BackgroundThe identification of inversions of DNA segments shorter than read length (e.g., 100 bp), defined as micro-inversions (MIs), remains challenging for next-generation sequencing reads. It is acknowledged that MIs are important genomic variation and may play roles in causing genetic disease. However, current alignment methods are generally insensitive to detect MIs. Here we develop a novel tool, MID (Micro-Inversion Detector), to identify MIs in human genomes using next-generation sequencing reads.ResultsThe algorithm of MID is designed based on a dynamic programming path-finding approach. What makes MID different from other variant detection tools is that MID can handle small MIs and multiple breakpoints within an unmapped read. Moreover, MID improves reliability in low coverage data by integrating multiple samples. Our evaluation demonstrated that MID outperforms Gustaf, which can currently detect inversions from 30 bp to 500 bp.ConclusionsTo our knowledge, MID is the first method that can efficiently and reliably identify MIs from unmapped short next-generation sequencing reads. MID is reliable on low coverage data, which is suitable for large-scale projects such as the 1000 Genomes Project (1KGP). MID identified previously unknown MIs from the 1KGP that overlap with genes and regulatory elements in the human genome. We also identified MIs in cancer cell lines from Cancer Cell Line Encyclopedia (CCLE). Therefore our tool is expected to be useful to improve the study of MIs as a type of genetic variant in the human genome. The source code can be downloaded from: http://cqb.pku.edu.cn/ZhuLab/MID.

BackgroundDNA methylation is an important epigenetic modification critical to the regulation of gene expression during development. To date, little is known about the role of DNA methylation in tooth development in large animal models. Thus, we carried out a comparative genomic analysis of genome-wide DNA methylation profiles in E50 and E60 tooth germ from miniature pigs using methylated DNA immunoprecipitation-sequencing (MeDIP-seq).ResultsWe observed different DNA methylation patterns during the different developmental stages of pig tooth germ. A total of 2469 differentially methylated genes were identified. Functional analysis identified several signaling pathways and 104 genes that may be potential key regulators of pig tooth development from E50 to E60.ConclusionsThe present study provided a comprehensive analysis of the global DNA methylation pattern of tooth germ in miniature pigs and identified candidate genes that potentially regulate tooth development from E50 to E60.

BackgroundIn diphyodont mammals, the additional molars (permanent molars) bud off from the posterior-free end of the primary dental lamina compared with successional teeth (replacement teeth) budding off from the secondary dental lamina. The diphyodont miniature pig has proved to be a valuable model for studying human molar morphogenesis. The additional molars show a sequential initiation pattern related to the specific tooth development stage of additional molars in miniature pigs during the morphogenesis of additional molars. However, the molecular mechanisms of the regulatory network of mRNAs and long non-coding RNAs during sequential formation of additional molars remain poorly characterized in diphyodont mammals. Here, we performed RNA-seq and microarray on miniature pigs at three key molar developmental stages to examine their differential gene expression profiles and potential regulatory networks during additional molar morphogenesis.ResultsWe have profiled the differential transcript expression and functional networks during morphogenesis of additional molars in miniature pigs. We also have identified the coding and long non-coding transcripts using Coding-Non-Coding Index (CNCI) and annotated transcripts through mapping to the porcine, Wuzhishan miniature pig, mice, cow and human genomes. Many new unannotated genes plus 450 putative long intergenic non-coding RNAs (lincRNAs) were identified. Detailed regulatory network analyses reveal that WNT and TGF-β pathways are critical in regulating sequential morphogenesis of additional molars.ConclusionsThis is the first study to comprehensively analyze the spatiotemporal dynamics of coding and long non-coding transcripts during morphogenesis of additional molars in diphyodont mammals. The miniature pig serves as a large model animal to elucidate the relationship between morphogenesis and transcript level during the cascade initiation of additional molars. Our data provide fundamental knowledge and a basis for understanding the molecular mechanisms governing cascade initiation of additional molars, but also provide an important resource for developmental biology research.

BackgroundBacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria.ResultsWe found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus.ConclusionsBacteria are genetically isolated into discrete clusters equivalent to natural species.