Unique Loci Research Articles

DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases.

BackgroundChronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is associated with chronic low-grade inflammation may reveal novel pathways or therapeutic targets for inflammation.ResultsWe performed a meta-analysis of epigenome-wide association studies (EWAS) of serum C-reactive protein (CRP), which is a sensitive marker of low-grade inflammation, in a large European population (n = 8863) and trans-ethnic replication in African Americans (n = 4111). We found differential methylation at 218 CpG sites to be associated with CRP (P < 1.15 × 10–7) in the discovery panel of European ancestry and replicated (P < 2.29 × 10–4) 58 CpG sites (45 unique loci) among African Americans. To further characterize the molecular and clinical relevance of the findings, we examined the association with gene expression, genetic sequence variants, and clinical outcomes. DNA methylation at nine (16%) CpG sites was associated with whole blood gene expression in cis (P < 8.47 × 10–5), ten (17%) CpG sites were associated with a nearby genetic variant (P < 2.50 × 10–3), and 51 (88%) were also associated with at least one related cardiometabolic entity (P < 9.58 × 10–5). An additive weighted score of replicated CpG sites accounted for up to 6% inter-individual variation (R2) of age-adjusted and sex-adjusted CRP, independent of known CRP-related genetic variants.ConclusionWe have completed an EWAS of chronic low-grade inflammation and identified many novel genetic loci underlying inflammation that may serve as targets for the development of novel therapeutic interventions for inflammation.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1119-5) contains supplementary material, which is available to authorized users.

Patient-Specific Bacteroides Genome Variants in Pouchitis.

ABSTRACTA 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

SummaryCharacterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.

Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life.

BackgroundDespite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level resolution, classification, and testing of important macroevolutionary hypotheses. Recently, alternative targeted sequence capture techniques have provided molecular systematics a powerful tool for resolving relationships across the Tree of Life. One of these approaches, Anchored Hybrid Enrichment (AHE), is designed to recover hundreds of unique orthologous loci from across the genome, for resolving both shallow and deep-scale evolutionary relationships within non-model systems. Herein we present a modification of the AHE approach that expands its use for application in spiders, with a particular emphasis on the infraorder Mygalomorphae.ResultsOur aim was to design a set of probes that effectively capture loci informative at a diversity of phylogenetic timescales. Following identification of putative arthropod-wide loci, we utilized homologous transcriptome sequences from 17 species across all spiders to identify exon boundaries. Conserved regions with variable flanking regions were then sought across the tick genome, three published araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa. Following development of the 585 target loci in the Spider Probe Kit, we applied AHE across three taxonomic depths to evaluate performance: deep-level spider family relationships (33 taxa, 327 loci); family and generic relationships within the mygalomorph family Euctenizidae (25 taxa, 403 loci); and species relationships in the North American tarantula genus Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were supported with high bootstrap support. Strong support was also found throughout the Euctenizidae, including generic relationships within the family and species relationships within the genus Aptostichus. As in the Euctenizidae, virtually identical topologies were inferred with high support throughout Aphonopelma.ConclusionsThe Spider Probe Kit, the first implementation of AHE methodology in Class Arachnida, holds great promise for gathering the types and quantities of molecular data needed to accelerate an understanding of the spider Tree of Life by providing a mechanism whereby different researchers can confidently and effectively use the same loci for independent projects, yet allowing synthesis of data across independent research groups.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0769-y) contains supplementary material, which is available to authorized users.

Genetic Networks in Mouse Retinal Ganglion Cells.

Retinal ganglion cells (RGCs) are the output neuron of the eye, transmitting visual information from the retina through the optic nerve to the brain. The importance of RGCs for vision is demonstrated in blinding diseases where RGCs are lost, such as in glaucoma or after optic nerve injury. In the present study, we hypothesize that normal RGC function is transcriptionally regulated. To test our hypothesis, we examine large retinal expression microarray datasets from recombinant inbred mouse strains in GeneNetwork and define transcriptional networks of RGCs and their subtypes. Two major and functionally distinct transcriptional networks centering around Thy1 and Tubb3 (Class III beta-tubulin) were identified. Each network is independently regulated and modulated by unique genomic loci. Meta-analysis of publically available data confirms that RGC subtypes are differentially susceptible to death, with alpha-RGCs and intrinsically photosensitive RGCs (ipRGCs) being less sensitive to cell death than other RGC subtypes in a mouse model of glaucoma.

