2) Xing-Xing Dong(þ¿¿) 3) Xi-Jie Zhan( ) Hai-Bin Zhang(

Simple sequence repeats (SSRs), also known as microsatellites, are ubiquitous short tandem duplications commonly found in genomes and/or transcriptomes of diverse organisms. They represent one of the most powerful molecular markers for genetic analysis and breeding programs because of their high mutation rate and neutral evolution. However, traditionally experimental screening of the SSR polymorphic status and their subsequent applicability to genetic studies are extremely labor-intensive and time-consuming. Thankfully, the recently decreased costs of next generation sequencing and increasing availability of large genome and/or transcriptome sequences have provided an excellent opportunity and sources for large-scale mining this type of molecular markers. However, current tools are limited. Thus we here developed a new pipeline, CandiSSR, to identify candidate polymorphic SSRs (PolySSRs) based on the multiple assembled sequences. The pipeline allows users to identify putative PolySSRs not only from the transcriptome datasets but also from multiple assembled genome sequences. In addition, two confidence metrics including standard deviation and missing rate of the SSR repetitions are provided to systematically assess the feasibility of the detected PolySSRs for subsequent application to genetic characterization. Meanwhile, primer pairs for each identified PolySSR are also automatically designed and further evaluated by the global sequence similarities of the primer-binding region, ensuring the successful rate of the marker development. Screening rice genomes with CandiSSR and subsequent experimental validation showed an accuracy rate of over 90%. Besides, the application of CandiSSR has successfully identified a large number of PolySSRs in the Arabidopsis genomes and Camellia transcriptomes. CandiSSR and the PolySSR marker sources are publicly available at: http://www.plantkingdomgdb.com/CandiSSR/index.html.

Substantial evidence has shown that DNA methylation regulates the initiation of ovarian and sexual maturation. Here, we investigated the genome-wide profile of DNA methylation in porcine ovaries at single-base resolution using reduced representation bisulfite sequencing. The biological variation was minimal among the three ovarian replicates. We found hypermethylation frequently occurred in regions with low gene abundance, while hypomethylation in regions with high gene abundance. The DNA methylation around transcriptional start sites was negatively correlated with their own CpG content. Additionally, the methylation level in the bodies of genes was higher than that in their 5′ and 3′ flanking regions. The DNA methylation pattern of the low CpG content promoter genes differed obviously from that of the high CpG content promoter genes. The DNA methylation level of the porcine ovary was higher than that of the porcine intestine. Analyses of the genome-wide DNA methylation in porcine ovaries would advance the knowledge and understanding of the porcine ovarian methylome.

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The rare decaysB → X s γ and B 0 s → μ + μ − are important to research new physics beyond the standard model (SM). In this work, we investigate two loop electroweak corrections toB → X s γ and B 0 s → μ + μ − in the minimal supersymmetric extension of the SM with local B − L gauge symmetry (B-LSSM), under a minimal flavor violating assumption for the soft breaking terms. In this framework, new particles and new definition of squarks can affect the theoretical predictions of these two processes, with respect to the MSSM. Considering the constraints from updated experimental data, the numerical results show that the B-LSSM can fit the experimental data for the branching ratios ofB → X s γ and B 0 s → μ + μ −. The results of the rare decays also further constrain the parameter space of the B-LSSM.

The theoretical predictions in the standard model (SM) and measurements on the anomalous magnetic dipole moments (MDM) of muon and electron have great precision, hence the MDMs of muon and electron have close relation with the new physics (NP) beyond the SM. Recently, a negative ∼ 2.4σ discrepancy between the measured electron MDM and the SM prediction results from a recent improved determination of the fine structure constant. Combined with the longlasting muon MDM discrepancy which is about ∼ 3.7σ, it is difficult to explain both the magnitude and opposite signs of the deviations in a consistent model, without introducing large flavourviolating effects. The analysis shows that they can be explained in the minimal supersymmetric extension (MSSM) of the SM with local B − L gauge symmetry (B-LSSM). Comparing with the MSSM, new parameters in the B-LSSM can affect the theoretical predictions on lepton MDMs, and the effects of them are explored. PACS numbers:

BackgroundCamellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic tolerance and biotic resistance and thus harbors valuable gene resources that may greatly benefit genetic improvement of cultivated tea tree. However, owning to a large genome size of ~3 Gb and structurally complex genome, there are fairly limited genetic information and particularly few genomic resources publicly available for this species. To better understand the key pathways determining tea flavor and enhance tea tree breeding programs, we performed a high-throughput transcriptome sequencing for C. taliensis.ResultsIn this study, approximate 241.5 million high-quality paired-end reads, accounting for ~24 Gb of sequence data, were generated from tender shoots, young leaves, flower buds and flowers using Illumina HiSeq 2000 platform. De novo assembly with further processing and filtering yielded a set of 67,923 transcripts with an average length of 685 bp and an N50 of 995 bp. Based on sequence similarity searches against public databases, a total of 39,475 transcripts were annotated with gene descriptions, conserved protein domains or gene ontology (GO) terms. Candidate genes for major metabolic pathways involved in tea quality were identified and experimentally validated using RT-qPCR. Further gene expression profiles showed that they are differentially regulated at different developmental stages. To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species. Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis.ConclusionWe reported the first large-coverage transcriptome datasets for C. taliensis using the next-generation sequencing technology. Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1494-4) contains supplementary material, which is available to authorized users.