BackgroundThe history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems.ResultsWe analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N’Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds.ConclusionsOur findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1153-y) contains supplementary material, which is available to authorized users.

Background The importance of cell type-specific epigenetic variation of non-coding regions in neuropsychiatric disorders is increasingly appreciated, yet data from disease brains are conspicuously lacking. We generate cell type-specific whole-genome methylomes ( N = 95) and transcriptomes ( N = 89) from neurons and oligodendrocytes obtained from brain tissue of patients with schizophrenia and matched controls. Results The methylomes of the two cell types are highly distinct, with the majority of differential DNA methylation occurring in non-coding regions. DNA methylation differences between cases and controls are subtle compared to cell type differences, yet robust against permuted data and validated in targeted deep-sequencing analyses. Differential DNA methylation between control and schizophrenia tends to occur in cell type differentially methylated sites, highlighting the significance of cell type-specific epigenetic dysregulation in a complex neuropsychiatric disorder. Conclusions Our results provide novel and comprehensive methylome and transcriptome data from distinct cell populations within patient-derived brain tissues. This data clearly demonstrate that cell type epigenetic-differentiated sites are preferentially targeted by disease-associated epigenetic dysregulation. We further show reduced cell type epigenetic distinction in schizophrenia. Electronic supplementary material The online version of this article (10.1186/s13059-019-1747-7) contains supplementary material, which is available to authorized users.

The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2472 completely sequenced prokaryotic genomes. This task is accomplished by reconstructing approximate maximum likelihood phylogenetic trees for each orthologous gene and corresponding 16S rRNA reference species sets and then reconciling the two trees under parsimony framework. The tree reconciliation method is generally considered to be a reliable way to detect HGT events but its practical use has remained limited because the method is computationally intensive and conceptually challenging. In this regard, HGTree (http://hgtree.snu.ac.kr) represents a useful addition to the biological community and enables quick and easy retrieval of information for HGT-acquired genes to better understand microbial taxonomy and evolution. The database is freely available and can be easily scaled and updated to keep pace with the rapid rise in genomic information.

Recently developed concepts in materials, manufacturing approaches and mechanics strategies open up opportunities for building optoelectronic systems with high performance, inorganic semiconductors in systems that afford exceptional levels of mechanical deformability (e.g., ability to bend and stretch), diversity in geometric layouts (e.g., large-area coverage, in dense or sparse coverages), and versatility in substrate choices (e.g., plastic, rubber). Each of these capabilities offers options in engineering design that are not easily addressed with conventional, wafer-based devices. [1][2][3][4][5][6] Some of the most successful demonstrations involve top-down methods to defi ne and release structures of active materials (or fully/partially formed devices) in ultrathin, microscale confi gurations from wafer hosts where they are deposited, grown and/or processed. Selective etching of a buried, sacrifi cial layer often enables this release, in schemes that use the techniques of transfer printing as routes to deterministic assembly on substrates of interest. [7][8][9] Key issues include, among others, (1) release layers and etching chemistries that do not degrade the active materials, (2) designs in structures (i.e. anchors) that tether released materials/devices to their lithographically defi ned locations, but that easily fracture during transfer printing and (3) schemes for interconnecting the materials/devices after their assembly on a target substrate. The present work presents two new concepts: the fi rst addresses topics of relevance to (2), in a way that signifi cantly relaxes requirements to achieve (1); the second relates to (3). Specifi cally, we propose and demonstrate engineering designs and materials that not only tether the materials/devices to the host substrate, but also simultaneously prevent their exposure to etchants applied during the release process. Further, an advanced interconnection scheme and vertical device layout facilitate electrical contacts and system integration. These two ideas are demonstrated with red emitting microscale light emitting diodes( μ -ILEDs) based on AlInGaP, both as individual devices and as interconnected arrays, on substrates ranging from glass to plastic. Comparisons to behaviors of devices formed using previous approaches illustrate the value of these techniques, both in performance and in integration schemes. [ 10 ] Thin epitaxial layers in stacks that consist of a p-spreading layer (Al 0.45 Ga 0.55 As:C)/p-cladding layer (In 0.5 Al 0.5 P:Zn)/quantum well (Al 0.25 Ga 0.25 In 0.5 P/In 0.56 Ga 0.44 P/ Al 0.25 Ga 0.25 In 0.5 P)/n-cladding (In 0.5 Al 0.5 P:Si)/n-spreading layer (Al 0.45 Ga 0.55 As:Si)/n-GaAs:Si, grown on a 500 nm thick sacrifi cial layer of Al 0.96 Ga 0.04 As on a GaAs wafer serve as active materials. This design allows selective elimination of the sacrifi cial layer with hydrofl uoric (HF) acid, to release arrays of individual, ultrathin, microscale devices (i.e. μ -ILEDs) from the underlying growth substrate. [ 11 ] Figure 1 illustrates key steps ...

