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Example sentences for: javanica
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We describe here a comprehensive two-step search for HGT candidates in M. incognita, M. javanica and M. hapla using EST data [ 22 28 29 ] . Genome-to-genome comparisons were made to discover patterns of presence and absence that would indicate horizontally acquired genes.
Sequences were obtained from the Parasitic Nematode Sequencing Project (PNSP) [ 30 ] including clustered Meloidogyne ESTs built with the NemaGene approach [ 28 ] . We analyzed 1,799 M. incognita (WMi) sequences and 3,119 M. javanica (WMj) sequences from these PNSP clusters.
Another RKN gene also postulated to have been acquired by HGT, and which encodes polyglutamate synthetase, was previously identified in M. artiellia [ 23 ] . Significantly, hybridization data showed that this particular gene is absent from both the M. javanica and G. rostochiensis genomes [ 23 ] . We speculate that acquisition of this gene by M. artiellia is a recent HGT event (event 'c', Figure 1), and thus it is truly absent from the Meloidogyne genomes from which our datasets were derived.
Following clustering, comparative analyses were performed using WU-BLASTX and WU-TBLASTX [ 92 93 ] with 1,798 contig consensus sequences (themselves grouped into 1,625 cluster groups) as queries versus multiple databases including SWIR v.21 (5/19/2000) non-redundant protein database and Wormpep v.54 C. elegans protein database (Wellcome Trust Sanger Institute, unpublished work), C. elegans mitochondrial protein sequences, and six internally constructed databases using intersections of data from the GenBank nucleotide database and dbEST [ 96 ] . These include: nemnoele (all nucleotide data from the phylum Nematoda with C. elegans removed); nemnoelenomi (nemnoele with M. incognita removed); nemnoelenomel (nemnoele with all Meloidogyne species removed); nemnoelenotyl (nemnoele with all Tylenchida species removed); yestylnomel (all Tylenchida species except Meloidogyne ); mj (only M. javanica sequences).
By creating intersections of various database search results, contigs/clusters could be organized by their distribution of homologies (for example, clusters which have M. javanica matches but not C. elegans matches).
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