Collembase: a repository for springtail genomics and soil quality assessment

<p>Abstract</p> <p>Background</p> <p>Environmental quality assessment is traditionally based on responses of reproduction and survival of indicator organisms. For soil assessment the springtail <it>Folsomia candida </it>(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.</p> <p>Description</p> <p>Collembase is a web-accessible database comprising springtail (<it>F. candida</it>) 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: <ext-link ext-link-type="gen" ext-link-id="EV473060">EV473060</ext-link> – <ext-link ext-link-type="gen" ext-link-id="EV481745">EV481745</ext-link>).</p> <p>Conclusion</p> <p>Collembase <url>http://www.collembase.org</url> is a resource of sequence data on the springtail <it>F. candida</it>. 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.</p

A genome-wide genetic map of NB-LRR disease resistance loci in potato

Like all plants, potato has evolved a surveillance system consisting of a large array of genes encoding for immune receptors that confer resistance to pathogens and pests. The majority of these so-called resistance or R proteins belong to the super-family that harbour a nucleotide binding and a leucine-rich-repeat domain (NB-LRR). Here, sequence information of the conserved NB domain was used to investigate the genome-wide genetic distribution of the NB-LRR resistance gene loci in potato. We analysed the sequences of 288 unique BAC clones selected using filter hybridisation screening of a BAC library of the diploid potato clone RH89-039-16 (S. tuberosum ssp. tuberosum) and a physical map of this BAC library. This resulted in the identification of 738 partial and full-length NB-LRR sequences. Based on homology of these sequences with known resistance genes, 280 and 448 sequences were classified as TIR-NB-LRR (TNL) and CC-NB-LRR (CNL) sequences, respectively. Genetic mapping revealed the presence of 15 TNL and 32 CNL loci. Thirty-six are novel, while three TNL loci and eight CNL loci are syntenic with previously identified functional resistance genes. The genetic map was complemented with 68 universal CAPS markers and 82 disease resistance trait loci described in literature, providing an excellent template for genetic studies and applied research in potato

Venn-diagram showing the cluster overlap between the three libraries for the total dataset: Cad: cadmium enriched library; Phe: phenanthrene enriched library; Nor: normalized library

<p><b>Copyright information:</b></p><p>Taken from "Collembase: a repository for springtail genomics and soil quality assessment"</p><p>http://www.biomedcentral.com/1471-2164/8/341</p><p>BMC Genomics 2007;8():341-341.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2234260.</p><p></p

Relative abundance of six cDNAs before (upper) and after (lower) normalization as measured using quantitative PCR

<p><b>Copyright information:</b></p><p>Taken from "Collembase: a repository for springtail genomics and soil quality assessment"</p><p>http://www.biomedcentral.com/1471-2164/8/341</p><p>BMC Genomics 2007;8():341-341.</p><p>Published online 27 Sep 2007</p><p>PMCID:PMC2234260.</p><p></p> Act: β-actin; 28S: 28S rDNA; De: RNA helicase Dead1; RXR: RXR-USP; Ub: Ultrabithorax; Kr: Kruppel

The genome of the stress-tolerant wild tomato species Solanum pennellii

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm