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Highlights • SSRs were used to identify fathers of tea individuals with valuable traits. • Paternity analyses showed that 8 individuals were derived from 'Ziyan' selfing. • The self-compatible 'Ziyan' is valuable for genetic studies and breeding in tea. Abstract Most tea plants (Camellia sinensis) are self-incompatible. Self-incompatibility is critical for preventing inbreeding depression and maintaining genetic diversity, but it can hinder breeding and genetic studies. Originally, the propose of this study was to identify fathers of 16 elite F 1 individuals derived from open-pollinated seeds of an anthocyanin-rich tea cultivar 'Ziyan'. In order to achieve this, 41 candidate parents and 16 F 1 individuals were genotyped with 15 polymorphic SSR markers. Using exclusion and likelihood methods, fathers of 12 individuals were identified at 95% level of confidence. Surprisingly, the results showed that eight individuals were from self-crossing of 'Ziyan'. Additional 36 SSR markers were used to further confirm selfing and the results were consistent, demonstrating that 'Ziyan' is self-compatible. As expected, the degrees of heterozygosity of the eight selfing individuals were significantly lower than 'Ziyan' and other tea accessions. This is the first report of a clonal cultivar of C. sinensis being self-compatible under open-pollination conditions and verified using DNA-based markers. Therefore, 'Ziyan' and its selfing offspring will be valuable materials for both genetic studies and breeding in C. sinensis. [ABSTRACT FROM AUTHOR]

Highlights • Simple protocol of Large-scale propagation of Prunus cerasifera was described. • Vigor vitroplants were produced, using Temporary Immersion Bioreactors. • The Temporary Immersion System improved the multiplication and rooting rates. • High percentage of genetic homogeneity of vitroplants was proved by ISSR analysis. Abstract An efficient protocol for the micropropagation of Prunus cerasifera using temporary immersion bioreactors was described. One-node cuttings excised from field-grown plants were successfully disinfected using 12% sodium hypochlorite for 10 min. Immersion duration, frequency and medium composition in Bioreactors type RITA® were evaluated. A high multiplication rate was obtained using RITA® bioreactors containing Murashige and Skoog's medium (MS) supplemented with 1 mg L−1 N6-benzyladenine (BAP) and 1 mg L−1 indole-3-butyric acid (IBA) with 20 min/12 h as immersion time. RITA®-derived shoots were found to be more vigorous than those regenerated using the standard procedure. Higher levels of photosynthetic pigments were observed in shoots cultured in bioreactors, during the proliferation and rooting stages, which proved a certain degree of photoautotrophy of RITA®-derived vitroplants. A high proportion of shoots was successfully rooted in an MS liquid medium supplemented with 1 g L−1 activated charcoal in RITA® bioreactors. During plant acclimatization, survival rates exceeding 80% were recorded. The genetic fidelity of micropropagated plants was investigated using inter simple sequence repeat (ISSR) markers. Results proved the generation of homogenous amplification profiles and thus supported the clonal fidelity of regenerated vitroplants. [ABSTRACT FROM AUTHOR]

Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby ( cis ) or physically separated from ( trans ) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis - and trans -modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients. [ABSTRACT FROM AUTHOR]

Among the many candidate genes analyzed in eating disorder (ED) patients, those involved in dopaminergic functions may be of special relevance, as dopamine is known to play a significant role in feeding behavior, the distortion of body image, hyperactivity and reward and reinforcement processes. We aimed to determine the effect of functional polymorphisms and haplotypes in the Dopamine Receptor D4 ( DRD4 ) gene on general psychopathological symptoms in ED patients. Two-hundred-and-seventy-three ED patients [199 with Anorexia Nervosa (AN) and 74 with Bulimia Nervosa (BN)] completed the SCL-90R inventory and were genotyped for four functional, clinically relevant DRD4 polymorphisms: three variants in the promoter region [120-bp tandem repeat (TR, long vs. short allele), C-616G and C-521 T] and a variable number of tandem repeats (VNTR) in exon 3 (7R vs. non-7R allele). After correcting for multiple testing, none of the assayed polymorphisms were individually associated with SCL-90R results. Four DRD4 haplotypes ( *1–*4 ) were detected in the patients with a frequency > 0.1. In the BN group, haplotype *2 (non7R-TR long-C-C) was associated with higher scores in the three global SCL-90R indices (GSI, PSDI and PST) after Bonferroni correction ( p  ≤ 0.01 in all instances). Furthermore, carriers of this haplotype displayed higher scores (worst symptomatology) in Somatization , Obsessive-Compulsive , Anxiety , Phobic anxiety , Paranoid ideation and the test additional items ( p -values for the differences between carriers vs. non-carriers ranging from 0.0001 to 0.0110). Certain combinations of DRD4 variants may contribute to psychopathological features in BN patients. [ABSTRACT FROM AUTHOR]

Leucine-rich repeats and WD repeat domain-containing protein 1 (LRWD1) is implicated in the regulation of signal transduction, transcription, RNA processing and tumor development. However, LRWD1 transcriptional regulation is not fully understood. This study aimed to investigate the relationship between LRWD1 expression and reactive oxygen species (ROS) level in human embryonal carcinoma cell line, NT2/D1 cells, which will help in understanding the transcriptional regulatory role of ROS in cells. Results showed that the exposure of NT2/D1 cells to various concentrations of hydrogen peroxide (H 2 O 2 ) and the nitric oxide (NO) donor sodium nitroprusside (SNP) caused a significant increase in the mRNA and protein expression of LRWD1. In addition, LRWD1 promoter luciferase reporter assay, and Chromatin Immunoprecipitation assay (CHIP assay) showed that nuclear factor erythroid-2-related factor (Nrf2) was involved in the regulation of LRWD1 expression in response to oxidative stress. The involvement of Nrf2 was confirmed by shRNA-mediated knockdown of Nrf2 in NT2/D1 cells, which caused a significant decrease in LRWD1 expression in response to oxidative stress. Similarly, LRWD1 knockdown resulted in the accumulation of H 2 O 2 and superoxide anion radical (O2-). Blocking ROS production by N-acetyl cysteine (NAC) protected NT2/D1 shLRWD1cells from H 2 O 2 -induced cell death. Collectively, oxidative stress increased LRWD1 expression through a Nrf2-dependent mechanism, which plays an important role in cellular adaptation to oxidative stress. These results highlight an evidence, on the molecular level, about LRWD1 transcriptional regulation under oxidative stress. [ABSTRACT FROM AUTHOR]

