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Comparative Sequence Analysis (comparative + sequence_analysis)
Selected AbstractsComparative Sequence Analysis of Coat Protein Gene of Iranian Citrus tristeza virus IsolatesJOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2005A. Barzegar Abstract Twenty-two isolates of Citrus tristeza virus (CTV) collected from two different geographical regions of Iran were characterized based on coat protein (CP) gene sequences. Thirteen virus isolates were collected from northern parts of Iran with high distribution of CTV infection and nine isolates were obtained from southern regions where the presence and aphid transmission of CTV was previously reported. All isolates were recovered from field trees showing varied CTV symptoms such as decline in most citrus varieties on sour orange rootstock, inverse pitting on some sour orange rootstocks below bud union, mild-to-moderate stem pitting on the trunk of some sweet orange. Isolates F, G, MB1, MB7, MB2, MB8, MB9, MB11 and MB17 were recovered from healthy looking Miyagawa Satsuma on trifoliate rootstock originally infected with CTV imported from Japan in late-1960s. The presence of virus in citrus samples was confirmed using polyclonal as well as monoclonal antibody. The CTV CP gene of all isolates was amplified by reverse transcriptase polymerase chain reaction (RT,PCR) using CP gene-specific primers yielding 672 bp amplicon. The restriction fragment length polymorphism (RFLP) profile, nucleotide and deduced amino acid sequences were analysed and compared with each other and also with some other exotic CP gene sequences of CTV isolates available in GenBank. Analysis of our data revealed that Iranian isolates have high similarity to California SY568 severe stem pitting and Japanese NUagA seedling yellows strains (up to 97%). The dendrogram generated from the deduced amino acid sequence could separate MB1, MB2, MB8, MB9, MB11 and MB17 isolates from others. However, no major dissociation between the isolates from northern and southern region could be obtained. [source] Dopamine Receptors in a Songbird BrainTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 6 2010Lubica Kubikova Dopamine is a key neuromodulatory transmitter in the brain. It acts through dopamine receptors to affect changes in neural activity, gene expression, and behavior. In songbirds, dopamine is released into the striatal song nucleus area X, and the levels depend on social contexts of undirected and directed singing. This differential release is associated with differential expression of activity-dependent genes, such as egr1 (avian zenk), which in mammalian brain are modulated by dopamine receptors. Here we cloned from zebra finch brain cDNAs of all avian dopamine receptors: the D1 (D1A, D1B, D1D) and D2 (D2, D3, D4) families. Comparative sequence analyses of predicted proteins revealed expected phylogenetic relationships, in which the D1 family exists as single exon and the D2 family exists as spliced exon genes. In both zebra finch and chicken, the D1A, D1B, and D2 receptors were highly expressed in the striatum, the D1D and D3 throughout the pallium and within the mesopallium, respectively, and the D4 mainly in the cerebellum. Furthermore, within the zebra finch, all receptors, except for D4, showed differential expression in song nuclei relative to the surrounding regions and developmentally regulated expression that decreased for most receptors during the sensory acquisition and sensorimotor phases of song learning. Within area X, half of the cells expressed both D1A and D2 receptors, and a higher proportion of the D1A-only-containing neurons expressed egr1 during undirected but not during directed singing. Our findings are consistent with hypotheses that dopamine receptors may be involved in song development and social context-dependent behaviors. J. Comp. Neurol. 