Drosophila Polymorphism Database (DPDB)A Portal for Nucleotide Polymorphism in Drosophila

As a growing number of haplotypic sequences from re-sequencing studies are now accumulating for Drosophila in the main primary sequence databases, collectively they can now be used to describe the general pattern of nucleotide variation across species and genes of this genus. The Drosophila Polymorphism Database (DPDB) is a secondary database that provides a collection of all well-annotated polymorphic sequences in Drosophila together with their associated diversity measures and options for re-analysis of the data that greatly facilitate both multi-locus and multi-species diversity studies in one of the most important group of model organisms. Here we describe the state-of-the-art of the DPDB database and provide a step-by-step guide to all its searching and analytic capabilities. Finally, we illustrate its usefulness through selected examples. DPDB is freely available at http://dpdb.uab.cat.     

Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach

Single nucleotide polymorphisms (SNPs) have rarely been exploited in nonhuman and nonmodel organism genetic studies. This is due partly to difficulties in finding SNPs in species where little DNA sequence data exist, as well as to a lack of robust and inexpensive genotyping methods. We have explored one SNP discovery method for molecular ecology, evolution, and conservation studies to evaluate the method and its limitations for population genetics in mammals. We made use of 'CATS' (or 'EPIC') primers to screen for novel SNPs in mammals. Most of these primer sets were designed from primates and/or rodents, for amplifying intron regions from conserved genes. We have screened 202 loci in 16 representatives of the major mammalian clades. Polymerase chain reaction (PCR) success correlated with phylogenetic distance from the human and mouse sequences used to design most primers; for example, specific PCR products from primates and the mouse amplified the most consistently and the marsupial and armadillo amplifications were least successful. Approximately 24% (opossum) to 65% (chimpanzee) of primers produced usable PCR product(s) in the mammals tested. Products produced generally high but variable levels of readable sequence and similarity to the expected genes. In a preliminary screen of chimpanzee DNA, 12 SNPs were identified from six (of 11) sequenced regions, yielding a SNP on average every 400 base pairs (bp). Given the progress in genome sequencing, and the large numbers of CATS-like primers published to date, this approach may yield sufficient SNPs per species for population and conservation genetic studies in nonmodel mammals and other organisms.     

A graphene-based platform for single nucleotide polymorphism (SNP) genotyping

A facile, rapid, stable and sensitive approach for fluorescent detection of single nucleotide polymorphism (SNP) is designed based on DNA ligase reaction and π-stacking between the graphene and the nucleotide bases. In the presence of perfectly matched DNA, DNA ligase can catalyze the linkage of fluorescein amidite-labeled single-stranded DNA (ssDNA) and a phosphorylated ssDNA, and thus the formation of a stable duplex in high yield. However, the catalytic reaction cannot effectively carry out with one-base mismatched DNA target. In this case, we add graphene to the system in order to produce different quenching signals due to its different adsorption affinity for ssDNA and double-stranded DNA. Taking advantage of the unique surface property of graphene and the high discriminability of DNA ligase, the proposed protocol exhibits good performance in SNP genotyping. The results indicate that it is possible to accurately determine SNP with frequency as low as 2.6% within 40 min. Furthermore, the presented flexible strategy facilitates the development of other biosensing applications in the future.     

dbSNP: a database of single nucleotide polymorphisms

In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Cancer for Biotechnology Information (NCBI) has established the dbSNP database. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. Submitted SNPs can also be downloaded via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/     

Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S)

The advent of complete-genome genotyping across phenotype cohorts has provided a rich source of information for bioinformaticians. However the search for SNPs from this data is generally performed on a study-by-study case without any specific hypothesis of the location for SNPs that are predictive for the phenotype. We have designed a method whereby very large SNP lists (several gigabytes in size), combining several genotyping studies at once, can be sorted and traced back to their ultimate consequence in protein structure. Given a working hypothesis, researchers are able to easily search whole genome genotyping data for SNPs that link genetic locations to phenotypes. This allows a targeted search for correlations between phenotypes and potentially relevant systems, rather than utilizing statistical methods only. HyDn-SNP-S returns results that are less data dense, allowing more thorough analysis, including haplotype analysis. We have applied our method to correlate DNA polymerases to cancer phenotypes using four of the available cancer databases in dbGaP. Logistic regression and derived haplotype analysis indicates that ～80 SNPs, previously overlooked, are statistically significant. Derived haplotypes from this work link POLL to breast cancer and POLG to prostate cancer with an increase in incidence of 3.01- and 9.6-fold, respectively. Molecular dynamics simulations on wild-type and one of the SNP mutants from the haplotype of POLL provide insights at the atomic level on the functional impact of this cancer related SNP. Furthermore, HyDn-SNP-S has been designed to allow application to any system. The program is available upon request from the authors.     

MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms

MonkeySNP is a web-based resource created by the Genetic Resource and Informatics Program at the Oregon National Primate Research Center to facilitate access to non-human primate (NHP) single nucleotide polymorphisms (SNP) data. MonkeySNP is a mirror of the NCBI dbSNP database and contains additional NHP subpopulation genotype data and visual genotype displays to support SNP review and selection. AVAILABILITY: http://monkeysnp.ohsu.edu/snp/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Characterization of single nucleotide polymorphism markers for eelgrass (Zostera marina)

We characterized 37 single nucleotide polymorphism (SNP) makers for eelgrass Zostera marina. SNP markers were developed using existing EST (expressed sequence tag)-libraries to locate polymorphic loci and develop primers from the functional expressed genes that are deposited in The ZOSTERA database (V1.2.1). SNP loci were genotyped using a single-base-extension approach which facilitated high-throughput genotyping with minimal optimization time. These markers show a wide range of variability among 25 eelgrass populations and will be useful for population genetic studies including evaluation of population structure, historical demography, and phylogeography. Potential applications include haplotype inference of physically linked SNPs and identification of genes under selection for temperature and desiccation stress.     

Single nucleotide polymorphism (SNP) discovery in porcine expressed genes

High-throughput genotyping of swine populations is a potentially efficient method for establishing animal lineage and identification of loci important to animal health and efficient pork production. Markers were developed based upon single nucleotide polymorphisms (SNPs), which are abundant and amenable to automated genotyping platforms. The focus of this research was SNP discovery in expressed porcine genes providing markers to develop the porcine/human comparative map. Locus specific amplification (LSA) and comparative sequencing were used to generate PCR products and allelic information from parents of a swine reference family. Discovery of 1650 SNPs in 403 amplicons and strategies for optimizing LSA-based SNP discovery using alternative methods of PCR primer design, data analysis, and germplasm selection that are applicable to other populations and species are described. These data were the first large-scale assessment of frequency and distribution of porcine SNPs.     

A database for the analysis of immunity genes in Drosophila: PADMA database

While microarray experiments generate voluminous data, discerning trends that support an existing or alternative paradigm is challenging. To synergize hypothesis building and testing, we designed the Pathogen Associated Drosophila MicroArray (PADMA) database for easy retrieval and comparison of microarray results from immunity-related experiments (www.padmadatabase.org). PADMA also allows biologists to upload their microarray-results and compare it with datasets housed within PADMA. We tested PADMA using a preliminary dataset from Ganaspis xanthopoda-infected fly larvae, and uncovered unexpected trends in gene expression, reshaping our hypothesis. Thus, the PADMA database will be a useful resource to fly researchers to evaluate, revise, and refine hypotheses.     

Characterization of 15 single nucleotide polymorphism markers for chimpanzees (Pan troglodytes)

We report the characterization of 15 new single nucleotide polymorphism markers for a threatened species, the chimpanzee (Pan troglodytes), developed using a targeted gene approach. These markers are derived from the Y chromosome and autosomal regions of the genome and show frequency differences between chimpanzee subspecies from central and western Africa. These single nucleotide polymorphism markers are the first to be designed for the genotyping of wild chimpanzee populations and will provide a useful addition to the genetic tools employed for the conservation management of this threatened species.     