Scab caused by the fungus Venturia inaequalis (Cook) G. Winter is the most devastating disease of the apple worldwide. To control the disease most efforts have been directed toward the breeding programmes by introgression of scab resistance genes from wild apples into commercial cultivars. Although, various apple genotypes exist in Iran, no comprehensive data regarding the possible presence of scab resistance genes is available. In this research the presence of five R genes ( Rvi2 , Rvi4 , Rvi6 , Rvi8 and Rvi11 ) was assessed in 28 wild and domestic apple genotypes using 13 SCAR and SSR markers. Sequencing and blastN results confirmed the identify of Rvi2 , Rvi6 , Rvi8 and Rvi11 genes. Based on the results, wild apples had more resistance genes and among foreign and autochthonous apples, ‘Golden Delicious’, ‘Malayer-1’ and ‘Shahroud-6’ carrying at least three R genes categorized as almost tolerant cultivars. However, ‘Gala’, ‘Boshghabi-e Damavand’, ‘Manouchehri’ and ‘Golab’ had just one R gene and classified as susceptible cultivars. The most frequent scab resistance breeding programmes rely on Rvi6 gene ( HcrVf2 gene), which was also detected in this study in crabapple Malus floribunda providing a rich resource for developing resistant apple cultivars in Iran. [ABSTRACT FROM AUTHOR]

The small leucine-rich proteoglycans (SLRPs) are important regulators of extracellular matrix assembly and cell signalling. We have determined crystal structures at ~ 2.2 Å resolution of human fibromodulin and chondroadherin, two collagen-binding SLRPs. Their overall fold is similar to that of the prototypical SLRP, decorin, but unlike decorin neither fibromodulin nor chondroadherin forms a stable dimer. A previously identified binding site for integrin α2β1 maps to an α-helix in the C-terminal cap region of chondroadherin. Interrogation of the Collagen Toolkits revealed a unique binding site for chondroadherin in collagen II, and no binding to collagen III. A triple-helical peptide containing the sequence GAOGPSGFQGLOGPOGPO (O is hydroxyproline) forms a stable complex with chondroadherin in solution. In fibrillar collagen I and II, this sequence is aligned with the collagen cross-linking site KGHR, suggesting a role for chondroadherin in cross-linking. [ABSTRACT FROM AUTHOR]

Since the discovery of repeat-associated non-ATG (RAN) translation, and more recently its association with amyotrophic lateral sclerosis/frontotemporal dementia, there has been an intense focus to understand how this process works and the downstream effects of these novel proteins. RAN translation across several different types of repeat expansions mutations (CAG, CTG, CCG, GGGGCC, GGCCCC) results in the production of proteins in all three reading frames without an ATG initiation codon. The combination of bidirectional transcription and RAN translation has been shown to result in the accumulation of up to six mutant expansion proteins in a growing number of diseases. This process is complex mechanistically and also complex from the perspective of the downstream consequences in disease. Here we review recent developments in RAN translation and their implications on our basic understanding of neurodegenerative disease and gene expression. [ABSTRACT FROM AUTHOR]

Myotonic dystrophy (DM) is a dominantly-inherited genetic disorder affecting skeletal muscle, heart, brain, and other organs. DM type 1 is caused by expansion of a CTG triplet repeat in DMPK , whereas DM type 2 is caused by expansion of a CCTG tetramer repeat in CNBP . In both cases the DM mutations lead to expression of dominant-acting RNAs. Studies of RNA toxicity have now revealed novel mechanisms and new therapeutic targets. Preclinical data have suggested that RNA dominance is responsive to therapeutic intervention and that DM therapy can be approached at several different levels. Here we review recent efforts to alleviate RNA toxicity in DM. [ABSTRACT FROM AUTHOR]

Patient carriers of a C9orf72 repeat expansion exhibit remarkable heterogeneous clinical and pathological characteristics suggesting the presence of modifying factors. In accordance with other repeat expansion diseases, repeat length is the prime candidate as a genetic modifier. Observations of earlier onset ages in younger generations of large families suggested a mechanism of disease anticipation. Yet, studies of repeat size and onset age have led to conflicting results. Also, the correlation between repeat size and diagnosis is poorly understood. We review what has been published regarding C9orf72 repeat size as modifier for phenotypic characteristics. Conclusive evidence is lacking, partly due to the difficulties in accurately defining the exact repeat size and the presence of repeat variability due to somatic mosaicism. [ABSTRACT FROM AUTHOR]

An isolate of the fungus Puccinia striiformis , causing yellow (stripe) rust on cereals and grasses, was selfed on the alternate (sexual) host, Berberis vulgaris . This enabled us to investigate genetic variability of progeny isolates within and among aecia. Nine aecial clusters each consisting of an aecium (single aecial cup) and nine clusters containing multiple aecial cups were selected from 18 B. vulgaris leaves. Aeciospores from each cluster were inoculated on susceptible wheat seedlings and 64 progeny isolates were recovered. Molecular genotyping using 37 simple sequence repeat markers confirmed the parental origin of all progeny isolates. Thirteen molecular markers, which were heterozygous in the parental isolate, were used to analyse genetic diversity within and among aecial cups. The 64 progeny isolates resulted in 22 unique recombinant multilocus genotypes and none of them were resampled in different aecial clusters. Isolates derived from a single cup were always of the same genotype whereas isolates originating from clusters containing up to nine aecial cups revealed one to three genotypes per cluster. These results implied that each aecium was the result of a successful fertilization in a corresponding pycnium and that an aecium consisted of genetically identical aeciospores probably multiplied via repetitive mitotic divisions. Furthermore, the results suggested that aecia within a cluster were the result of independent fertilization events often involving genetically different pycniospores. The application of molecular markers represented a major advance in comparison to previous studies depending on phenotypic responses on host plants. The study allowed significant conclusions about fundamental aspects of the biology and genetics of an important cereal rust fungus. [ABSTRACT FROM AUTHOR]

Advances in wheat genomics have lagged behind other major cereals ( e.g. , rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs. Key functional genomic resources will enable this, including sequenced mutant populations and gene editing technologies which are now available in wheat. Training the next-generation of genomics-enabled researchers will be essential to ensure these advances are quickly translated into farmers’ fields. [ABSTRACT FROM AUTHOR]

Introduction The aim of this study was to evaluate the diversity and similarity of Enterococcus faecalis genotype isolates from multiple oral sites using repetitive sequence-based polymerase chain reaction and arbitrarily primed polymerase chain reaction (AP-PCR). Methods Forty-two endodontically treated teeth with apical periodontitis were selected. A total of 126 microbial samples were collected from 3 different sites (saliva, pulp chamber, and root canals, all n = 42) during the nonsurgical retreatment procedures. After growth on m-Enterococcus agar, the colonies were isolated, characterized as gram-positive catalase negative cocci, and identified using an API 20 Strep kit (bioMérieux, Marcy-l'Etoile, France). Seventy-four colonies from 10 patients were confirmed as E. faecalis by polymerase chain reaction (16S ribosomal RNA). Repetitive sequence-based polymerase chain reactions using ERIC and AP-PCR using RW3A primers were performed in all 74 colonies. Fingerprints were analyzed and separated into genotypic groups based on the Dice coefficient percentage of similarity (82% or greater) as determined by ERIC reproducibility assays involving E. faecalis controls. Results Seven different E. faecalis genotypes (GTs) (GT1 = 27%, GT2 = 17.6%, GT3 = 1.3%, GT4 = 18.9%, GT5 = 9.5%, GT6 = 14.9%, and GT7 = 10.8%) were observed in different subjects and oral sites associated with endodontic failure. Remarkably, in 4 of 5 patients, the same GTs present in the infected root canals were also isolated from either the pulp chamber or the saliva samples. In particular, GT6 was detected in all 3 oral sites of patient 37. Conclusions E. faecalis GTs isolated from saliva, the pulp chamber, and the root canal were similar using the Rep-PCR and AP-PCR methods. These findings suggest that coronal microleakage is a conceivable cause of endodontic failure. [ABSTRACT FROM AUTHOR]