Assessment of genetic diversity using DNA markers among Brassica rapa var. yellow sarson germplasm lines collected from Eastern Uttar Pradesh and Uttarakhand hills

The genetic diversity and the relatedness among thirty-one germplasm lines of yellow sarson collected from eastern UP were evaluated using morphological characters and Random Amplified Polymorphic DNA (RAPD) markers. Molecular parameters, viz. A total number of bands, average polymorphic band, average percent polymorphism, average polymorphic information content (PIC), Jaccard’s similarity coefficient, Principal Coordinate Analysis (PCA) and dendrogram generated using RAPD markers. A total of 148 different polymorphic amplification products were obtained using 10 selected decamer primers. The Jaccard similarity coefficient ranged from 0.557-0.899. Maximum polymorphism detected was 100 %.The range of amplification was from 190bp to 9 kb. Some unique bands were also reported with different primers that can be used for the identification of particular accession. PYSC-11-11 and PYSC-11-36 genotypes showed a maximum number of unique loci of different size. 31 germplasm lines grouped into two major clusters I and II based on RAPD profiling. Morphological characterization was done on the basis of leaf, petal and beak characteristics. The similarity value among the germplasm lines ranged from 0.222 to 1.000 using morphological descriptors. The dendrogram generated grouped the germplasm accession into two major groups at 44% similarity value. The cluster analysis was comparable up to some extent with Principal Coordinate Analysis (PCA) of two and three-dimensional plots. The variability revealed by morphological and molecular profile were found to be non-comparable. This study indicated the presence of high genetic diversity among collected yellow sarson germplasm, which could be used for developing for breeding and germplasm management purposes.

Genetic Association Studies in Uterine Fibroids: Risk Alleles Presage the Path to Personalized Therapies.

Uterine leiomyoma (UL) is the most common tumor of the female reproductive system. Epidemiological analyses, including familial aggregation, twin studies, and racial discrepancies in disease prevalence and morbidity, indicated genetic factors influence risk for developing UL. Genome-wide association studies (GWASs) are a powerful method for identifying genetic variants that are associated with elevated risk for a common, complex disease. To date, three genome-wide scans for UL have been performed: a GWAS in Japanese women, a genome-wide linkage and association study in women of European decent, and an admixture-based analysis in African American women. Results from each of the three genome-wide scans performed have had varying success in identifying unique loci associated with predisposition to developing UL. Here, we address the evidence for a genetic basis for UL risk, discuss genetic association studies and their results, and identify challenges and future directions for UL GWAS analyses.

Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.

Two bottlenecks impeding the genetic analysis of complex traits in rodents are access to mapping populations able to deliver gene-level mapping resolution, and the need for population specific genotyping arrays and haplotype reference panels. Here we combine low coverage sequencing (0.15X) with a novel method to impute the ancestral haplotype space in 1,887 commercially available outbred mice. We mapped 156 unique quantitative trait loci for 92 phenotypes at 5% false discovery rate. Gene-level mapping resolution was achieved at about a fifth of loci, implicating Unc13c and Pgc1-alpha at loci for the quality of sleep, Adarb2 for home cage activity, Rtkn2 for intensity of reaction to startle, Bmp2 for wound healing, Il15 and Id2 for several T-cell measures and Prkca for bone mineral content. These findings have implications for diverse areas of mammalian biology and demonstrate how GWAS can be extended via low-coverage sequencing to species with highly recombinant outbred populations.

Use of Random Amplified Polymorphic DNA (RAPD) Technique to Study the Genetic Diversity of Eight Aloe Species.

