model species of invertebrates must be urgently corrected. To address this challenge, we propose in this study to focus further on a ubiquitous earthworm species (Lumbricus rubellus) which, in common with other members of its taxon, is a keystone ecological-engineering organism and whose particular ecophysiological traits enable it to be a pioneering colonizer of stress-laden brownfield and abandoned industrial soils, as well as a denizen of clean acidic upland and chalky soils. Surprisingly little is known of the genetics of L. rubellus or any other earthworm. In a previous NERC-funded (EcoWorm) programme we generated the first large dataset of annelid DNA sequences, now totalling > 20,000 EST sequences, clustered into 8,000 'gene objects'. This dataset (deposited in a public-access database called LumbriBASE, www.earthworms.org.) is estimated to represent only ~40% of the genes expressed by this environmental sentinel organism, and has already facilitated the identification of key response pathways conserved across unrelated taxa. Furthermore, the information promises to allow the genotypic, phenotypic and ecological consequences of soil pollution to be linked. The present proposed sequencing programme intends using the strategic investment and resources gleaned within EcoWorm as springboards to expand the sequence knowledge-base for L. rubellus. L. rubellus is estimated to possess a genome of 430 Mb (http://www.genomesize.com/annelids.htm) distributed over 18 chromosome pairs. We will screen a BAC library or ~50,000 clones with average size of 100 Kb, which represents ~15-fold coverage of the earthworm genome, for targets with known environmental response profiles. Our proposal is, however, far more than an exercise in genetic accretion; it promises a quantum enhancement in our ability to describe the functional basis of resistance or vulnerability to environmental change and impact in a conspicuously important soil-dwelling macroinvertebrate. By exploiting informatic tools generated within EcoWorm, transcript data can be converted into resources which support efforts to understand the interactions between environmental perturbations and both the transcriptome and proteome Furthermore, we aim to reveal the functional pathways that underlie altered genome expression based on non-coding sequences, thus providing the necessary precursor data for whole-genome sequencing.
Organisations
People |
ORCID iD |
Peter Kille (Principal Investigator) | |
Mark Blaxter (Co-Investigator) |
Publications
Anderson C
(2013)
Life-history effects of arsenic toxicity in clades of the earthworm Lumbricus rubellus
in Environmental Pollution
Andre J
(2009)
Accumulated metal speciation in earthworm populations with multigenerational exposure to metalliferous soils: cell fractionation and high-energy synchrotron analyses.
in Environmental science & technology
Andre J
(2010)
Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape.
in Environmental pollution (Barking, Essex : 1987)
Blaxter M
(2023)
The genome sequence of the common earthworm, Lumbricus terrestris (Linnaeus, 1758)
in Wellcome Open Research
Jones G
(2016)
The worm has turned: Behavioural drivers of reproductive isolation between cryptic lineages
in Soil Biology and Biochemistry
Kille P
(2013)
DNA sequence variation and methylation in an arsenic tolerant earthworm population
in Soil Biology and Biochemistry
Liebeke M
(2014)
Identifying biochemical phenotypic differences between cryptic species.
in Biology letters
Novo M
(2015)
Different routes, same pathways: Molecular mechanisms under silver ion and nanoparticle exposures in the soil sentinel Eisenia fetida.
in Environmental pollution (Barking, Essex : 1987)
Schultz C
(2015)
Analytical approaches to support current understanding of exposure, uptake and distributions of engineered nanoparticles by aquatic and terrestrial organisms.
in Ecotoxicology (London, England)
Short S
(2023)
The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843)
in Wellcome Open Research
Spurgeon D
(2016)
Ecological drivers influence the distributions of two cryptic lineages in an earthworm morphospecies
in Applied Soil Ecology
Stürzenbaum S
(2008)
Earthworm genomes, genes and proteins: the (re)discovery of Darwin's worms
in Proceedings of the Royal Society B: Biological Sciences
Description | Final project report provided to NERC together with detailed OPMs. |
Exploitation Route | Substantial genetic resources generated. |
Sectors | Environment |
Title | Lumbricus rubellus Genome sequencing and assembly |
Description | NCBI Bioproject: PRJNA391583 : Lumbricus rubellus Genome sequencing and assembly (TaxID: 35632) |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Earthworm Genome sequence |
URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA391583 |
Title | PRJNA596978 : Lumbricus rubellus Arsenic Transcriptome (TaxID: 35632) |
Description | Lumbricus rubellus Arsenic Transcriptome Biosamples: 1. Invertebrate sample from Lumbricus rubellus - 125 mg/kg Exposure Identifiers: BioSample: SAMN13649404; Sample name: Lumbricus rubellus - 125 mg/kg Arsenic Exposure; SRA: SRS5873818 Organism: Lumbricus rubellus isolate: Surplied by Lasebo, Netherlands Package: Invertebrate; version 1.0 Accession: SAMN13649404 ID: 13649404 2. Invertebrate sample from Lumbricus rubellus - 36 mg/kg Exposure Identifiers: BioSample: SAMN13649388; Sample name: Lumbricus rubellus - 36 mg/kg Arsenic Exposure; SRA: SRS5873550 Organism: Lumbricus rubellus isolate: Surplied by Lasebo, Netherlands Package: Invertebrate; version 1.0 Accession: SAMN13649388 ID: 13649388 3. Invertebrate sample from Lumbricus rubellus - Control Exposure Identifiers: BioSample: SAMN13648696; Sample name: Lumbricus rubellus - Control Arsenic Exposure; SRA: SRS5873542 Organism: Lumbricus rubellus isolate: Surplied by Lasebo, Netherlands Package: Invertebrate; version 1.0 Accession: SAMN13648696 ID: 13648696 SRA Experiment Accession Experiment Title Organism Name Instrument Submitter Study Accession Study Title Sample Accession Sample Title Total Size, Mb Total RUNs Total Spots Total Bases Library Name Library Strategy Library Source Library Selection SRX7427885 Lumbricus rubellus As Exposure 125 mg/kg Lumbricus rubellus Illumina HiSeq 2000 Cardiff University SRP238477 Lumbricus rubellus Genome sequencing and assembly SRS5873818 16551.85 1 114220774 23072596348 Lrub_T_As125_140711 RNA-Seq TRANSCRIPTOMIC RT-PCR SRX7427617 Lumbricus rubellus As exposure 36 mg/kg Lumbricus rubellus Illumina HiSeq 2000 Cardiff University SRP238474 Lumbricus rubellus Arsenic Transcriptome SRS5873550 8783.6 1 60373451 12195437102 Lrub_T_As36_140711 RNA-Seq TRANSCRIPTOMIC RT-PCR SRX7427609 As Control Lumbricus rubellus Illumina HiSeq 2000 Cardiff University SRP238474 Lumbricus rubellus Arsenic Transcriptome SRS5873542 3315.76 1 21928948 4429647496 Lrub_T_As0_140711 RNA-Seq TRANSCRIPTOMIC RT-PCR |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Lumbricus rubellus Arsenic Transcriptome |
URL | https://www.ncbi.nlm.nih.gov/bioproject/PRJNA596978 |
Description | Review of the sequencing technology, it's strengths and Weaknesses / Sequencing technology and its impact on experimental design |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | NERC-MDIBL Environmental Genomics and Metabolomics Training course |
Year(s) Of Engagement Activity | 2016 |
URL | http://www.birmingham.ac.uk/schools/biosciences/news/2016/06Mar-NERC-MDIBL-Environmental-Genomics-Me... |