Parent-of-origin methylation arises when the methylation patterns of a particular allele is dependent on the parent it was inherited from. Previous work in honey bees has shown evidence of parent-of-origin specific expression, yet the mechanisms regulating such pattern remains unknown in honey bees. In mammals and plants, DNA methylation is known to regulate parent-of-origin effects such as genomic imprinting. Here, we utilize genotyping of reciprocal European and Africanized honey bee crosses to study genome-wide allele-specific methylation patterns in sterile and reproductive individuals. Our data confirms the presence of allele-specific methylation in honey bees in lineage-specific contexts but also importantly, though to a lesser degree, parent-of-origin contexts. We show that the majority of allele-specific methylation occur due to lineage rather than parent-of-origin factors, regardless of reproductive state. Interestingly, genes affected by allele-specific DNA methylation often exhibit both lineage and parent-of-origin effects, indicating that they are particularly labile in terms of DNA methylation patterns. Additionally, we re-analyzed our previous study on parent-of-origin specific expression in honey bees and found little association with parent-of-origin specific methylation. These results indicate strong genetic background effects on allelic DNA methylation, and suggest that while parent-of-origin effects are manifested in both DNA methylation and gene expression, they are not directly associated with each other.

BackgroundNatural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data.ResultsWe generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism.ConclusionsResults revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0265-1) contains supplementary material, which is available to authorized users.

Ginsenosides can be classified on the basis of the skeleton of their aglycones. Here, we hypothesized that the sugar moieties attached to the dammarane backbone enable binding of the ginsenosides to the sweet taste receptor, eliciting glucagon-like peptide-1 (GLP-1) secretion in the enteroendocrine L cells. Using the human enteroendocrine NCI-H716 cells, we demonstrated that 15 ginsenosides stimulate GLP-1 secretion according to the position of their sugar moieties. Through a pharmacological approach and RNA interference technique to inhibit the cellular signal cascade and using the Gαgust−/− mice, we elucidated that GLP-1 secreting effect of Rg3 mediated by the sweet taste receptor mediated the signaling pathway. Rg3, a ginsenoside metabolite that transformed the structure through a steaming process, showed the strongest GLP-1 secreting effects in NCI-H716 cells and also showed an anti-hyperglycemic effect on a type 2 diabetic mouse model through increased plasma GLP-1 and plasma insulin levels during an oral glucose tolerance test. Our study reveals a novel mechanism where the sugar moieties of ginsenosides Rg3 stimulates GLP-1 secretion in enteroendocrine L cells through a sweet taste receptor-mediated signal transduction pathway and thus has an anti-hyperglycemic effect on the type 2 diabetic mouse model.

Horizontal gene transfer (HGT) is widespread in the evolution of prokaryotes, especially those associated with the human body. Here, we implemented large-scale gene-species phylogenetic tree reconstructions and reconciliations to identify putative HGT-derived genes in the reference genomes of microbiota isolated from six major human body sites by the NIH Human Microbiome Project. Comparisons with a control group representing microbial genomes from diverse natural environments indicated that HGT activity increased significantly in the genomes of human microbiota, which is confirmatory of previous findings. Roughly, more than half of total genes in the genomes of human-associated microbiota were transferred (donated or received) by HGT. Up to 60% of the detected HGTs occurred either prior to the colonization of the human body or involved bacteria residing in different body sites. The latter could suggest ‘genetic crosstalk’ and movement of bacterial genes within the human body via hitherto poorly understood mechanisms. We also observed that HGT activity increased significantly among closely-related microorganisms and especially when they were united by physical proximity, suggesting that the ‘phylogenetic effect’ can significantly boost HGT activity. Finally, we identified several core and widespread genes least influenced by HGT that could become useful markers for building robust ‘trees of life’ and address several outstanding technical challenges to improve the phylogeny-based genome-wide HGT detection method for future applications.