The genus Aloe comprises over 400 species of flowering succulent plants. Aloe leaves are used in the treatment of asthma, gastrointestinal ulcers, cardiovascular disease, tumors, burns, and diabetes. They are rich in anthraquinones, such as aloin, aloe-emodin, chrysophanol, aloinoside A, and aloinoside B. The various species of Aloe show chemical and morphological similarity and diversity, which depend on the genotype and environmental conditions. In a continuity to our interest in the genus Aloe, this study targets the authentication of eight different Aloe species, Aloe vera (A1), Aloe arborescens (A2), Aloe eru (A3), Aloe grandidentata (A4), Aloe perfoliata (A5), Aloe brevifolia (A6), Aloe saponaria (A7), and Aloe ferox (A8), grown in Egypt by using the technique of random amplified polymorphic DNA. Twelve decamer primers were screened in amplification with genomic DNA extracted from all species, of which five primers yielded species-specific reproducible bands. Out of 156 loci detected, the polymorphic, monomorphic, and unique loci were 107, 26, and 23, respectively. Based on a dendrogram and similarity matrix, the eight Aloe species were differentiated from each other and showed more divergence. Aloe species prevailed similarity coefficients of 54-70 % by which they could be classified into three major groups. Thus, this technique may contribute to the identification of these Aloe species that have great morphological similarity in the Egyptian local markets.

Genome-Wide SNP Discovery, Genotyping and Their Preliminary Applications for Population Genetic Inference in Spotted Sea Bass (Lateolabrax maculatus).

Next-generation sequencing and the collection of genome-wide single-nucleotide polymorphisms (SNPs) allow identifying fine-scale population genetic structure and genomic regions under selection. The spotted sea bass (Lateolabrax maculatus) is a non-model species of ecological and commercial importance and widely distributed in northwestern Pacific. A total of 22 648 SNPs was discovered across the genome of L. maculatus by paired-end sequencing of restriction-site associated DNA (RAD-PE) for 30 individuals from two populations. The nucleotide diversity (π) for each population was 0.0028±0.0001 in Dandong and 0.0018±0.0001 in Beihai, respectively. Shallow but significant genetic differentiation was detected between the two populations analyzed by using both the whole data set (FST = 0.0550, P < 0.001) and the putatively neutral SNPs (FST = 0.0347, P < 0.001). However, the two populations were highly differentiated based on the putatively adaptive SNPs (FST = 0.6929, P < 0.001). Moreover, a total of 356 SNPs representing 298 unique loci were detected as outliers putatively under divergent selection by FST-based outlier tests as implemented in BAYESCAN and LOSITAN. Functional annotation of the contigs containing putatively adaptive SNPs yielded hits for 22 of 55 (40%) significant BLASTX matches. Candidate genes for local selection constituted a wide array of functions, including binding, catalytic and metabolic activities, etc. The analyses with the SNPs developed in the present study highlighted the importance of genome-wide genetic variation for inference of population structure and local adaptation in L. maculatus.

Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci

The genus Bradyrhizobium contains predominantly nitrogen-fixing legume symbionts. Phylogenetic analysis of the genes responsible for their symbiotic abilities (i.e., those encoded on the nodulation [nod] and nitrogen-fixation [nif] loci) has facilitated the development of an extensive phylogeographic framework for the genus. This framework however contains only a few nodulating isolates from Africa. Here we focused on nodulating Bradyrhizobium isolates associated with native southern African legumes in the tribes Genisteae and Crotalarieae found along the Great Escarpment in the Mpumalanga Province of South Africa. The aims of this study were to: (1) obtain rhizobial isolates from legumes in the Genisteae and Crotalarieae; (2) verify their nodulation ability; (3) characterize them to species level based on phylogenetic analyses of several protein coding gene regions (atpD, dnaK, glnII, recA, rpoB and gyrB) and (4) determine their placement in the phylogeographic framework inferred from the sequences of the symbiotic loci nodA and nifD. Twenty of the 21 Bradyrhizobium isolates belonged to six novel species, while one was conspecific with the recently described B. arachidis. Among these isolates, the nodA phylogeny revealed several new clades, with 18 of our isolates found in Clades XIV and XV, and only three forming part of the cosmopolitan Clade III. These strains formed predominantly the same groups in the nifD phylogeny although with slight differences; indicating that both vertical and horizontal inheritance of the symbiotic loci occurred. These findings suggest that the largely unexplored diversity of indigenous African rhizobia are characterized by unique ancestries that might mirror the distribution of their hosts and the environmental factors driving their evolution.

