Fast and accurate reference-guided scaffolding of draft genomes, bioRxiv, 2019-01-14

Background As the number of new genome assemblies continues to grow, there is increasing demand for methods to coalesce contigs from draft assemblies into pseudomolecules. Most current methods use genetic maps, optical maps, chromatin conformation (Hi-C), or other long-range linking data, however these data are expensive and analysis methods often fail to accurately order and orient a high percentage of assembly contigs. Other approaches utilize alignments to a reference genome for ordering and orienting, however these tools rely on slow aligners and are not robust to repetitive contigs.Results We present RaGOO, an open-source reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in just minutes. With the pseudomolecules constructed, RaGOO identifies structural variants, including those spanning sequencing gaps that are not reported by alternative methods. We show that RaGOO accurately orders and orients contigs into nearly complete chromosomes based on de novo assemblies of Oxford Nanopore long-read sequencing from three wild and domesticated tomato genotypes, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open-source with an MIT license at httpsgithub.commalongeRaGOO.Conclusions We demonstrate that with a highly contiguous assembly and a structurally accurate reference genome, reference-guided scaffolding with RaGOO outperforms error-prone reference-free methods and enable rapid pan-genome analysis.

biorxiv bioinformatics 100-200-users 2019

Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification Supplementary Figures, bioRxiv, 2019-01-14

Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.

biorxiv developmental-biology 200-500-users 2019

Single-Cell Transcriptomic Evidence for Dense Intracortical Neuropeptide Networks, bioRxiv, 2019-01-14

BrieflyAnalysis of single-cell RNA-Seq data from mouse neocortex exposes evidence for local neuropeptidergic modulation networks that involve every cortical neuron directly.Data Highlights<jatslist list-type=bullet><jatslist-item>At least 98% of mouse neocortical neurons express one or more of 18 neuropeptide precursor proteins (NPP) genes.<jatslist-item><jatslist-item>At least 98% of cortical neurons express one or more of 29 neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes.<jatslist-item><jatslist-item>Neocortical expression of these 18 NPP and 29 NP-GPCR genes is highly neuron-type-specific and permits exceptionally powerful differentiation of transcriptomic neuron types.<jatslist-item><jatslist-item>Neuron-type-specific expression of 37 cognate NPP NP-GPCR gene pairs predicts modulatory connectivity within 37 or more neuron-type-specific intracortical networks.<jatslist-item>SummarySeeking insight into homeostasis, modulation and plasticity of cortical synaptic networks, we analyzed results from deep RNA-Seq analysis of 22,439 individual mouse neocortical neurons. This work exposes transcriptomic evidence that all cortical neurons participate directly in highly multiplexed networks of modulatory neuropeptide (NP) signaling. The evidence begins with a discovery that transcripts of one or more neuropeptide precursor (NPP) and one or more neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes are highly abundant in nearly all cortical neurons. Individual neurons express diverse subsets of NP signaling genes drawn from a palette encoding 18 NPPs and 29 NP-GPCRs. Remarkably, these 47 genes comprise 37 cognate NPPNP-GPCR pairs, implying a strong likelihood of dense, cortically localized neuropeptide signaling. Here we use neuron-type-specific NP gene expression signatures to put forth specific, testable predictions regarding 37 peptidergic neuromodulatory networks that may play prominent roles in cortical homeostasis and plasticity.

biorxiv neuroscience 100-200-users 2019

Does testosterone impair mens' cognitive empathy? Evidence from two large-scale randomized controlled trials Supplementary material, bioRxiv, 2019-01-13

The capacity to infer the mental states of others (known as cognitive empathy) is essential for social interactions, and a well-known theory proposes that it is negatively affected by intrauterine testosterone exposure. Furthermore, previous studies reported that testosterone administration impaired cognitive empathy in healthy adults, and that a biomarker of prenatal testosterone exposure (finger digit ratios) moderated the effect. However, empirical support for the relationship has relied on small-sample studies with mixed evidence. We investigate the reliability and generalizability of the relationship in two large-scale double-blind placebo-controlled experiments in young men (N=243 and N=400), using two different testosterone administration protocols. We find no evidence that cognitive empathy is impaired by testosterone administration or associated with digit ratios. With an unprecedented combined sample size, these results counter current theories and previous high-profile reports, and demonstrate that previous investigations of this topic have been statistically underpowered.

biorxiv neuroscience 200-500-users 2019

Does testosterone impair men’s cognitive empathy? Evidence from two large-scale randomized controlled trials, bioRxiv, 2019-01-13

AbstractThe capacity to infer others’ mental states (known as “mind reading” and “cognitive empathy”) is essential for social interactions across species, and its impairment characterizes psychopathological conditions such as autism spectrum disorder and schizophrenia. Previous studies reported that testosterone administration impaired cognitive empathy in healthy humans, and that a putative biomarker of prenatal testosterone exposure (finger digit ratios) moderated the effect. However, empirical support for the relationship has relied on small-sample studies with mixed evidence. We investigate the reliability and generalizability of the relationship in two large-scale double-blind placebo-controlled experiments in young men (N=243 and N=400), using two different testosterone administration protocols. We find no evidence that cognitive empathy is impaired by testosterone administration or associated with digit ratios. With an unprecedented combined sample size, these results counter current theories and previous high-profile reports, and demonstrate that previous investigations of this topic have been statistically underpowered.

biorxiv neuroscience 200-500-users 2019

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome, bioRxiv, 2019-01-13

AbstractThe major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.

biorxiv genomics 200-500-users 2019