Sequencing a Soil Sentinel (SeqaWorm)

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

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.

Publications

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Anderson CJ (2013) Life-history effects of arsenic toxicity in clades of the earthworm Lumbricus rubellus. in Environmental pollution (Barking, Essex : 1987)

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Andre J (2010) Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape. in Environmental pollution (Barking, Essex : 1987)

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St├╝rzenbaum SR (2009) Earthworm genomes, genes and proteins: the (re)discovery of Darwin's worms. in Proceedings. 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...