Discovery of unfixed endogenous retrovirus insertions in diverse human populations

Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome. The majority of these elements lack function due to accumulated mutations or internal recombination resulting in a solitary (solo) LTR, although members of one group of human ERVs (HERVs), HERV-K, were recently active with members that remain nearly intact, a subset of which is present as insertionally polymorphic loci that include approximately full-length (2-LTR) and solo-LTR alleles in addition to the unoccupied site. Several 2-LTR insertions have intact reading frames in some or all genes that are expressed as functional proteins. These properties reflect the activity of HERV-K and suggest the existence of additional unique loci within humans. We sought to determine the extent to which other polymorphic insertions are present in humans, using sequenced genomes from the 1000 Genomes Project and a subset of the Human Genome Diversity Project panel. We report analysis of a total of 36 nonreference polymorphic HERV-K proviruses, including 19 newly reported loci, with insertion frequencies ranging from <0.0005 to >0.75 that varied by population. Targeted screening of individual loci identified three new unfixed 2-LTR proviruses within our set, including an intact provirus present at Xq21.33 in some individuals, with the potential for retained infectivity.

Genetic dissection of plant architecture and yield-related traits in Brassica napus.

An optimized plant architecture (PA) is fundamental for high-yield breeding but the genetic control of the important trait is largely unknown in rapeseed. Here plant architecture factors (PAFs) were proposed to consist of main inflorescence length proportion (MILP), branch height proportion (BHP), and branch segment proportion (BSP). Comparison of different genotypes in a DH population grown in diverse environments showed that an optimized PAF performance with MILP and BHP between 0.3–0.4 was important for high yield potential. In total, 163 unique quantitative trait loci (QTLs) for PA- and plant yield (PY)-related traits were mapped onto a high-density genetic map. Furthermore, 190 PA-related candidate genes for 91 unique PA QTLs and 2350 PY epistatic interaction loci-pairs were identified, which explain 2.8–51.8% and 5.2–23.6% of phenotypic variation, respectively. Three gene categories, transcription factor, auxin/IAA, and gibberellin, comprise the largest proportions of candidate genes for PA-related QTLs. The effectiveness of QTL candidate genes prediction was demonstrated by cloning of three candidate genes, Bna.A02.CLV2, Bna.A09.SLY2, and Bna.C07.AHK4. The study thus outlines a gene network for control of PA-related traits and provides novel information for understanding the establishment of ideal PA and for developing effective breeding strategies for yield improvement in rapeseed and other crops.

Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and unique plasmid-encoded locus.

Anal�za polymorfizmu miRNA vo vybran�ch v�vojov�ch �t�di�ch lanu siateho

MicroRNAs represent small non-coding RNAs that play important role in regulating gene expression under various biotic and abiotic stresses as well as in different developmental stages of plants. They are involved in wide variety of biological and metabolic pathways of plants. The research was focused on the potential of selected miRNA-based molecular markers (miR156 and miR168) to map the polymorphism level of flax genome in the selected developmental stages (flower bud - flowering – boll development) as a reflection of the activity of specific miRNAs in these flax organs and tissues. The miRNA polymorphism was evaluated on 8 flax genotypes by miRNA-based molecular marker assays and data were supported by the morphology measurements on buds, flowers, petals and developing bolls. Extent of PCR amplification of miRNA fragments ranged from 40 bp to 200 bp (miR168a-F/miR-R primer pair) or 35 bp to 120 bp (miR156b-F/miR-R primer pair), respectively. MiRNAbased primers amplified in total 196, respectively 158 miRNA loci. Based on the results can be concluded that the representation of miR168 loci have increased according to developmental stages ascending (stage of bud, flower and boll). In overall miRNA156b loci profile in all three analyzed developmental stages is possible to observe the increase of miRNA loci amplification almost in all genotypes. Taking into account the genetic background of genotypes, based on the peak analysis profile of amplified miRNA loci, implemented by GeneTools software, was possible to identified unique loci in linseed and intermediate genotypes in individual developmental stages. Have been found out that only the genotype Bolley Golden differ from other genotypes in both analysis (molecular and morphological) if the variability of miR168 loci number in the flower bud growing stage was compared to the variability in trait petals colour in bud.