518:741,769, 2010. © 2009 Wiley-Liss, Inc. [source] Dopamine receptors in a songbird brainTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 6 2010Lubica Kubikova Abstract Dopamine is a key neuromodulatory transmitter in the brain. It acts through dopamine receptors to affect changes in neural activity, gene expression, and behavior. In songbirds, dopamine is released into the striatal song nucleus Area X, and the levels depend on social contexts of undirected and directed singing. This differential release is associated with differential expression of activity-dependent genes, such as egr1 (avian zenk), which in mammalian brain are modulated by dopamine receptors. Here we cloned from zebra finch brain cDNAs of all avian dopamine receptors: the D1 (D1A, D1B, D1D) and D2 (D2, D3, D4) families. Comparative sequence analyses of predicted proteins revealed expected phylogenetic relationships, in which the D1 family exists as single exon and the D2 family exists as spliced exon genes. In both zebra finch and chicken, the D1A, D1B, and D2 receptors were highly expressed in the striatum, the D1D and D3 throughout the pallium and within the mesopallium, respectively, and the D4 mainly in the cerebellum. Furthermore, within the zebra finch, all receptors, except for D4, showed differential expression in song nuclei relative to the surrounding regions and developmentally regulated expression that decreased for most receptors during the sensory acquisition and sensorimotor phases of song learning. Within Area X, half of the cells expressed both D1A and D2 receptors, and a higher proportion of the D1A-only-containing neurons expressed egr1 during undirected but not during directed singing. Our findings are consistent with hypotheses that dopamine receptors may be involved in song development and social context-dependent behaviors. J. Comp. Neurol. 518:741,769, 2010. © 2009 Wiley-Liss, Inc. [source] Conservation and expression of IQ-domain-containing calpacitin gene products (neuromodulin/GAP-43, neurogranin/RC3) in the adult and developing oscine song control systemDEVELOPMENTAL NEUROBIOLOGY, Issue 2-3 2009David F. Clayton Abstract Songbirds are appreciated for the insights they provide into regulated neural plasticity. Here, we describe the comparative analysis and brain expression of two gene sequences encoding probable regulators of synaptic plasticity in songbirds: neuromodulin (GAP-43) and neurogranin (RC3). Both are members of the calpacitin family and share a distinctive conserved core domain that mediates interactions between calcium, calmodulin, and protein kinase C signaling pathways. Comparative sequence analysis is consistent with known phylogenetic relationships, with songbirds most closely related to chicken and progressively more distant from mammals and fish. The C-terminus of neurogranin is different in birds and mammals, and antibodies to the protein reveal high expression in adult zebra finches in cerebellar Purkinje cells, which has not been observed in other species. RNAs for both proteins are generally abundant in the telencephalon yet markedly reduced in certain nuclei of the song control system in adult canaries and zebra finches: neuromodulin RNA is very low in RA and HVC (relative to the surrounding pallial areas), whereas neurogranin RNA is conspicuously low in Area X (relative to surrounding striatum). In both cases, this selective downregulation develops in the zebra finch during the juvenile song learning period, 25,45 days after hatching. These results suggest molecular parallels to the robust stability of the adult avian song control circuit. © 2008 Wiley Periodicals, Inc. Develop Neurobiol, 2009 [source] Retrieval of first genome data for rice cluster I methanogens by a combination of cultivation and molecular techniquesFEMS MICROBIOLOGY ECOLOGY, Issue 2 2005Christoph Erkel Abstract We report first insights into a representative genome of rice cluster I (RC-I), a major group of as-yet uncultured methanogens. The starting point of our study was the methanogenic consortium MRE50 that had been stably maintained for 3 years by consecutive transfers to fresh medium and anaerobic incubation at 50 °C. Process-oriented measurements provided evidence for hydrogenotrophic CO2 -reducing methanogenesis. Assessment of the diversity of consortium MRE50 suggested members of the families Thermoanaerobacteriaceae and Clostridiaceae to constitute the major bacterial component, while the archaeal population was represented entirely by RC-I. The RC-I population amounted to more than 50% of total cells, as concluded from fluorescence in situ hybridization using specific probes for either Bacteria or Archaea. The high enrichment status of RC-I prompted construction of a large insert fosmid library from consortium MRE50. Comparative sequence analysis of internal transcribed spacer (ITS) regions revealed that three different RC-I rrn operon variants were present in the fosmid library. Three, approximately 40-kb genomic fragments, each representative for one of