Biology subjects

Chen, D.

Publications and source records attributed to Chen, D..

At least 415 records · Page 23Linked to original sources

bioRxiv2019

Comparative identification of microRNAs in Apis cerana cerana workers'midguts responding to Nosema ceranae invasion

MicroRNAs (miRNAs) are endogenous small noncoding RNAs that post transcriptionally regulate gene expression and are involved in many biological processes including host-pathogen interactions. However, the potential role of miRNAs in the responses of eastern honeybees to Nosema ceranae invasion is completely unknown. Here, the expression profiles and differentially expressed miRNAs (DEmiRNAs) in the midguts of Apis cerana cerana workers 7 and 10 days post infection (dpi) with N. ceranae were investigated via small RNA sequencing and bioinformatics. In total, 529 miRNAs highly conserved between various species and 25 novel miRNAs with varied expressions were identified for the first time. In addition, stem-loop RT-PCR confirmed the expression of 16 predicted miRNAs, validating their existence. Eight up-regulated miRNAs and six down-regulated miRNAs were detected in midguts at 7 dpi, while nine and three miRNAs were significantly up-regulated and down-regulated, respectively, in midguts at 10 dpi. In addition, Venn analysis showed that five DEmiRNAs were shared, while nine and seven DEmiRNAs were specifically expressed in midguts at 7 and 10 dpi, respectively. Gene ontology analysis suggested that a portion of the DEmiRNAs and corresponding target genes were involved in various biological processes, cellular components, and molecular functions including immune system processes and response to stimulus and signaling. Moreover, KEGG pathway analysis shed light on the potential functions of some DEmiRNAs in the regulation of target genes engaged in material and energy metabolism, cellular immunity such as endocytosis and phagosome, and the humoral immune system, including the Jak-STAT and MAPK signaling pathways. Further investigation demonstrated a complex regulation network between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x and miR-3654-y at the center of the network, implying their key parts in host responses. This comprehensive miRNA transcriptome analysis demonstrated that N. ceranae invasion influenced the expression of miRNAs in the midguts of A. c. ceranae workers; the results can not only facilitate future exploration of the regulatory roles and mechanisms of miRNAs in hosts responses, especially their immune responses to N. ceranae, but also provide potential candidates for further investigation of the molecular mechanisms underlying eastern honeybee-microsporidian interactions.

bioinformatics↗

bioRxiv2019

Multi-locus characterization and phylogenetic inference of Leishmania spp. in snakes from Northwest China

BackgroundLeishmaniasis caused by protozoan parasite Leishmania is a neglected disease which is endemic in the northwest of China. Reptiles were considered to be the potential reservoir hosts for mammalian Leishmaniasis, and Leishmania had been detected in lizards from the epidemic area in the northwest of China. To date, few studies are focused on the natural infection of snakes with Leishmania.\n\nMethodsIn this study, 15 snakes captured from 10 endemic foci in the northwest of China were detected Leishmania spp. on the base of mitochondrial cytochrome b, heat shock protein 70 gene and ribosomal internal transcribed spacer 1 regions, and identified with phylogenetic and network analyses.\n\nResultIn total, Leishmania gene was found in 7 snakes. The phylogenetic inference trees and network analysis suggests that the species identification was confirmed as Leishmania donovani, Leishmania turanica and Leishmania sp.\n\nConclusionOur work is the first time to investigate the natural Leishmania spp. infection of snakes in the northwest of China. Mammalian Leishmania was discovered in snakes and the reptilian Leishmania was closely related to the clinical strains both prompt the importance of snakes in the disease cycle. To indicate the epidemiological involvement of snakes, a wide sample size in epidemic area and the pathogenic features of reptilian Leishmania promastigotes are recommended in the future research.

evolutionary biology↗

bioRxiv2018

Coding advantage of grid cell orientation under noisy conditions

Grid cells constitute a crucial component of the \"GPS\" in the mammalian brain. Recent experiments revealed that grid cell activity is anchored to environmental boundaries. More specifically, these results revealed a slight yet consistent offset of 8 degrees relative to boundaries of a square environment. The causes and possible functional roles of this orientation are still unclear. Here we propose that this phenomenon maximizes the spatial information conveyed by grid cells. Computer simulations of the grid cell network reveal that the universal grid orientation at 8 degrees optimizes spatial coding specifically in the presence of noise. Our model also predicts the minimum number of grid cells in each module. In addition, analytical results and a dynamical reinforcement learning model reveal the mechanism underlying the noise-induced orientation preference at 8 degrees. Together, these results suggest that the experimentally observed common orientation of grid cells serves to maximize spatial information in the presence of noise.\n\nAuthor summarySpatial navigation depends on several specialized cell types including place and grid cells. Grid cells have multiple firing fields that are arranged in a regular hexagonal pattern. The axes of this pattern are anchored to environmental boundaries at a universal angle of 8{degrees}. Here, we combine computer simulations of the grid cell network with analytical derivations and a reinforcement learning model to explain the functional relevance of this universal grid cell orientation. We show that spatial information provided by grid cells is maximized at the experimentally observed grid orientation within a broad parameter range. This relationship occurs only in the presence of noise. The model allows for several experimentally testable predictions including the number of grid cells.