Overcompensation as a mechanism for maintaining polymorphism: egg-to-adult viability in Drosophila

Frequency-dependent selection may be accounted for, in ecological terms, by the differential effectiveness of alternative genotypes in exploiting limiting environmental resources. Differentiation in resource exploitation among genotypes implies in turn that a mix of genotypes may exploit more fully the resources than a genetically uniform population, a phenomenon called overcompensation Experiments designed to test for overcompensation whow that highly polymorphic populations can support larger numbers of individuals per food unit than less polymorphic populations. This difference cannot be attributed to the level of individual heterozygosity, which is the same in both types of populations.     

FlyBase: a Drosophila database. Flybase Consortium.

FlyBase (http://flybase.bio.indiana.edu/) is a comprehensive database of genetic and molecular data concerning Drosophila . FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (with phenotypes), aberrations, transposons, pointers to sequence data, gene products, maps, clones, stock lists, Drosophila workers and bibliographic references.     

PIP: a database of potential intron polymorphism markers

MOTIVATION: With the recent progress made in large-scale plant functional genome sequencing projects, a great amount of EST (express sequence tag) data is becoming available. With the help of complete genomic sequence information of model plants (rice and Arabidopsis), it is possible to predict the joints between adjacent exons after splicing (or termed 'intron positions' for short) in homologous ESTs of other plants. This would allow developing potential intron polymorphism (PIP) markers in these plants by designing primers in exons flanking the target intron. RESULTS: We have extracted a total of 57,658 PIP markers in 59 plant species and created a web-based database platform named PIP to provide detailed information of these PIP markers and homologous relationships among PIP markers from different species. The platform also provides a function of online designing of PIP markers based on cDNA/EST sequences submitted by users. With evaluations performed in silico, we have found that the intron position prediction is highly reliable and the polymorphism level of PIP markers is high enough for practical need. AVAILABILITY: http://ibi.zju.edu.cn/pgl/pip/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Highly selective single nucleotide polymorphism recognition by a chiral (5S) PNA beacon

A chiral peptide nucleic acid (PNA) beacon containing a C-5 modified monomer based on L-lysine was synthesized. The terminal amino group of the lysine side chain was linked to a spacer for future applications on surfaces. The PNA beacon bears a carboxyfluorescein fluorophore and a dabcyl quencher at opposite ends. The DNA binding properties were compared with those of a homologous PNA beacon containing only achiral monomers. Both beacons underwent a fluorescence increase in the presence of complementary DNA, with higher efficiency and higher selectivity (evaluated using single mismatched DNA sequences) observed for the chiral monomer containing PNA. Ion exchange (IE) HPLC with fluorimetric detection was used in combination with the beacon for the selective detection of complementary DNA. A fluorescent peak corresponding to the PNA beacon:DNA duplex was observed at a very low detection limit (1 nM). The discriminating capacity of the chiral PNA beacon for a single mismatch was found to be superior to those observed with the unmodified one, thus confirming the potency of chirality for increasing the affinity and specificity of DNA recognition.     

Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai)

The development of single nucleotide polymorphism (SNP) markers in Japanese pear (Pyrus pyrifolia Nakai) offers the opportunity to use DNA markers for marker-assisted selection in breeding programs because of their high abundance, codominant inheritance, and potential for automated high-throughput analysis. We developed a 1,536-SNP bead array without a reference genome sequence from more than 44,000 base changes on the basis of a large-scale expressed sequence tag (EST) analysis combined with 454 genome sequencing data of Japanese pear ‘Housui’. Among the 1,536 SNPs on the array, 756 SNPs were genotyped, and 609 SNP loci were mapped to linkage groups on a genetic linkage map of ‘Housui’, based on progeny of an interspecific cross between European pear (Pyrus communis L.) ‘Bartlett’ and ‘Housui’. The newly constructed genetic linkage map consists of 951 loci, comprising 609 new SNPs, 110 pear genomic simple sequence repeats (SSRs), 25 pear EST–SSRs, 127 apple SSRs, 61 pear SNPs identified by the “potential intron polymorphism” method, and 19 other loci. The map covers 22 linkage groups spanning 1341.9 cM with an average distance of 1.41 cM between markers and is anchored to reference genetic linkage maps of European pears and apples. A total of 514 contigs containing mapped SNP loci showed significant similarity to known proteins by functional annotation analysis.