the three different rrn operon variants, were recovered and sequenced. Computational analysis of the sequence data resulted in two major findings: (i) consortium MRE50 most likely harbours only a single RC-I genotype, which is characterized by multiple rrn operon copies; (ii) seven genes were identified to possess a strong phylogenetic signal (eIF2a, dnaG, priA, pcrA, gatD, gatE, and a gene encoding a putative RNA-binding protein). Trees exemplarily computed for the deduced amino acid sequences of eIF2a, dnaG, and priA corroborated a specific phylogenetic association of RC-I with the Methanosarcinales. [source] A 76-residue polypeptide of colicin E9 confers receptor specificity and inhibits the growth of vitamin B12 -dependent Escherichia coli 113/3 cellsMOLECULAR MICROBIOLOGY, Issue 3 2000Christopher N. Penfold The mechanism by which E colicins recognize and then bind to BtuB receptors in the outer membrane of Escherichia coli cells is a poorly understood first step in the process that results in cell killing. Using N- and C-terminal deletions of the N-terminal 448 residues of colicin E9, we demonstrated that the smallest polypeptide encoded by one of these constructs that retained receptor-binding activity consisted of residues 343,418. The results of the in vivo receptor-binding assay were supported by an alternative competition assay that we developed using a fusion protein consisting of residues 1,497 of colicin E9 fused to the green fluorescent protein as a fluorescent probe of binding to BtuB in E. coli cells. Using this improved assay, we demonstrated competitive inhibition of the binding of the fluorescent fusion protein by the minimal receptor-binding domain of colicin E9 and by vitamin B12. Mutations located in the minimum R domain that abolished or reduced the biological activity of colicin E9 similarly affected the competitive binding of the mutant colicin protein to BtuB. The sequence of the 76-residue R domain in colicin E9 is identical to that found in colicin E3, an RNase type E colicin. Comparative sequence analysis of colicin E3 and cloacin DF13, which is also an RNase-type colicin but uses the IutA receptor to bind to E. coli cells, revealed significant sequence homology throughout the two proteins, with the exception of a region of 92 residues that included the minimum R domain. We constructed two chimeras between cloacin DF13 and colicin E9 in which (i) the DNase domain of colicin E9 was fused onto the T+R domains of cloacin DF13; and (ii) the R domain and DNase domain of colicin E9 were fused onto the T domain of cloacin DF13. The killing activities of these two chimeric colicins against indicator strains expressing BtuB or IutA receptors support the conclusion that the 76 residues of colicin E9 confer receptor specificity. The minimum receptor-binding domain polypeptide inhibited the growth of the vitamin B12 -dependent E. coli 113/3 mutant cells, demonstrating that vitamin B12 and colicin E9 binding is mutually exclusive. [source] Identification and gene expression profiling of the Pum1 and Pum2 members of the Pumilio family in the chickenMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 1 2008Jee Young Lee Abstract Members of the Pumilio (Pum) family of RNA-binding proteins act as translational repressors and are required for germ cell development and asymmetric division. We identified the chicken Pum1 and Pum2 genes and analyzed their expression patterns in various tissues. Comparative sequence analysis of the Pum1 and Pum2 proteins from the drosophila, chicken, mouse, and human revealed a high degree of evolutionary conservation in terms of the levels of homology of the peptide sequences and the structure of Pumilio homology domain (PUM-HD), C-terminal RNA-binding domain, with similar spacing between the adjacent Pum eight tandem repeats. In addition, phylogenetic patterns of pumilio family showed that Pum 1 and 2 of chicken are more closely related to those of mouse and human than other species and Pum1 is more conserved than Pum2. Using real-time RT-PCR, the expression levels of the Pum1 and Pum2 genes were found to be highest in hatched female gonads, and high-level expression of Pum2 was detected in 12-day and hatched gonads among the various chicken embryonic tissues tested. In adult tissues, the expression levels of Pum1 and Pum2 were expressed at higher levels in the testis and muscle than in any other tissue. The characteristics of the tissue-specific expression