Spinocerebellar ataxia type 6 (SCA6) is an autosomal dominant neurodegenerative disorder. However, it remains unclear whether SCA6 shows a gene dosage effect, defined by earlier age-of-onset in homozygotes than heterozygotes. Herein, we retrospectively analyzed four homozygous SCA6 subjects from our single institution cohort of 120 SCA6 subjects. We also performed a neuropathological investigation into an SCA6 individual with compound heterozygous expansions. In the 116 heterozygotes, there was an inverse correlation of age-of-onset with the number of CAG repeats in the expanded allele, and with the total number of CAG repeats, in both normal and expanded alleles. The age-of-onset in the four homozygotes was within the 95% confidence interval of the age-of-onset versus the repeat-lengths correlations determined in the 116 heterozygotes. Nevertheless, all homozygotes had earlier onset than their parents, and showed rapid disease progression. Neuropathology revealed neuronal loss, as well as α1A-calcium channel protein aggregates in Purkinje cells, a few α1A-calcium channel protein aggregates in the neocortex and basal ganglia, and neuronal loss in Clarke's column and the globus pallidus not seen in heterozygotes. These data suggest a mild clinical and neuropathological gene dosage effect in SCA6 subjects. [ABSTRACT FROM AUTHOR]

The aim of this study was to detect Trichinella spiralis DNA in mouse feces during the early stages of infection using PCR. The target gene fragment, a 1.6 kb repetitive sequence of T. spiralis genome, was amplified by PCR from feces of mice infected with 100 or 300 larvae at 3–24 h post infection (hpi) and 2–28 dpi. The sensitivity of PCR was 0.016 larvae in feces. The primers used were highly specific for T. spiralis . No cross-reactivity was observed with the DNA of other intestinal helminths. T. spiralis DNA was detected in 100% (12/12) of feces of mice infected with 100 or 300 larvae as early as 3 hpi, with the peak detection lasting to 12–24 hpi, and then fluctuating before declining gradually. By 28 dpi, the detection rate of T. spiralis DNA in feces of the two groups of infected mice decreased to 8.33% and 25%, respectively. PCR detection of T. spiralis DNA in feces is simple and specific; it might be useful for the early diagnosis of Trichinella infection. [ABSTRACT FROM AUTHOR]

The elongate loach ( Leptobotia elongata ) is a typical migratory fish that was formerly found in abundance throughout the upper and middle reaches of the Yangtze River but is now classified as a highly threatened fish on the China Species Red List. Here, a comparative study of microsatellite loci was performed to evaluate the genetic diversity and analyze the population structure in seven locations in the upper reaches of the Yangtze River, China. The results showed that genetic diversity of L . elongata is generally still at a high level. Populations from Xinshi, Panzhihua, Hechuan and Chishui, were found to have lower levels of genetic diversity than those that lived in Leshan, Yibin and Jiangjin. The IAM model indicated that populations from Panzhihua, Xinshi and Hechuan have undergone recent bottlenecks. AMOVA analysis revealed a small amount of differentiation among populations (3.6%), but most of the total variation occurred within populations (96.4%). Pairwise comparisons of populations confirmed a low population differentiation. STRUCTURE analysis showed no obvious genetic structure among populations, indicating that L . elongata living in the main stem of the river and its tributaries should be considered a single management unit. [ABSTRACT FROM AUTHOR]

Somatic instability of CAG repeats has been associated with the clinical progression of CAG repeat diseases. Aging and DNA repair processes influence the somatic stability of CAG repeat in disease and in mouse models. However, most of the studies have focused on genetically engineered transgenic repeats and little is known about the stability of naturally polymorphic CAG repeats. To study whether age and/or DNA repair activity have an effect on the somatic stability of CAG repeats, we analyzed variations of the length of naturally polymorphic CAG repeats in the striatum of young and aged WT and ogg1 KO mice. Some multiple and long polymorphic CAG repeats were observed to have variable length in the striatum of aged mice. Interestingly, a low level of repeat variability was detected in the CAG repeat located in tbp, the only mouse polymorphic CAG repeat that is associated with a trinucleotide disease in humans, in the striatum of aged mice and not in young mice. We propose that age may have an effect on the somatic stability of polymorphic CAG repeats and that such an effect depends on intrinsic CAG repeat characteristics. [ABSTRACT FROM AUTHOR]

Charcoal rot caused by Macrophomina phaseolina in castor is one of the major pathogenic determinants for extreme yield loss. The charcoal rot resistance trait is complex and controlled by quantitative trait locis (QTLs). This study was aimed to develop linkage map and to identify novel QTLs associated with charcoal rot resistance in castor. A mapping population (F 2:3 ) derived from the cross between two castor inbred lines JI 357 (Resistant genotype) and SKI 338 (Susceptible genotype) was developed and screened in the sick plot using randomised block design. After screening 920 (520 RAPD, 100 ISSR, 300 SSR) primers among the parental lines, 336 polymorphic markers were identified to be used for genotyping the mapping population to develop genetic linkage map. The genetic map consisting of 10 linkage group covering a total map length of 1833.4 centimorgan (cM) with average marker interval of 6.93 cM was developed. The length of linkage groups varied from 121.5 cM for linkage group 10 (C10) to 278.7 cM for linkage group 9 (C9). The average marker interval was maximum in C3 (8.23 cM) while it was lowest in C10 (5.78 cM). Analysing genotypic data along with phenotypic data collected from mapping population against charcoal rot in sick plot, identified three novel QTLs explaining 11.3–71.2% of phenotypic variation. One major QTL with LOD score of 6.5 was identified on linkage group 2 explaining 71.2% of phenotypic variation, is a most promising QTL for molecular breeding. This is the first study reporting novel QTLs for charcoal rot resistance in castor and thus future studies will be conducted to refine these QTLs. [ABSTRACT FROM AUTHOR]

Cymbopogon , an important genus of the family Poaceae, cultivated mainly for its essential oil, is a valuable medicinal and aromatic plant. Essential oils from this crop found a wide range of application including medicine, perfumery, ornamental, flavouring and therapeutic uses in pharmaceuticals and is emerging crop for bio fuel production. Many species of Cymbopogon cultivated worldwide but their identification is somewhat difficult since they do not have suitable genomic diversity information. Assessment of genetic diversity is therefore essential for conservation and management of this species. A total of 20 Randomly Amplified Polymorphic DNA (RAPD) and 15 Inter Simple Sequence Repeats (ISSR) primers were examined, of which 26 primers (13 RAPD and 13 ISSR) showed amplification and were used for further study. Unweighted Pair Group Method of Arithmetic Mean (UPGMA) derived dendrogram in both the analysis was more or less similar and cluster analysis (CA) based on RAPD, ISSR and their combined data clearly discriminated the genotypes into different clusters. Result of principal component analysis (PCA) was in agreement with cluster analysis with a few exceptions. DNA based markers (RAPD and ISSR) could be effectively used for genetic diversity evaluation among Cymbopogon species. Results of this study will help in the conservation and Cymbopogon improvement/breeding programe. [ABSTRACT FROM AUTHOR]

