Collembase: a repository for springtail genomics and soil quality assessment.
Collembase: a repository for springtail genomics and soil quality assessment.
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Collembase：Springtail基因组学和土壤质量评估的存储库。
DOI：
10.1186/1471-2164-8-341
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发表时间：
2007-09-27
期刊：
影响因子：
4.4
通讯作者：
Roelofs, Dick
中科院分区：
文献类型：
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作者：
Timmermans, Martijn J T N;de Boer, Muriel E;Nota, Benjamin;de Boer, Tjalf E;Marien, Janine;Klein-Lankhorst, Rene M;van Straalen, Nico M;Roelofs, Dick
传统的环境质量评价是基于指示生物的繁殖和生存反应。对于土壤评估，跳虫Folsomia candida（弹尾目）是公认的标准测试生物。我们认为，环境质量评估的指示生物暴露于测试基板的基因表达谱是更敏感，更有毒的具体和显着快于目前的风险评估方法。为了将该物种作为土壤质量检测的基因组模型，我们进行了EST测序项目，并开发了一个在线数据库。Collembase是一个可通过网络访问的数据库，包括弹簧尾（F。念珠菌属）基因组数据。目前，该数据库包含8686个EST的信息，这些EST被组装成5952个独特的基因对象。在这些基因对象中，约40%显示出与GenBank中可获得的其他蛋白质序列的同源性（blastx分析;非冗余（nr）数据库;期望值< 10-5）。应用软件推断蛋白质序列。推定的肽，其平均长度为115个氨基酸（范围在23和440之间），用基因本体（GO）术语进行注释。总共10 - 25个肽（约17%的基因对象）被分配至少一个GO术语（期望值< 10-25）。在Collembase内，可以基于BLAST和GO注释、簇名称或使用BLAST服务器进行搜索。该系统还可以轻松检索功能基因组和定量PCR实验的序列。将序列提交至GenBank（登录号：EV 473060-EV 481745）。Collembase是一个关于弹尾F的序列数据资源。念珠菌。数据库中的信息将链接到基于Agilent平台的定制微阵列，该微阵列可用于土壤质量检测。此外，Collembase还为相关科学学科提供了有价值的信息，如分子生态学，生态基因组学，分子进化和遗传学。
Environmental quality assessment is traditionally based on responses of reproduction and survival of indicator organisms. For soil assessment the springtail Folsomia candida (Collembola) is an accepted standard test organism. We argue that environmental quality assessment using gene expression profiles of indicator organisms exposed to test substrates is more sensitive, more toxicant specific and significantly faster than current risk assessment methods. To apply this species as a genomic model for soil quality testing we conducted an EST sequencing project and developed an online database. Collembase is a web-accessible database comprising springtail (F. candida) genomic data. Presently, the database contains information on 8686 ESTs that are assembled into 5952 unique gene objects. Of those gene objects ~40% showed homology to other protein sequences available in GenBank (blastx analysis; non-redundant (nr) database; expect-value < 10-5). Software was applied to infer protein sequences. The putative peptides, which had an average length of 115 amino-acids (ranging between 23 and 440) were annotated with Gene Ontology (GO) terms. In total 1025 peptides (~17% of the gene objects) were assigned at least one GO term (expect-value < 10-25). Within Collembase searches can be conducted based on BLAST and GO annotation, cluster name or using a BLAST server. The system furthermore enables easy sequence retrieval for functional genomic and Quantitative-PCR experiments. Sequences are submitted to GenBank (Accession numbers: EV473060 – EV481745). Collembase is a resource of sequence data on the springtail F. candida. The information within the database will be linked to a custom made microarray, based on the Agilent platform, which can be applied for soil quality testing. In addition, Collembase supplies information that is valuable for related scientific disciplines such as molecular ecology, ecogenomics, molecular evolution and phylogenetics.