of Pum genes suggest that Pum1 and Pum2 have effects crucially in particular stage during development of chicken gonads depending on sexual maturation. Mol. Reprod. Dev. 75: 184,190, 2008. © 2007 Wiley-Liss, Inc. [source] Phylogeography of the Angolan black and white colobus monkey, Colobus angolesnsis palliatus, in Kenya and TanzaniaAMERICAN JOURNAL OF PRIMATOLOGY, Issue 8 2010Monica M. McDonald Abstract Little is known about genetic variation in the 6,8 subspecies of Colobus angolensis, currently distinguished by pelage differences. We present a comparative genetic analysis of one of these subspecies, C. a. palliatus, in Kenya and Tanzania that assesses evolutionary relationships and patterns of mitochondrial genetic diversity in 103 individuals across its geographic range. Fecal samples from approximately 156 individuals were collected in four localities: (1) Diani Forest, Kenya; (2) Shimoni, Kenya; (3) Udzungwa Mountains National Park, Eastern Arc Mountains, Tanzania; and (4) Mount Rungwe, Southern Highlands, Tanzania. These samples represent at least six groups, with 5,15 samples from each. Comparative sequence analysis of a 1,795 base pair mtDNA fragment revealed 19 unique haplotypes in four populations. Phylogenetic analyses suggest that sampled Kenyan haplotypes are paraphyletic, with one Kenyan haplotype basal to all other sampled haplotypes. Analysis of molecular variance (AMOVA) suggests high levels of genetic variation among populations (,ST 0.72, P<0.001). Genetic data are concordant with a subspecies level differentiation between C. a. palliatus populations in Kenya and those in Central and southern Tanzania, as earlier suggested based on pelage differences. This study highlights the evolutionary distinctiveness of Kenyan populations of C. a. palliatus relative to Tanzanian populations. Although C. a. palliatus habitat in Tanzania is currently better protected than in Kenya, our results suggest Kenyan and Tanzanian populations should be considered distinct units, and the protection of C. a. palliatus habitat in Kenya, as well as habitat connectivity between Kenyan populations, should be prioritized for conservation and management. Am. J. Primatol. 72:715,724, 2010. © 2010 Wiley-Liss, Inc. [source] Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotesENVIRONMENTAL MICROBIOLOGY, Issue 2 2009Alexander Loy Summary Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB -encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment. [source] Multiple bacterial symbionts in two species of co-occurring gutless oligochaete worms from Mediterranean sea grass sedimentsENVIRONMENTAL MICROBIOLOGY, Issue 12 2008Caroline Ruehland Summary Gutless oligochaete worms are found worldwide in the pore waters of marine sediments and live in symbiosis with chemoautotrophic sulfur-oxidizing bacteria. In the Mediterranean, two species of gutless oligochaete worms, Olavius algarvensis and O. ilvae, co-occur in sediments around sea grass beds. These sediments have extremely low sulfide concentrations (< 1 ,M), raising the question if O. ilvae, as shown previously for O. algarvensis, also harbours sulfate-reducing symbionts that provide its sulfur-oxidizing symbionts with reduced sulfur compounds. In this study, we used fluorescence in situ hybridization (FISH) and comparative sequence analysis of genes for 16S rRNA, sulfur metabolism (aprA and dsrAB), and autotrophic carbon fixation (cbbL) to examine the microbial community of O. ilvae and re-examine the O. algarvensis symbiosis. In addition to the four previously described symbionts of O. algarvensis, in this study a fifth symbiont belonging to the Spirochaetes was found in these hosts. The symbiotic community of O. ilvae was similar to that of O. algarvensis and also included two gammaproteobacterial sulfur oxidizers and two deltaproteobacterial sulfate reducers, but not a spirochete. The phylogenetic and metabolic similarity of the symbiotic communities in these two co-occurring host species that are not closely related to each other indicates that syntrophic sulfur cycling provides a strong selective advantage to these worms in their sulfide-poor environment. [source] Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plantFEMS MICROBIOLOGY ECOLOGY, Issue 1 2009Babur S. Mirza Abstract The ability of Frankia strains to grow in the rhizosphere of a nonactinorhizal plant, Betula pendula, in surrounding bulk soil and in soil amended with leaf litter was