Black tiger shrimp ( Penaeus monodon ) is an economically important species for aquaculture in Vietnam; however, very little information is available regarding its transcriptome. In this study, we sequenced four transcriptome libraries from mRNA of heart, muscle, hepatopancreas, and eyestalk tissues of P. monodon individuals using the Illumina MiSeq® platform, yielding 78,575,346 raw paired-end reads. After quality control, a total of 62,327,726 paired-end reads were de novo assembled into 69,089 unigenes with an average size of 447.89 bp, N50 of 481 bp, and transcriptome size of 30.94 Mb. Comparisons of the assembled unigenes against five public protein databases identified 165 unigenes related to growth and development, and expression analysis revealed that 14,229 unigenes were differentially expressed among tissues. In addition, we detected 12,768 simple sequence repeats (SSRs) in 11,173 unigenes. This work provides candidate genes for trait mapping, marker-assisted breeding, genetic studies and functional genome annotation of P. monodon . Statement of relevance This paper is relevant for the Shrimp Industry. [ABSTRACT FROM AUTHOR]

The complete mitochondrial (mt) genome of the trematode Echinochasmus japonicus Tanabe, 1926 was fully determined and annotated. The circular mt molecule of this species is 15,865 bp in length, containing 12 protein-coding genes (arranged in the following order: cox 3- cob - nad 4L- nad 4- atp 6- nad 2- nad 1- nad 3- cox 1- cox 2- nad 6- nad 5), two ribosomal RNA genes ( rrn L and rrn S) and 22 transfer RNA genes ( trn H; trn Q; trn F; trn M; trn V; trn A; trn D; trn N; trn P; trn I; trn K; trn S 1(AGN) ; trn W; trn T; trn C; trn L 1(CUN) ; trn S 2(UCN) ; trn L 2(UUN) ; trn G; and trn E). The atp 8 gene is absent. The 3′ end of nad 4L overlaps the 5′ end of nad 4 by 40 bp. An array of eight identical tandem repeats (240 bp each) was found between trn G and trn E in the long non-coding region of the individual worm sequenced. Numbers of these repeats varied among E. japonicus samples. Phylogenetic analysis of concatenated mt protein sequences of 40 trematode species/strains supports the elevation of Echinochasminae Odhner, 1910 to family rank, close to the families Echinostomatidae and Fasciolidae. As echinochasmid and echinostomatid species can parasitize humans, the future characterization of additional mt genomes is needed for development of mt markers for identification and phylogenetic, population, epidemiological and hybridization studies. [ABSTRACT FROM AUTHOR]

DNA methylation is a key epigenetic mechanism, needed for proper control over the expression of genetic information and silencing of repetitive elements. Exposure to ionizing radiation, aside from its strong genotoxic potential, may also affect the methylation of DNA, within the repetitive elements, in particular. In this study, we exposed C57BL/6J male mice to low absorbed mean doses of two types of space radiation—proton (0.1 Gy, 150 MeV, dose rate 0.53 ± 0.08 Gy/min), and heavy iron ions ( 56 Fe) (0.5 Gy, 600 MeV/n, dose rate 0.38 ± 0.06 Gy/min). Radiation-induced changes in cardiac DNA methylation associated with repetitive elements were detected. Specifically, modest hypomethylation of retrotransposon LINE-1 was observed at day 7 after irradiation with either protons or 56 Fe. This was followed by LINE-1, and other retrotransposons, ERV2 and SINE B1, as well as major satellite DNA hypermethylation at day 90 after irradiation with 56 Fe. These changes in DNA methylation were accompanied by alterations in the expression of DNA methylation machinery and affected the one-carbon metabolism pathway. Furthermore, loss of transposable elements expression was detected in the cardiac tissue at the 90-day time-point, paralleled by substantial accumulation of mRNA transcripts, associated with major satellites. Given that the one-carbon metabolism pathway can be modulated by dietary modifications, these findings suggest a potential strategy for the mitigation and, possibly, prevention of the negative effects exerted by ionizing radiation on the cardiovascular system. Additionally, we show that the methylation status and expression of repetitive elements may serve as early biomarkers of exposure to space radiation. [ABSTRACT FROM AUTHOR]

Transposable elements and other repeated sequences are predominant contributors to most plant genomes. The vast majority of repeated elements accumulate mutations to the extent of becoming anonymous sequences, also known as ‘genomic dark matter’ which is also thought to contribute significantly to the composition of plant genomes. This review aims to highlight recent methods and analyses suggesting that ancient repeats have profound effects on plant genome biology. [ABSTRACT FROM AUTHOR]

An astonishing number of neurological diseases result from expansion of unstable repetitive sequences causing alterations in key neuronal processes. Some are progressive late-onset conditions related to aging, such as the spinocerebellar ataxias. In several of these pathologies, the expanded repeat is transcribed, producing an expanded RNA repeat that causes neurodegeneration by a complex mechanism, comprising 3 main pathways. These include (1) accumulation in the nucleus of RNA foci, resulting from sequestration of RNA-binding proteins functioning in important neuronal cascades; (2) decrease in availability of RNA-binding proteins, such as splicing factors, causing alternative splicing misregulation with imbalance in the expression ratio of neuronal isoforms; and (3) generation of neurotoxic peptides, produced from repeat-associated non-ATG-initiated translation across the RNA repeat, in all reading frames. Recently, 2 pathologies characterized by impaired motor function, cognitive decline, or/and degeneration of motor neurons have been found that have broaden our understanding of these diseases. Moreover, the finding of compromised nucleocytoplasmic transport opens new avenues for research. This review will cover the amazing progress regarding these conditions. [ABSTRACT FROM AUTHOR]

Genome sequencing has not only extended our understanding of the blueprints of many plant species but has also revealed the secrets of coding and non-coding genes. We present here a brief introduction to and personal account of key RNA-based technologies, as well as their development and applications for functional genomics of plant coding and non-coding genes, with a focus on short tandem target mimics (STTMs), artificial microRNAs (amiRNAs), and CRISPR/Cas9. In addition, their use in multiplex technologies for the functional dissection of gene networks is discussed. [ABSTRACT FROM AUTHOR]

