The Eastern Italian Alps (South Tyrol) is a connection area between continental Italy and the northern Alps. Various local factors, such as the heterogeneous environment, complex historical events, and different mobility patterns, may have influenced the genetic makeup of early medieval alpine groups. However, no ancient genetic data from these groups are currently available. This study provides a first picture of the ancient mitochondrial DNA (mtDNA) diversity of alpine groups from four locations in South Tyrol (Adige, Isarco, Venosta, and Merano). In total, 94 ancient mitogenomes of individuals (dated from 400 to 1100AD) were reconstructed by shotgun sequencing and a mtDNA capture approach. Moreover, stable isotope ratios (δ13C, δ15N, δ34S) were analyzed in a subset of 32 individuals. The results indicate different mtDNA haplogroup distributions among the alpine locations and the presence of rare lineages besides a possible maternal relatedness between individuals buried in the same and in diverse archaeological contexts. The study also shows differences in the genetic and mobility patterns (δ34S) between individuals from the central and north-eastern parts (Adige, Merano, Isarco) and those from the north-western part of South Tyrol (Venosta). These results suggest genetic exchanges with allochthonous people in the first group probably linked to high mobility and to geomorphological, historical, and socio-cultural factors. Comparisons extended to present-day alpine populations also suggested maternal genetic continuity in this alpine area. Finally, stable isotope (δ13C, δ15N, δ34S) data provided further support for regional differences in the diet of past alpine groups possibly linked to altitude and/or social status.

Cell-free (cf)DNA signatures are quickly becoming the target of choice for non-invasive screening, diagnosis, treatment and monitoring of human tumors. DNA methylation changes occur early in tumorigenesis and are widespread, making cfDNA methylation an attractive cancer biomarker. Already a proven technology for targeted genome sequencing, hybridization probe capture is emerging as a method for high-throughput targeted methylation profiling suitable to liquid biopsy samples. However, to date there are no reports describing the performance of this approach in terms of reproducibility, scalability, and accuracy. In the current study we performed hybridization probe capture using the myBaits® Custom Methyl-seq kit on 172 plasma samples and standards to evaluate its performance on cfDNA methylation analysis. The myBaits® assay showed high target recovery (>90%), demonstrated excellent reproducibility between captures (R2 = 0.92 on average), and was unaffected by increasing the number of targets in a capture. Finally, myBaits® accurately replicated ‘gold standard’ beta values from WGBS (average R2 = 0.79). The results of this study show that custom targeted methylation sequencing with myBaits® offers a cost-effective, reliable platform to profile DNA methylation at a set of discrete custom regions, with potential applicability to liquid biopsies for cancer monitoring.

Abstract Cell-free protein synthesis has been widely used as a “breadboard” for design of synthetic genetic networks. However, due to a severe lack of modularity, forward engineering of genetic networks remains challenging. Here, we demonstrate how a combination of optimal experimental design and microfluidics allows us to devise dynamic cell-free gene expression experiments providing maximum information content for subsequent non-linear model identification. Importantly, we reveal that applying this methodology to a library of genetic circuits, that share common elements, further increases the information content of the data resulting in higher accuracy of model parameters. To show modularity of model parameters, we design a pulse decoder and bistable switch, and predict their behaviour both qualitatively and quantitatively. Finally, we update the parameter database and indicate that network topology affects parameter estimation accuracy. Utilizing our methodology provides us with more accurate model parameters, a necessity for forward engineering of complex genetic networks.

The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.

Abstract The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub-Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.

Clades of marine fishes exhibit many patterns of diversification, ranging from relatively constant throughout time to rapid changes in the rates of speciation and extinction. The goatfishes (Syngnatharia: Mullidae) are a family of marine, reef associated fishes with a relatively recent origin, distributed globally in tropical and temperate waters. Despite their abundance and economic importance, the goatfishes remain one of the few coral reef families for which the species level relationships have not been examined using genomic techniques. Here we use phylogenomic analysis of ultra-conserved elements (UCE) and exon data to resolve a well-supported, time-calibrated phylogeny for 72 species of goatfishes, supporting a recent crown age of the goatfishes at 21.9 million years ago. We used this framework to test hypotheses about the associations among body shape morphometrics, taxonomy, and phylogeny, as well as to explore relative diversification rates across the phylogeny. Body shape was strongly associated with generic-level taxonomy of goatfishes, with morphometric analyses showing evidence for high phylogenetic signal across all morphotypes. Rates of diversification in this clade reveal a recent sharp increase in lineage accumulation, with 92% of the goatfish species sampled across all clades and major body plans having originated in just the past 5 million years. We suggest that habitat diversity in the early Pliocene oceans and the generalist ecology of goatfishes are key factors in the unusual evolutionary tempo of the family Mullidae.

North American river sturgeons of the genus Scaphirhynchus include three species: S. platorynchus, S. albus and S. suttkusi that live in the Missouri, Mississippi, and Mobile basin. All species of Scaphirhynchus are threatened, endangered or critically endangered due to a combination of factors including of habitat loss and over-harvesting. Genetic tools have been applied for conservation studies in this group, however, the tetrapolyploid nature of the genome of these species have brought a huge challenge to development of nuclear markers for these species and limited knowledge that could be obtained, such as the phylogenetic intrarelationships and population genetics of this genus. Moreover, unintentional hybridization arose from two species of Scaphirhynchus (S. platorynchus and S. albus) that share the same spawning space. To address the problem of species identification and provide genetic markers for population genetic studies on Scaphirhynchus, we developed a bioinformatics pipeline to find SNP markers, based on comparison between single-copy loci of diploid gar and two released autotetraploid genomes of Acipenseriformes. We found 77 SNPs at single-copy loci and 642 SNPs at double-copy loci after filtering. Both the single-copy and double-copy loci supported the same phylogenetic relationship among the three species, in which S. albus and S. platorynchus were more closely related to each other than either of them to S. suttkusi. The principal component analysis using these SNPs also showed that S. albus and S. platorynchus were close to each other. The SNP markers developed in this study should facilitate further researches on population genetics and conservation of the Scaphirhynchus sturgeons.

The monocot family Costaceae Nakai consists of seven genera but their mutual relationships have not been satisfactorily resolved in previous studies employing classical molecular markers. Phylogenomic analyses of 365 nuclear genes and nearly-complete plastome data provides almost fully resolved insights into their diversification. Paracostus is identified as sister to all other taxa, followed by several very short branches leading to discrete lineages, suggesting an ancient rapid radiation of these early lineages and leaving the exact relationships among them unresolved. Relationships among Chamaecostus, Dimerocostus and Monocostus confirmed earlier findings that these genera form a monophyletic group. The Afro-American Costus is also monophyletic. By contrast, Tapeinochilos appeared as a well-supported crown lineage of Cheilocostus rendering it paraphyletic. As these two genera differ morphologically from one another owing to a shift from insect- to bird-pollination, we propose to keep both names. The divergence time within Costaceae was estimated using penalized likelihood utilizing two fossils within Zingiberales, †Spirematospermum chandlerae and †Ensete oregonense, indicated a relatively recent diversification of Costaceae, between 18–9 Mya. Based on these data, the current pantropical distribution of the family is hypothesized to be the result of several long-distance intercontinental dispersal events, which do not correlate with global geoclimatic changes.