analyzed 6 weeks after inoculation of pure cultures by in situ hybridization. Growth responses were related to taxonomic position as determined by comparative sequence analysis of nifH gene fragments and of an actinomycetes-specific insertion in Domain III of the 23S rRNA gene. Phylogenetic analyses confirmed the basic classification of Frankia strains by host infection groups, and allowed a further differentiation of Frankia clusters within the Alnus host infection group. Except for Casuarina -infective Frankia strains, all other strains of the Alnus and the Elaeagnus host infection groups displayed growth in the rhizosphere of B. pendula, and none of them grew in the surrounding bulk soil that was characterized by a very low organic matter content. Only a small number of strains that all belonged to a distinct phylogenetic cluster within the Alnus host infection group grew in soil amended with ground leaf litter from B. pendula. These results demonstrate that saprotrophic growth of frankiae is a common trait for most members of the genus, and the supporting factors for growth (i.e. carbon utilization capabilities) varied with the host infection group and the phylogenetic affiliation of the strains. [source] Phylogenetic reconstruction of Gram-positive organisms based on comparative sequence analysis of molecular chaperones from the ruminal microorganism Ruminococcus flavefaciens FD-1FEMS MICROBIOLOGY LETTERS, Issue 1 2003Dionysios A. Antonopoulos Abstract Primers designed on the basis of nucleotide sequences conserved in DnaK and GroEL from Gram-positive organisms were used to PCR amplify internal regions of the cognate genes from the anaerobic ruminal cellulolytic bacterium Ruminococcus flavefaciens FD-1. Genome walking was then utilized to elucidate the remainder of the sequences in addition to upstream and downstream regions. The full sequence of the gene encoding the GroES protein (groES) was found directly upstream from groEL. The deduced amino acid sequence of the groEL gene showed the highest homology with the amino acid sequence of the Clostridium thermocellum GroEL protein (72% amino acid identity). Similarly, translation of the groES nucleotide sequence showed highest homology to the C. thermocellum GroES protein (61% amino acid identity). Analysis of the upstream region of this chaperonin operon revealed a CIRCE regulatory element 45 bp upstream from the putative start of the groES ORF. The deduced amino acid sequence of the putative dnaK gene showed the highest homology with the amino acid sequence of the Clostridium acetobutylicum DnaK protein (68% amino acid identity). Phylogenetic analyses based on the translated sequences reiterate this relationship between R. flavefaciens and the Clostridia. However, when the nucleotide sequences of Gram-positive organisms are analyzed, a different topology occurs of the relationship between high- and low-G+C Gram-positive organisms to the 16S rRNA interpretation. [source] Advances in molecular ecology: tracking trophic links through predator,prey food-websFUNCTIONAL ECOLOGY, Issue 5 2005S. K. SHEPPARD Summary 1It is not always possible to track trophic interactions between predators and prey by direct observation. This is especially true when observing small or elusive animals with cryptic food-web ecology. Gut and/or faecal analysis can sometimes allow prey remains to be identified visually but is only possible when a component of the diet is resistant to digestion. In some cases there are no solid remains, and when there are it can lead to bias in interpretation of prey choice. 2Numerous invasive and non-invasive methods have been developed to characterize predator,prey interactions but two principal areas dominate ,molecular' research. These are reviewed under the headings of monoclonal antibodies and DNA-based techniques. 3Early ,molecular' studies of predator,prey food webs were dominated by the development of monoclonal antibodies. These methods continue to be used for mass-screening of field-collected arthropods for insect-specific proteins. 