Sequencing a Soil Sentinel (SeqaWorm)

对土壤哨兵进行测序 (SeqaWorm)

• 批准号: NE/F001185/1
• 负责人: Peter Kille
• 金额: $ 7.03万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FF001185%2F1
• 关键词: Sequencing; Soil; Sentinel; SeqaWorm

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.

通过使用当代生态毒理学基因组学技术（转录组学、蛋白质组学和代谢组学）监测自由生活受体生物的表现指标来评估生态系统健康的努力，至少在两种基本方法上努力模仿人类医学中的分子诊断原理。首先，越来越强调从分子角度描述化学中毒导致生理过程中断的机制，从发育、生存、生长到繁殖。其次，人们正在利用技术逐步废除传统的“基因用于”方法，转而采用包含复杂、模块化、基因-蛋白质网络的系统观点。毫无疑问，环境诊断学正在接近一个令人兴奋的阶段，它将成为一门强大的、可预测的科学。然而，为了从现有的技术平台中获得最大的利益，很明显，在非模式无脊椎动物物种中缺乏完全注释的序列数据必须立即纠正。为了应对这一挑战，我们建议在本研究中进一步关注一种无处不在的蚯蚓物种（Lumbricus rubellus），它与其分类单元的其他成员一样，是一种重要的生态工程生物，其特殊的生态生理特性使其成为充满压力的棕地和废弃工业土壤的先驱殖民者，以及清洁酸性高地和白垩土的居民。令人惊讶的是，人们对风疹乳杆菌或任何其他蚯蚓的遗传学知之甚少。在之前nerc资助的（EcoWorm）项目中，我们生成了第一个环节动物DNA序列的大型数据集，现在总共有20万个EST序列，聚集到8000个“基因对象”中。这个数据集（存放在一个名为LumbriBASE的公共访问数据库中，www.earthworms.org.）估计只代表了这种环境哨兵生物表达的约40%的基因，并且已经促进了在不相关的分类群中保守的关键反应途径的鉴定。此外，这些信息有望将土壤污染的基因型、表型和生态后果联系起来。目前拟议的测序计划打算利用在EcoWorm中收集的战略投资和资源作为跳板，扩大风疹螺旋体的序列知识库。据估计，风疹乳杆菌拥有430 Mb的基因组（http://www.genomesize.com/annelids.htm），分布在18对染色体上。我们将筛选一个BAC文库或约50,000个平均大小为100 Kb的克隆，这代表了蚯蚓基因组的约15倍覆盖率，以寻找具有已知环境响应谱的靶点。然而，我们的建议远不止是基因增加的练习；它保证了我们描述一种非常重要的土栖大型无脊椎动物对环境变化和影响的抵抗力或脆弱性的功能基础的能力的量子增强。通过利用EcoWorm生成的信息工具，转录数据可以转化为资源，支持理解环境扰动与转录组和蛋白质组之间的相互作用。此外，我们的目标是揭示基于非编码序列的基因组表达改变的功能途径，从而为全基因组测序提供必要的前体数据。

项目成果

Identifying biochemical phenotypic differences between cryptic species.

识别隐秘物种之间的生化表型差异。

• DOI: 10.1098/rsbl.2014.0615
• 发表时间: 2014
• 期刊: Biology letters
• 影响因子: 3.3
• 作者: Liebeke M

DNA sequence variation and methylation in an arsenic tolerant earthworm population

• DOI: 10.1016/j.soilbio.2012.10.014
• 发表时间: 2013-02-01
• 期刊: SOIL BIOLOGY & BIOCHEMISTRY
• 影响因子: 9.7
• 作者: Kille, Peter;Andre, Jane;Spurgeon, David J.
• 通讯作者: Spurgeon, David J.

The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843)

红色堆肥蚯蚓 Lumbricus rubellus 的基因组序列（Hoffmeister，1843）

• DOI: 10.12688/wellcomeopenres.19834.1
• 发表时间: 2023
• 期刊: Wellcome Open Research
• 作者: Short S

The worm has turned: Behavioural drivers of reproductive isolation between cryptic lineages

• DOI: 10.1016/j.soilbio.2016.03.015
• 发表时间: 2016-07-01
• 期刊: SOIL BIOLOGY & BIOCHEMISTRY
• 影响因子: 9.7
• 作者: Jones, G. L.;Wills, A.;Novo, M.
• 通讯作者: Novo, M.