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 2019Single-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 2019Tumor mutational landscape is a record of the pre-malignant state, bioRxiv, 2019-01-12
Chromatin structure has a major influence on the cell-specific density of somatic mutations along the cancer genome. Here, we present a pan-cancer study in which we searched for the putative cancer cell-of-origin of 2,550 whole genomes, representing 32 cancer types by matching their mutational landscape to the regional patterns of chromatin modifications ascertained in 104 normal tissue types. We found that, in almost all cancer types, the cell-of-origin can be predicted solely from their DNA sequences. Our analysis validated the hypothesis that high-grade serous ovarian cancer originates in the fallopian tube and identified distinct origins of breast cancer subtypes. We also demonstrated that the technique is equally capable of identifying the cell-of-origin for a series of 2,044 metastatic samples from 22 of the tumor types available as primaries. Moreover, cancer drivers, whether inherited or acquired, reside in active chromatin regions in the respective cell-of-origin. Taken together, our findings highlight that many somatic mutations accumulate while the chromatin structure of the cell-of-origin is maintained and that this historical record, captured in the DNA, can be used to identify the often elusive cancer cell-of-origin.
biorxiv genomics 100-200-users 2019Chloroplasts navigate towards the pathogen interface to counteract infection by the Irish potato famine pathogen, bioRxiv, 2019-01-10
Chloroplasts are light harvesting organelles that arose from ancient endosymbiotic cyanobacteria. Upon immune activation, chloroplasts switch off photosynthesis, produce anti-microbial compounds, and develop tubular extensions called stromules. We report that chloroplasts navigate to the pathogen interface to counteract infection by the Irish potato famine pathogen Phytophthora infestans, physically associating with the specialised membrane that engulfs pathogen haustoria. Outer envelope protein, chloroplast unusual positioning1 (CHUP1), anchors chloroplasts to the host-pathogen interface. Stromules are induced during infection in a CHUP1-dependent manner, embracing haustoria and interconnecting chloroplasts, to form dynamic organelle clusters. Infection-triggered reprogramming of chloroplasts relies on surface immune signalling, whereas pathogen effectors subvert these immune pulses. Chloroplast are deployed focally, and coordinate to restrict pathogen entry into plant cells, a process actively countered by parasite effectors.
biorxiv plant-biology 100-200-users 2019Multiplexed electron microscopy by fluorescent barcoding allows screening for ultrastructural phenotype, bioRxiv, 2019-01-09
Genetic screens performed using high-throughput fluorescent microscopes have generated large datasets that have contributed many insights into cell biology. However, such approaches typically cannot tackle questions requiring knowledge of ultrastructure below the resolution limit of fluorescent microscopy. Electron microscopy (EM) is not subject to this resolution limit, generating detailed images of cellular ultrastructure, but requires time consuming preparation of individual samples, limiting its throughput. Here we overcome this obstacle and describe a robust method for screening by high-throughput electron microscopy. Our approach uses combinations of fluorophores as barcodes to mark the genotype of each cell in mixed populations, and correlative light and electron microscopy to read the fluorescent barcode of each cell before it is imaged by electron microscopy. Coupled with an easy-to-use software workflow for correlation, segmentation and computer image analysis, our method allows to extract and analyze multiple cell populations from each EM sample preparation. We demonstrate the method on several organelles with samples that each contain up to 15 different yeast variants. The methodology is not restricted to yeast, can be scaled to higher-throughput, and can be utilized in multiple ways to enable electron microscopy to become a powerful screening methodology.
biorxiv cell-biology 100-200-users 2019