4The application of species-specific primer design, polymerase chain reaction (PCR), restriction fragment length polymorphism analysis (RFLP), DNA cloning and sequencing, comparative sequence analysis (e.g. BLAST; basic local alignment search tool), high-resolution gel electrophoresis, Temperature/denaturing gradient gel electrophoresis (TGGE/DGGE) and automated fragment analysis with fluorescent probes is reviewed. The development of molecular techniques for use in predator,prey studies is primarily limited by their cost and the development of new procedures and equipment that complement them. [source] Zebrafish cnbp intron1 plays a fundamental role in controlling spatiotemporal gene expression during embryonic developmentJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2009Andrea M.J. Weiner Abstract Cellular nucleic acid binding protein (CNBP) is a strikingly conserved zinc-finger nucleic acid chaperone required for forebrain development. Its depletion causes forebrain truncation mainly as a consequence of a reduction in size of craniofacial structures and neural crest derivatives. The CNBP expression pattern is complex and highly dynamic, but little is known of the underlying mechanisms regulating its spatiotemporal pattern. CNBP expression is highly conserved between all vertebrates characterized. In this study we have combined comparative sequence analysis and in vivo testing of DNA fragments in zebrafish to identify evolutionarily constrained regulatory motifs that likely control expression of the cnbp gene in embryos. We found a novel exon sequence located 5, upstream of the Exon1-sequence reported in most databases, and two transcription start sites that generate two primary-transcripts that differ in their 5,UTRs and expression profile during zebrafish embryonic development. Furthermore, we found a region inside the intron1 sequence that controls the cnbp developmental-specific transcriptional activation. Conserved binding sites for neural crest transcription factors were identified in this region. Mutagenesis analysis of the regulatory region revealed that Pax6/FoxD3 binding sites are required for proper zygotic cnbp expression. This is the first study that identifies, in vivo, cis -regulatory sequences inside intron sequences and typical neural crest transcription factors involved in cnbp spatiotemporal specific transcriptional control during vertebrate embryonic development. J. Cell. Biochem. 108: 1364,1375, 2009. © 2009 Wiley-Liss, Inc. [source] Characterization of the 3p12.3-pcen region associated with tumor suppression in a novel ovarian cancer cell line model genetically modified by chromosome 3 fragment transferMOLECULAR CARCINOGENESIS, Issue 12 2009Neal A.L. Cody Abstract The genetic analysis of nontumorigenic radiation hybrids generated by transfer of chromosome 3 fragments into the tumorigenic OV-90 ovarian cancer cell line identified the 3p12.3-pcen region as a candidate tumor suppressor gene (TSG) locus. In the present study, polymorphic microsatellite repeat analysis of the hybrids further defined the 3p12.3-pcen interval to a 16.1 Mb common region containing 12 known or hypothetical genes: 3ptel - ROBO2-ROBO1-GBE1-CADM2-VGLL3-CHMP2B-POU1F1-HTR1F-CGGBP1-ZNF654-C3orf38-EPHA3 -3pcen. Seven of these genes, ROBO1, GBE1, VGLL3, CHMP2B, CGGBP1, ZNF654, and C3orf38, exhibited gene expression in the hybrids, placing them as top TSG candidates for further analysis. The expression of all but one (VGLL3) of these genes was also detected in the parental OV-90 cell line. Mutations were not identified in a comparative sequence analysis of the predicted protein coding regions of these candidates in OV-90 and donor normal chromosome 3 contig. However, the nondeleterious sequence variants identified in the transcribed regions distinguished parent of origin alleles for ROBO1, VGLL3, CHMP2B, and CGGBP1 and cDNA sequencing of the hybrids revealed biallelic expression of these genes. Interestingly, underexpression of VGLL3 and ZNF654 were observed in malignant ovarian tumor samples as compared with primary cultures of normal ovarian surface epithelial cells or benign ovarian tumors, and this occurred regardless of allelic content of 3p12.3-pcen. The results taken together suggest that dysregulation of VGLL3 and/or ZNF654 expression may have affected pathways important in ovarian tumorigenesis which was offset by the transfer of chromosome 3 fragments in OV-90, a cell line hemizygous for 3p. Mol. Carcinog. © 2009 Wiley-Liss, Inc. [source] First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genomePLANT BIOTECHNOLOGY JOURNAL, Issue 6 2003Andreas M. Rickert Summary A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (, = 0.72 × 10,3) was lower when compared with diploid genotypes (, = 2.31 × 10,3). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet. [source] | ||||||||||||||||||||||