Pyropia haitanensis is one of the most economically important mariculture crops of southern China. Core collection construction is important for the study, management and utilization of germplasm resources of P. haitanensis . In this study, methods for the construction of a core collection of P. haitanensis based on SSR marker data were developed and a core collection was created. Using 126 SSR alleles of 77 strains of P. haitanensis , 30 core subsets were constructed by stepwise clustering using two sampling strategies (random sampling and preferred sampling), three genetic distances (Nei & Li genetic distance (ND), simple matching genetic distance (SM), and Jaccard genetic distance (JD)) and five sample sizes (10%, 15%, 20%, 25%, 30%). Three parameters (Ne, H, and I) of genetic diversity were used to evaluate the genetic diversity of the 30 core subsets. The core subset that was constructed using preferred sampling at 15% of sample size with the SM genetic distance best represented the initial collection of the 30 core subsets and is recommended to be used as the core collection of P. haitanensis . Statement of relevance Pyropia haitanensis is one of the most economically important mariculture crops of southern China. Core collection construction is important for the study, management and utilization of germplasm resources of P. haitanensis . [ABSTRACT FROM AUTHOR]

Simple sequence repeats (SSRs) play specific roles in many biological activities. In this paper, we focused on SSRs in the genome of Pleurotus ostreatus , which is a widely cultivated edible mushroom. The distribution curves of SSRs and exons are opposite throughout the genome, which means that SSRs are mostly located in non-coding regions. A comparative analysis of nine fungi suggests that Agaricomycotina fungi have similar SSR distributions. Functional enrichment analysis on the SSR-containing gene set uncovers enriched functions about environmental interactions and important cellular functions for life. Trinucleotide SSRs account for an extremely high fraction of all SSRs, and in exonic regions, they are equivalent to inserting repeating amino acids (RAAs) into the protein sequences. The RAA indel could partly explain some enriched functions of the genes they modify. Agaricomycotina fungi have similar distributions of RAAs, indicating that this may be a potential common mechanism for some specific functions. [ABSTRACT FROM AUTHOR]

DNA has the ability to form a variety of secondary structures in addition to the normal B-form DNA, including hairpins and quadruplexes. These structures are implicated in a number of neurological diseases and cancer. Expansion of a GGGGCC repeat located at C9orf72 is associated with familial amyotrophic lateral sclerosis and frontotemporal dementia. This repeat expands from two to 24 copies in normal individuals to several hundreds or thousands of repeats in individuals with the disease. Biochemical studies have demonstrated that as little as four repeats have the ability to form a stable DNA secondary structure known as a G-quadruplex. Quadruplex structures have the ability to disrupt normal DNA processes such as DNA replication and transcription. Here we examine the role of GGGGCC repeat length and orientation on DNA replication using an SV40 replication system in human cells. Replication through GGGGCC repeats leads to a decrease in overall replication efficiency and an increase in instability in a length-dependent manner. Both repeat expansions and contractions are observed, and replication orientation is found to influence the propensity for expansions or contractions. The presence of replication stress, such as low-dose aphidicolin, diminishes replication efficiency but has no effect on instability. Two-dimensional gel electrophoresis analysis demonstrates a replication stall with as few as 20 GGGGCC repeats. These results suggest that replication of the GGGGCC repeat at C9orf72 is perturbed by the presence of expanded repeats, which has the potential to result in further expansion, leading to disease. [ABSTRACT FROM AUTHOR]

Purine repeat sequences present in the human genome are known to act as hotspots for mutations leading to chromosomal imbalances. It is established that large purine repeats (PRs) form stable DNA triplex structure which can inhibit gene expression. Friedreich's ataxia (FRDA), the autosomal neurodegenerative disorder is the only human disease known so far, where a large purine ( GAA ) repeat in the FXN gene is known to inhibit the expression of frataxin protein. We explored the hidden purine repeats (PR n with n ≥ 200) if any, in the human genome to find out how they are associated with neurological disorders. The results showed 28 PRs, which are mostly restricted to the intronic regions. Interestingly, the transcriptome expression analysis of PR-carrying genes (PR-genes) revealed that most of them are down-regulated in neurological disorders (autism, Alzheimer's disease, schizophrenia, epilepsy, mental retardation, Parkinson's disease, brain tumor) as compared to that in healthy controls. The altered gene expression in brain disorders can be interpreted in terms of a possible expansion of purine repeats leading to formation of very stable DNA-triplex and/or alleviation of the repair enzymes and/or other unknown cellular factors. Interactome analysis identified four PR-genes in signaling pathways whose dysregulation is correlated directly with pathogenesis: GRK5 and KLK6 in Alzheimer's disease; FGF14 in craniosynostosis, mental retardation and FLT1 in neuroferritinopathy. By virtue of being mutational hotspots and their ability to form DNA-triplex, purine repeats in genome disturb the genome integrity and interfere with the transcriptional regulation. However, validation of the disease linkage of PR-genes can be validated using knock-out techniques. [ABSTRACT FROM AUTHOR]

High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads to properly reconstruct repetitive sequences. The mathematical model for error-free input data shows the upper limits of accuracy of the results as a function of read coverage. For high coverage, the estimation error depends linearly on repetitive sequence length and inversely proportional to the sequencing coverage. The model depicts, the smaller de Bruijn graph dimensions, the more accurate assembly of long repetitive regions. The algorithm requires high read depth, provided by the next-generation sequencers and could use the existing data. The tests on errorless reads, generated in silico from several model genomes, pointed the properly reconstructed repetitive sequences, where existing assemblers fail. The C++ sources, the Python scripts and the additional data are available at http://dnaasm.sourceforge.net . [ABSTRACT FROM AUTHOR]

Melon ( Cucumis melo L.) is one of the most important commercial vegetable crops grown in Iran. Very few studies on the genetic structure and diversity of melon landraces of Iran are available in the literature. In addition, it is susceptible to a number of diseases causing reduction in both productivity and quality of the crop. In this study we applied inter retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and inter simple sequence repeat (ISSR) molecular markers to investigate genetic diversity and its association with populations resistant to ZYMV in 11 Iranian melon populations and 12 commercial lines. Significant differences (P ≤ 0.01) were detected among populations for reaction to ZYMV infection. No symptoms observed on inbred line PI414723, while variety Charentais T showed the highest value of virus infection (1.87). Based on five IRAP, 15 REMAP and 20 ISSR primers, a total of 656 reproducible and scorable loci were generated, among them 75.41% were polymorphic. Population structure analysis using STRUCTURE software identified K = 10 as the reliable value for the number of clusters. Associations between molecular markers and populations resistant to ZYMV were tested using mixed linear model (MLM) approach that accounts for population structure. Highly significant associations were found for seven REMAP and four ISSR markers affecting ZYMV resistance (P ≤ 0.01). This study provides evidence that using natural germplasms, the diversity can be enhanced for marker-trait associations that can be validated in segregating populations and exploited through marker-assisted selection. [ABSTRACT FROM AUTHOR]

Structure-prone DNA repeats are common components of genomic DNA in all kingdoms of life. In humans, these repeats are linked to genomic instabilities that result in various hereditary disorders, including many cancers. It has long been known that DNA repeats are not only highly polymorphic in length but can also cause chromosomal fragility and stimulate gross chromosomal rearrangements, i.e., deletions, duplications, inversions, translocations and more complex shuffles. More recently, it has become clear that inherently unstable DNA repeats dramatically elevate mutation rates in surrounding DNA segments and that these mutations can occur up to ten kilobases away from the repetitive tract, a phenomenon we call repeat-induced mutagenesis (RIM). This review describes experimental data that led to the discovery and characterization of RIM and discusses the molecular mechanisms that could account for this phenomenon. [ABSTRACT FROM AUTHOR]

Immunoglobulin (Ig) heavy chains undergo class switch recombination (CSR) to change the heavy chain isotype from IgM to IgG, A or E. The switch regions are several kilobases long, repetitive, and G-rich on the nontemplate strand. They are also relatively depleted of CpG (also called CG) sites for unknown reasons. Here we use synthetic switch regions at the IgH switch alpha (Sα) locus to test the effect of CpG sites and to try to understand why the IgH switch sequences evolved to be relatively depleted of CpG. We find that even just two CpG sites within an 80 bp synthetic switch repeat iterated 15 times (total switch region length of 1200 bp containing 30 CpG sites) are sufficient to dramatically reduce both Ig CSR and transcription through the switch region from the upstream Iα sterile transcript promoter, which is the promoter that directs transcripts through the Sα region. De novo DNA methylation occurs at the four CpG sites in and around the Iα promoter when each 80 bp Iα switch repeat contains the two CpG sites. Thus, a relatively low density of CpG sites within the switch repeats can induce upstream CpG methylation at the IgH alpha locus, and cause a substantial decrease in transcription from the sterile transcript promoter. This effect is likely the reason that switch regions evolved to contain very few CpG sites. We discuss these findings as they relate to DNA methylation and to Ig CSR. [ABSTRACT FROM AUTHOR]

Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disease caused by the expansion of a CAG repeat within the ataxin 7 gene, leading to a pathogenic polyglutamine tract within the ataxin 7 protein. SCA7 patients suffer from progressive cerebellar ataxia and macular degeneration. SCA7 is considered to be rare, although founder effects have been reported in South Africa, Scandinavia and Mexico. The South African SCA7-associated haplotype has not been investigated in any other populations, and there have been limited reports of SCA7 patients from other African countries. Here, we describe the first two ethnic Zambian families with confirmed SCA7. Haplotype analysis showed that the South African SCA7 haplotype alleles were significantly associated with the pathogenic expansion in affected Zambian individuals, providing strong evidence for a shared founder effect between South African and Zambian SCA7 patients. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) comprise a group of repetitive sequences that bring positive, negative, as well as neutral effects to the host organism. Earlier considered as “junk DNA,” TEs are now well-accepted driving forces of evolution and critical regulators of the expression of genetic information. Their activity is regulated by epigenetic mechanisms, including methylation of DNA and histone modifications. The loss of epigenetic control over TEs, exhibited as loss of DNA methylation and decondensation of the chromatin structure, may result in TEs reactivation, initiation of their insertional mutagenesis (retrotransposition) and has been reported in numerous human diseases, including cancer. Accumulating evidence suggests that these alterations are not the simple consequences of the disease, but often may drive the pathogenesis, as they can be detected early during disease development. Knowledge derived from the in vitro , in vivo , and epidemiological studies, clearly demonstrates that exposure to ubiquitous environmental stressors, many of which are carcinogens or suspected carcinogens, are capable of causing alterations in methylation and expression of TEs and initiate retrotransposition events. Evidence summarized in this review suggests that TEs are the sensitive endpoints for detection of effects caused by such environmental stressors, as ionizing radiation (terrestrial, space, and UV-radiation), air pollution (including particulate matter [PM]-derived and gaseous), persistent organic pollutants, and metals. Furthermore, the significance of these effects is characterized by their early appearance, persistence and presence in both, target organs and peripheral blood. Altogether, these findings suggest that TEs may potentially be introduced into safety and risk assessment and serve as biomarkers of exposure to environmental stressors. Furthermore, TEs also show significant potential to become invaluable surrogate biomarkers in clinic and possible targets for therapeutic modalities for disease treatment and prevention. [ABSTRACT FROM AUTHOR]

Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon's diversity index ( I ) of 0.748 and the heterozygosity ( He ) of 0.434. In each regional population, I value varied widely. The widest range of I (0.228–0.489) was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea (0.168–0.270). The F -statistics of regional populations ( Fis , Fit and Fst ) also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea. All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China. [ABSTRACT FROM AUTHOR]

The diacylglycerol-O-transferase 1 gene is a positional and functional candidate for milk composition traits. The objective of this study was to evaluate the segregation of the variable number of tandem repeat polymorphisms in the regulatory region of diacylglycerol-O-transferase 1 gene in a water buffalo herd, and to assess the association of this mutation with milk production traits. For this purpose, 196 Murrah buffalo cows were genotyped by PCR. The association of the marker with total milk, fat, and protein yields at 305 d of lactation, milk fat and protein percentage, and somatic cell scores were evaluated by single-trait analyses using a generalized mixed model. Two segregating alleles were identified in the population. The allele with 2 repeats affected fat percentage favorably. The present results suggest that this polymorphism is an interesting marker to include in the genetic evaluation of buffaloes. [ABSTRACT FROM AUTHOR]

PCR-based typing methods, such as repetitive sequence-based PCR (rep-PCR), may facilitate the identification of Shiga toxin-producing Escherichia coli (STEC) by serving as screening methods to reduce the number of isolates to be processed for further confirmation. In this study, we used a commercial rep-PCR typing system to generate DNA fingerprint profiles for STEC 0157 (n = 60) and non-0157 (n = 91) isolates from human, food, and animal samples and then compared the results with those obtained from pulsed-field gel electrophoresis (PFGE). Fifteen serogroups were analyzed using the Kullback Leibler or extended Jaccard statistical method, and the unweighted pair group method of averages algorithm was used to create dendrograms. Among the 151 STEC isolates tested, all were typeable by rep-PCR. Among the non-0157 isolates, rep-PCR clustered 79 (88.8%) of 89 isolates according to serogroup status, with peak differences ranging from 1 (96.4% similarity) to 12 (58.7% similarity). The genetic relatedness of the non-0157 serogroups mirrored the branching of distinct clonal groups elucidated by other investigators. Although the discriminatory power of rep-PCR (Simpson's index of diversity [SID] = 0.954) for the 0157 isolates was less than that of PFGE (SID = 0.993), rep-PCR was able to identify 29 pattern types, suggesting that this method can be used for strain typing; although not to the same level as PFGE. Similar results were obtained from analysis of the non-0157 isolates. With rep-PCR, we assigned non-0157 isolates to 46 pattern types with a SID of 0.977. By PFGE, non-0157 STEC strains were divided into 77 pattern types with a SID of 0.996. Together, these results indicate the ability of the rep-PCR typing system to distinguish between and within 0157 and non-0157 STEC groups. Rapid PCR-based typing methods could be invaluable tools for use in outbreak investigations by excluding unrelated STEC isolates within 24 h. [ABSTRACT FROM AUTHOR]

Eukaryotic genomes contain millions of copies of repetitive elements (RE). Although the euchromatic parts of most genomes are clearly annotated, the repetitive/heterochromatic parts are poorly defined. It is estimated that between 50 and 70% of the human genome is composed of REs. Despite this, we know surprisingly little about the physiological relevance, molecular regulation and the composition of these regions. This primarily reflects the difficulty that REs pose for PCR-based assays, and their poor map-ability in next generation sequencing experiments. Here we first summarize the nature and classification of REs and then examine how this has been used in the recent years to broaden our understanding of mechanisms that keep the repetitive regions of our genomes silent and stable. [ABSTRACT FROM AUTHOR]

An exploratory study in five conventional pig production clusters was carried out to investigate the dynamic and diversity of Salmonella spp. within different production stages and sample site categories (pooled feces, direct and non-direct environment). Observing two production cycles per production cluster, a total of 1276 samples were collected along the pig production chain. Following a microbiological examination via culture, 2246 subcultures were generated out of 285 Salmonella positive samples and analysed by pheno- and genotyping methods. Based on a combination of serotyping, MLVA (multiple-locus variable-number tandem repeat (VNTR) analysis), PFGE (pulse-field gel electrophoresis) and MLST (multilocus sequence typing), an amount of 22.3% Salmonella positive samples were characterized in clonal lineages and its variants. Within each production cluster, one main clonal lineage could be identified and persisted over both production cycles with a large diversity of variants and a wide distribution in sample site categories and production stages. Results underline the importance of biosecurity with emphasis on the environment to prevent persistence and circulation of Salmonella within herds. Furthermore, the combined implementation of MLVA, PFGE and MLST with conventional culture techniques for isolate classification could be successfully applied as an effective and valuable tool for identifying similar pattern of Salmonella occurrence within pig production clusters. [ABSTRACT FROM AUTHOR]

Genetic heterogeneity of Mycoplasma hyopneumoniae in pigs has been reported, however there has been limited reproducibility on the molecular methods employed so far. The aim of this study was to modify and standardize a high-resolution multiple locus variable number tandem repeat analysis (MLVA), to investigate the genetic variability of M. hyopneumoniae circulating in the United States of America (USA), Brazil, Mexico and Spain. The MLVA was standardized on the basis of the number of tandem repeats in two Mycoplasma adhesins, P97 and P146, which are proteins involved in the adherence of the pathogen to cilia. A total of 355 samples obtained from the four countries were analyzed. The Simpson's diversity index for the assay was D = 0.976 when samples from all countries were combined. A large number of MLVA types ( n = 139) were identified, suggesting that multiple M. hyopneumoniae variants are circulating in swine. The locus P97 had 17 different types with 2–18 repeats. The P146 locus showed higher heterogeneity, with 34 different types, ranging from 7 to 48 repeats. MLVA types that presented more than 30 repeats in P146 were found in Spain and Brazil, while shorter repeats were observed in the USA and Mexico. This simplified MLVA method proved to be an efficient tool for typing M. hyopneumoniae with a high degree of stability, repeatability, and discriminatory power. In conclusion, M. hyopneumoniae showed a high variable number tandem repeat heterogeneity and this assay can be applied in molecular epidemiology investigations within farms and productions systems. [ABSTRACT FROM AUTHOR]

Background: There is a significant comorbidity between mood disorders and tobacco use disorder (TUD), which may be related to both genetic and environmental factors. Gene variants of the 5-HT transporter, such as STin2 VNTR (a variable number of tandem repeats in the functional serotonin transporter intron 2) may be associated with mood disorders and TUD.Aims: This study aimed to delineate the association between the STin2 genetic polymorphism and comorbid TUD and mood disorders, including depression or bipolar disorder.Methods: We examined the STin2 VNTR polymorphism in never-smokers (n=113); patients with mood disorders without TUD (n=62); patients with TUD without mood disorders (n=90); and patients with both disorders (n=95).Results: We found a significant association between the STin2 genetic polymorphism and the above diagnostic groups whereby the STin2.12 allele shows a positive association with comorbid TUD and mood disorders (Odds ratio=3.07, 95% CI=1.41-6.68), while the STin2.10/10 homozygous genotype shows a negative association (Odds ratio=0.34, 95% CI=0.16-0.74). Adjusting for years of education, age, gender, marital status and ethnicity did not change these results, but showed that TUD was associated with lower education levels and less stable relationships, whereas mood disorders were related to female gender. A family history of TUD was significantly associated with TUD in subjects without mood disorders only.Conclusions: The STin2.12 allele is positively and the STin2.10/10 genotype is negatively associated with comorbid TUD and mood disorders, depression or bipolar depression, suggesting that biological endophenotypes, e.g. disorders in serotonin metabolism, may in part underpin this comorbidity. [ABSTRACT FROM AUTHOR]

Manglietia patungensis Hu is an endangered plant native to China. Knowledge of its genetic diversity and structure would aid its conservation. This study assessed nine natural populations of M . patungensis using two methods: inter simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Using 10 ISSR primer pairs, 334 bands were generated, and 10 SRAP primer pairs generated 276 bands. The percent of polymorphic bands (91.32% and 93.48%), Nei's genetic diversity (0.3448 and 0.3323), and Shannon's information index (0.5075 and 0.4935) revealed a high level of genetic diversity at the species level. Total heterozygosity was 0.3439 by ISSR and 0.3281 by SRAP. The mean heterozygosity was 0.2323 by ISSR and 0.2521 by SRAP. The coefficient of genetic differentiation among natural populations was 0.3245 by ISSR and 0.2316 by SRAP. These data indicated higher levels of genetic diversity of M . patungensis within, rather than among, populations. Estimates of gene flow among natural populations were 1.0411 and 1.0589, which implied a certain amount of gene exchange among populations. A Mantel test revealed no significant correlation between genetic and geographic distance. ISSR and SRAP markers are both effective for genetic diversity research in M. Patungensis . Based on these results, conservation of M . patungensis should be performed both in situ and ex situ. [ABSTRACT FROM AUTHOR]

There is a need for an appropriate evaluation of Hemarthria germplasm resources using genetic analysis. Understanding their genetic background will promote effective development and utilization of its germplasm resources in plant breeding. We examined the genetic diversity and relationships among 46 Hemarthria germplasm resources from four continents. Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) and Start Codon Targeted (SCoT) markers were used to investigate species Hemarthria altissima (36), Hemarthria compressa (8) and Hemarthria uncinata (2). We selected 19 EST-SSR primers and generated 550 polymorphic (94.7%). Twenty one SCoT primers were selected and amplified to produce 597 bands with 89.4% of polymorphic bands. The Mantel test between EST-SSR and SCoT matrices revealed significant correlations ( r = 0.854) and the data from both markers were combined for cluster analysis. The 46 materials were clustered into two main groups by UPGMA clustering with a similarity coefficient ranging from 0.573 to 0.940 and the dendrogram was basically concordant with geographical origins and species. Among the three Hemarthria species, H. altissima was genetically closest to H. compressa while it was not close to H. uncinata . When the utility of the two markers were compared, we found EST-SSR to be more efficient than SCoT in determining the genetic diversity study of Hemarthria species. [ABSTRACT FROM AUTHOR]

In this study, we have aimed to genetically characterize Ginkgo biloba . Nine G. biloba samples from different places of China were collected, and DNA was extracted from the leaves of these samples for inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analysis. ISSR analysis showed high genetic variation among the nine varieties of G. biloba ; the polymorphism and similarity coefficients were 87% and 0.40–0.84, respectively. RAPD analysis also showed 93% polymorphism, and the similarity coefficients ranged from 0.44 to 0.87. Persistent genetic isolation that developed for millions of years might influence the genetic variability between the samples of G. biloba . This study generates a genetic map of G. biloba , and reports the highly variable intra-species genetic characteristics of this living fossil among different geographical locations of China. Our study also suggests that ISSR and the improved RAPD markers are useful molecular tools for the genetic characterization of plants. [ABSTRACT FROM AUTHOR]

Assuming systematic exchanges between nucleotides (swinger RNAs) resolves genomic ‘parenthood’ of some orphan mitochondrial transcripts. Twenty-three different systematic nucleotide exchanges (bijective transformations) exist. Similarities between transcription and replication suggest occurrence of swinger DNA. GenBank searches for swinger DNA matching the 23 swinger versions of human and mouse mitogenomes detect only vertebrate mitochondrial swinger DNA for swinger type AT + CG (from five different studies, 149 sequences) matching three human and mouse mitochondrial genes: 12S and 16S ribosomal RNAs, and cytochrome oxidase subunit I. Exchange A<->T + C<->G conserves self-hybridization properties, putatively explaining swinger biases for rDNA, against protein coding genes. Twenty percent of the regular human mitochondrial 16S rDNA consists of short swinger repeats (from 13 exchanges). Swinger repeats could originate from recombinations between regular and swinger DNA: duplicated mitochondrial genes of the parthenogenetic gecko Heteronotia binoei include fewer short A<->T + C<->G swinger repeats than non-duplicated mitochondrial genomes of that species. Presumably, rare recombinations between female and male mitochondrial genes (and in parthenogenetic situations between duplicated genes), favors reverse-mutations of swinger repeat insertions, probably because most inserts affect negatively ribosomal function. Results show that swinger DNA exists, and indicate that swinger polymerization contributes to the genesis of genetic material and polymorphism. [ABSTRACT FROM AUTHOR]

Boule is responsible for meiotic arrest of sperms and male sterility during mammalian spermatogenesis. In the present study, we first identified yak b-Boule gene and its two alternative splice variants. The full length coding region of yak b-Boule is 888 bp and encodes a 295-amino acid protein with a typical RNA-recognition motif (RRM) and a Deleted in Azoospermia (DAZ) repetitive sequence motif. Two alternative splice variants of yak b-Boule were generated following the consensus “GT-AG” rule and named b-Boule1 (36 bp deletion in exon 3) and b-Boule2 (deletion of integral exon 7), respectively. In male yak, b-Boule , b-Boule1 and b-Boule2 were found to be exclusively expressed in the testes at a ratio of 81:0.1:1. Intriguingly, the mRNA expression levels of b-Boule and b-Boule1 in yak testis were significantly higher than those in cattle–yak, although no significant difference was observed for b-Boule2 expression between the yak and cattle–yak. These results suggest that b-Boule gene, which is partially regulated by alternative splicing, may be involved in the process of yak spermatogenesis. [ABSTRACT FROM AUTHOR]

Background Prenatal exposure to endocrine disrupting compounds (EDCs) has previously shown to alter epigenetic marks. Objectives In this work we explore whether prenatal exposure to mixtures of xenoestrogens has the potential to alter the placenta epigenome, by studying DNA methylation in retrotransposons as a surrogate of global DNA methylation. Methods The biomarker total effective xenoestrogen burden (TEXB) was measured in 192 placentas from participants in the longitudinal INMA Project. DNA methylation was quantitatively assessed by bisulfite pyrosequencing on 10 different retrotransposons including 3 different long interspersed nuclear elements (LINEs), 4 short interspersed nuclear elements (SINEs) and 3 human endogenous retroviruses (HERVs). Associations were tested using linear mixed-effects regression models and sex interaction was evaluated. Results A significant sex interaction was observed for AluYb8 (p-value for interaction < 0.001, significant at Bonferroni corrected p-value threshold of 0.0025). Boys with the highest TEXB-alpha levels of exposure (third tertile) presented on average a decrease of 0.84% in methylation compared to those in the first tertile (p-value<0.001), while no significant effects were found in girls (p-value=0.134). Conclusions Our findings suggest that boys may be more susceptible to the effect of exposure to xenoestrogens during prenatal development, producing shifts in DNA methylation of certain sensitive genomic repetitive sequences in a tissue important for fetal growth and development. [ABSTRACT FROM AUTHOR]

Species of Ganoderma are used in traditional medicines. An improved random amplified polymorphic DNA (RAPD) analysis, where the RAMP time is prolonged, has been used to characterize the genetic variation in some well known species of Ganoderma . The DNA materials were collected from ten Ganoderma strains, amplified with randomly selected 24 RAPD primers and evaluated by agarose gel electrophoresis. A cluster dendrogram was constructed for genetic analysis on the basis of amplification results. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 316 bands were found with 93% polymorphism. There was a significant genetic distance between the different strains of Ganoderma , with an index of similarity coefficient in the range of 0.52–0.74. The inter-simple sequence repeat (ISSR) analysis of the Ganoderma DNA samples showed similar trend results to the RAPD analysis with 0.49–0.81 similarity coefficients. This study reports the high level of genetic differences between different species or strains of a single species of Ganoderma and confirms the significance of the improved RAPD method in genetic characterization of organisms. Therefore, the improved RAPD combined with ISSR techniques might be used for the genetic characterization of organisms. [ABSTRACT FROM AUTHOR]

Armillaria luteo-virens is a type of ectomycorrhiza whose fruit body is widely used as an edible mushroom in the Qinghai-Tibetan Plateau. In total, 404 individuals of A. luteo-virens from 23 geographically separate populations were analyzed using eight pairs of SSR markers. The average number of alleles among nine populations was 28.65 with a range from 20 to 38. The mean observed ( H O ) and expected ( H E ) heterozygosity ranged from 0.446 to 0.501 and from 0.499 to 0.554, respectively. An analysis of molecular variance (AMOVA) showed that most genetic variation occurred within populations (83.32%). The mean value of F ST (0.176) suggested low genetic differentiation among populations. The 23 studied populations were divided into two main clusters based on the NJ dendrogram, which was also confirmed by STRUCTURE analysis. This study may aid in not only the protection of this species but also the management of genetic resources for future artificial cultivation. [ABSTRACT FROM AUTHOR]