Genetic distances of three venerid species identified by PCR analysis

The seven selected primers BION-13, BION-29, BION-61, BION-64, BION-68, BION-72 and BION-80 generated the total number of loci, average number of loci per lane and specific loci in Meretrix lusoria (ML), Saxidomus purpuratus (SP) and Cyclina sinensis (CS) species. Here, the complexity of the banding patterns varied dramatically between the primers from the three venerid clam species. The higher fragment sizes (> 1,000 bp) are much more observed in the SP species. The primer BION-68 generated 21 unique loci to each species, which were ascertaining each species, approximately 150 bp, 300 bp and 450 bp, in the ML species. Remarkably, the primer BION-80 detected 7 shared loci by the three clam species, major and/or minor fragments of sizes 500 bp, which were matching in all samples. As regards average bandsharing value (BS) results, individuals from CS clam species (0.754) exhibited higher bandsharing values than did individuals from SP clam species (0.607) (P < 0.05). In this study, the dendrogram obtained by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (LUSORIA01-LUSORIA07), cluster 2 (PURPURATUS08-PURPURATUS14), cluster 3 (SINENSIS15- SINENSIS21). Among the twenty one venerid clams, the shortest genetic distance that displayed significant molecular differences was between individuals 18 and 20 from the CS species (genetic distance = 0.071), while the longest genetic distance among the twenty-one individuals that displayed significant molecular differences was between individuals LUSORIA no. 02 and PURPURATUS no. 09 (genetic distance = 0.778). Relatively, individuals of SP venerid species were appropriately closely related to that of CS species, as shown in the hierarchical dendrogram of genetic distances. Eventually, PCR fragments exposed in the present study may be worthwhile as a DNA marker the three venerid clam species to discriminate.

Geographical Variations and Genetic Distances of Three Saxidomus purpuratus Populations ascertained by PCR Analysis.

Genomic DNA samples isolated from geographical purplish Washington clam (Saxidomus purpuratus) were obtained from three different regions in the Korean Peninsula: Geoje (Geoje population; GJP), Gunsan (Gunsan population; GSP) and a site of North Korea (North Korea population; NKP). The seven primers generated the total 369 loci that can be scored from the GSP clam population. 356 fragments were generated from the NKP clam population. The complexity of the banding patterns varies dramatically between the primers and three localities. In this study, 319 loci were identified in the purplish Washington clam from Geoje and 369 in the clam population from Gunsan: 221 specific loci (69.3%) in the GJP clam population and 300 (81.3%) in the GSP population. These results demonstrate that the primer detected a large quantity of specific fragments, suggesting that the genetic variation in the GSP is higher than in the GJP population. In particular, the BION-28 primer gave DNA profiles with more fragments than the other six primers in the NKP population. The oligonucleotides primer BION-75 produced 21 unique loci to each population, which were ascertaining each population, approximately 250 bp, 300 bp and 400 bp, in the GJP population. Outstandingly, the primer BION-50 detected 21 shared loci by the three populations, major and/or minor fragments of sizes 150 bp, which were matching in all samples. With regard to average bandsharing value (BS) results, individuals from GJP population (0.743) displayed higher bandsharing values than did individuals from GSP population (0.606). In the present study, the dendrogram gained by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (GEOJE 01 ~ GEOJE 07), cluster 2 (GUNSAN 08 ~ GUNSAN 14), cluster 3 (N.KOREA 15 ~ N.KOREA 21). Among the twenty one clams, the shortest genetic distance that revealed significant molecular differences was between individuals 08 and 09 from the NKP population (genetic distance = 0.073), while the longest genetic distance among the twenty-one individuals that demonstrated significant molecular differences was between individuals GEOJE no. 03 and GUNSAN no. 09 (genetic distance = 0.669). Comparatively, individuals of GJP population were properly closely related to that of NKP population, as revealed in the hierarchical dendrogram of genetic distances. In due course, PCR analysis has revealed the significant genetic distance among three purplish Washington clam populations. PCR fragments discovered in this study could be valuable as a DNA marker of the three geographical clam populations to distinguish.

Genetic import and phenotype specific alleles associated with hyper-invasion in Campylobacter jejuni.

BackgroundCampylobacter jejuni is a major zoonotic pathogen, causing gastroenteritis in humans. Invasion is an important pathogenesis trait by which C. jejuni causes disease. Here we report the genomic analysis of 134 strains to identify traits unique to hyperinvasive isolates.MethodsA total of 134 C. jejuni genomes were used to create a phylogenetic tree to position the hyperinvasive strains. Comparative genomics lead to the identification of mosaic capsule regions. A pan genome approach led to the discovery of unique loci, or loci with unique alleles, to the hyperinvasive strains.ResultsPhylogenetic analysis showed that the hyper-invasive phenotype is a generalist trait. Despite the fact that hyperinvasive strains are only distantly related based on the whole genome phylogeny, they all possess genes within the capsule region with high identity to capsule genes from C. jejuni subsp. doylei and C. lari. In addition there were genes unique to the hyper-invasive strains with identity to non-C. jejuni genes, as well as allelic variants of mainly pathogenesis related genes already known in the other C. jejuni. In particular, the sequence of flagella genes, flgD-E and flgL were highly conserved amongst the hyper-invasive strains and divergent from sequences in other C. jejuni. A novel cytolethal distending toxin (cdt) operon was also identified as present in all hyper-invasive strains in addition to the classic cdt operon present in other C. jejuni.ConclusionsOverall, the hyper-invasive phenotype is strongly linked to the presence of orthologous genes from other Campylobacter species in their genomes, notably within the capsule region, in addition to the observed association with unique allelic variants in flagellar genes and the secondary cdt operon which is unlikely under random sharing of accessory alleles in separate lineages.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2087-y) contains supplementary material, which is available to authorized users.

Unique hue data and CIECAM02: A comment on Xiao et al

AbstractThis letter to the editor notes the offsets from the origin of unique hue loci in the recent article, Unique Hue Data for Colour Appearance Models. Part III: Comparison with NCS Unique Hues by Xiao et al. [Color Res Appl 2015;40:256–263] and suggests that modifications to the cone response function in CIECAM02 be explored. © 2015 Wiley Periodicals, Inc. Col Res Appl, 2015

Development of genomewide simple sequence repeat fingerprints and highly polymorphic markers in cucumbers based on next‐generation sequence data

AbstractCucumbers are one of the most important vegetable crops worldwide. The molecular markers have substantial potential to improve the efficiency of conventional cucumber breeding. In this study, a total of 101 157 simple sequence repeats (SSRs) were identified across the cucumber 9930 genome. Most (69 526 of 76 103 or 91.36%) SSRs with unique flanking sequences (unique SSRs) had polymorphisms among 103 cucumber genomes; the number of alleles ranged from 2 to 34 with an average of 4.70. Next, we selected 7486 unique SSR loci with polymorphism information content (PIC) ≥0.5 and major allele differences (the size difference between the alleles with the highest and the second highest frequency) ≥3 bp to design primers. The SSR marker polymorphisms were experimentally validated; 50 highly polymorphic SSR markers had polymorphisms with an average PIC of 0.44. PCR analysis also indicated that these SSR markers could be effectively used as molecular markers. The SSR fingerprints and polymorphic SSR markers with large major allele differences could enhance the efficiency of genetic research and marker‐assisted breeding in cucumbers.