MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea

Abstract

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

Construction of a Spinach Bacterial Artificial Chromosome (BAC) Library as a Resource for Gene Identification and Marker Development

“…BLASTx analysis indicated that 70 sequences (2.06 %) were associated with chloroplasts, and 12 sequences (0.35 %) consisted of mitochondrial genes. These percentages of chloroplast and mitochondrial contamination are similar to what has been reported for other plant BAC libraries (Lijavetzky et al 1999;O'Sullivan et al 2001;Tomkins et al 2001;Martin et al 2002;Allouis et al 2003;Xia et al 2005). In addition to providing new sequence information for genome analysis and marker development, these BAC end sequences will be particularly useful to help reduce the number of scaffolds created during de novo sequencing of the spinach genome.…”

Gene expression analysis of plant host–pathogen interactions by SuperSAGE

“…Blast disease is a devastating rice disease caused by the ascomycete fungus M. grisea. Whole genome sequences are available for both rice (11,12) and the blast fungus (13), so that the rice-blast fungus interaction system offers to test the utility of genomic information for understanding host-pathogen interactions.…”

Serial Analysis of Gene Expression (SAGE) of Magnaporthe grisea: genes involved in appressorium formation

“…Another 28 tags could be successfully annotated by consulting genomic sequences ( Table 2). As the genome size of M. grisea is small (40 Mb, Martin et al 2002), the chance that a 14-bp tag sequence occurs only once in the genome is theoretically high. This is because the possible number of tag sequences (4 14 =268,435,456), assuming that all four bases are represented equally in the M. grisea genome and in a random sequence, is far higher than the total number of nucleotides in the genome (40,000,000), so that the probability that a given 14mer sequence exactly matches a single sequence in the genome by chance is low.…”