Assembly of 4?coverage of the S. salmonicida genome indicates distinc…

Assembly of 4?coverage of the S. salmonicida genome indicates distinct upstream sequences for two paralogs (unpublished data). Thus, ourRoxstr -Lindquist et al. BMC Genomics 2010, 11:258 http://www.biomedcentral.com/1471-2164/11/Page 8 ofTable 1: PCR amplifications of regions with SNPs observed in the EST data.Gene speciesa length Enolase Enolase Ribosomal protein S2 Ribosomal protein S2 Glutamate dehydrogenase Glutamate dehydrogenase HSP70 HSP70 Pyruvate kinase Pyruvate kinasea)PCR #clones 14 10 10 10 13 13 67d 10 68d 10 PCR 4 0 0 0 6 10 5 0 13#SNP EST 4 0 0 0 2 N/Ac 5 N/Ac 9 0 shared 4 0 0 0 1 N/Ac 4 N/Ac 9#alleles PCR total 4 1 1 1 2 3 6 1 11 1 majorb 3 1 1 1 2 2 5 1 3#clones major and (minor) allelesSB SS SB SS SB SS SB SS SB SS566 566 496 499 549 549 514 514 4666,4,3 (1) 10 10 10 9,4 8,4 (1) 54,5,4,2,1 (1) 10 43,8,6 (2,2,2,1,1,1,1,1)SB: Spironucleus barkhanus, SS: Spironucleus salmonicida b) Major alleles are the minimal set of alleles observed in the PCR experiments to explain all SNPs present in the data. c) No S. salmonicida ESTs were available for these two genes. d) From two independent PCR reactions.study indicates a low level of allelic sequence divergence in S. salmonicida, as suggested by the previous genomic survey [14]. Available sequences from the genome project of S. vortens [44] were used to test whether allelic variation is present in this Spironucleus species. Sequences covering the homologous region of the five genes were identified among the >200,000 genomic survey sequences (GSS) and >25,000 EST sequences available at the NCBI [45]. No sequences were found for glutamate dehydrogenase, whereas between five and 32 GSSs, and between nine and hundreds of ESTs were found for the other four genes (Table 2). The number of identified SNPs varied extensively between the four genes; none were found for the enolase gene, whereas more than 60 SNPs were present in the pyruvate kinase sequences (Table 2). The number of alleles appeared to be high for the three genes for which SNPs were found (data not shown). Thus, extensive allelic sequence variation is present in S. vortens.An emerging picture of allelic sequence variation in diplomonadsOur data indicate large variations in the degree of allelic sequence variation between different genes and different member of the genus Spironucleus. This is similar to the situation in G. intestinalis; WB (genotype A) and GS (genotype B) showed PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/16989806 from patient samples in epidemiological studies of Giardia than genotype A isolates [46,47]. The allelic sequence divergence in G. intestinalis GS is non-randomly distributed along the chromosomes with large regions with very Lenalidomide low frequencies of SNPs followed by large regions with high divergence [7]. Similarly, some Spironucleus genes lack SNPs, whereas others have large numbers (Tables 1, 2 and Additional file 5). In G. intestinalis GS most genes with SNPs seem to group into two, or sometimes three alleles [7]. Our data suggest higher numbers of alleles for many of the S. barkhanus genes (Table 1 and Additional file 5). Ten proteins are represented by five or more closely related sequences which correspond to alleles and/or paralogs. An additional nine proteins with three or four highly similar contig sequences show allelic variation within individual c.