neuroscience↗

bioRxiv2018

Whole-tree heartwood inducing technique for Dalbergia odorifera

The dried heartwood of Dalbergia odorifera is a very important traditional Chinese medicine. In nature, D. odorifera heartwood forms slowly over several decades, and excessive harvesting has caused large-scale reductions of its wild populations. To date, there have been no studies on artificial methods to induce heartwood formation in trees that have not already begun producing heartwood. We have published a patent for a whole-tree heartwood inducing technique for D. odorifera (the \"Dodor-Wit\" method); here, we describe and analyze its efficacy. Trees in four plantations in China were treated using this method. After two years, in 2016 and 2017, they were harvested and analyzed. Average heartwood yield per tree was 3,161.95 g. Heartwood induction rate (dry heartwood weight to total dry trunk weight after peeling) was 21.60%. Average volatile oil content per tree was 1.42%. Alcohol-soluble extract of the induced heartwood was 15.77%, exceeding the Chinese Pharmacopoeia standard. This is the first report on the Dodor-Wit method and heartwood induction in D. odorifera trees aged 5-8 years. The heartwood induced by Dodor-Wit satisfies the requirements of the Chinese Pharmacopoeia. The Dodor-Wit method has an important role in solving the extreme scarcity of Chinese medicinal herbs.

plant biology↗

bioRxiv2018

The α-tubulin of Laodelphax striatellus facilitates the passage of rice stripe virus (RSV) and enhances horizontal transmission

Rice stripe virus (RSV), causal agent of rice stripe disease, is transmitted by the small brown planthopper (SBPH, Laodelphax striatellus) in a persistent manner. The midgut and salivary glands of SBPH are the first and last barriers in viral circulation and transmission, respectively; however, the precise mechanisms used by RSV to cross these organs and re-inoculate rice have not been fully elucidated. We obtained full-length cDNA of L. striatellus -tubulin 2 (LsTUB) and found that RSV infection increased the level of LsTUB in vivo. Furthermore, LsTUB was shown to bind the RSV nonstructural protein 3 (NS3) in vitro. RNAi was used to reduce LsTUB expression, which caused a significant reduction in RSV titer, NS3 expression, RSV inoculation rates, and transmission to healthy plants. Electrical penetration graphs (EPG) showed that LsTUB knockdown by RNAi did not impact SBPH feeding; therefore, the reduction in RSV inoculation rate was likely caused by the decrease in RSV transmission. These findings suggest that LsTUB mediates the passage of RSV through midgut and salivary glands and leads to successful horizontal transmission.

pathology↗

bioRxiv2018

Oxytocin involves in chronic stress-evoked melanoma metastasis via β-arrestin 2 mediated-pathways

Stress is associated with an increased risk of lung metastasis in melanoma. However, the underlying mechanism is elusive. Oxytocin (OXT), a neurohormone produced by the hypothalamus, plays a vital role in laboring induction and lactation. Emerging evidence suggests that OXT also regulates human emotions, social cognition, social behaviors and stress-related disorders. Here, we reported that a significant up-regulation of oxytocin receptors (OXTRs) was observed in malignant melanoma. The activation of oxytocin receptors (OXTRs) dramatically promoted migration, invasion and angiogenesis but not the proliferation of melanoma cells in vitro and in vivo via {beta}-arrestin 2-dependent ERK-VEGF/ MMP-2 pathway. Next, chronic restraint stress significantly elevated the plasma level of OXT. Notably, 21 days chronic restraint stress facilitated lung metastasis of melanoma and reduced overall survival in mice, which were largely abrogated by knocking down either OXTR or {beta}-arrestin 2. These findings provide evidence that chronic stress hormone-OXT promotes lung metastasis of melanoma via a {beta}-arrestin 2-dependent mechanism and suggest that OXT, a novel pro-metastasis factor, is a potential therapeutic target for melanoma.\n\nImportance of the StudyOxytocin, a neuropeptide produced in the hypothalamus that is involved in lactation and parturition, play a vital role in chronic stress-evoked melanoma metastasis via {beta}-arrestin 2-mediated ERK signaling pathway, which provides a potential therapeutic target for melanoma.

cancer biology↗

bioRxiv2018

Construction of a germline-specific RNAi tool in C. elegans

Analysis of complex biological functions usually requires tissue-specific genetic manipulations in multicellular organisms. The C. elegans germline plays regulatory roles not only in reproduction, but also in metabolism, stress response and aging. Previous studies have used mutants of rrf-1, which encodes an RNA-directed RNA polymerase, as a germline-specific RNAi tool. However, the rrf-1 mutants showed RNAi efficiency in somatic tissues. Here we constructed a germline-specific RNAi strain by combining an indel mutation of rde-1, which encodes an Argonaute protein that functions cell autonomously to ensure RNAi efficiency, and a single-copy rde-1 transgene driven by the sun-1 germlinespecific promoter. The germline RNAi efficiency and specificity are confirmed by RNAi phenocopy of known mutations, knockdown of GFP reporter expression, as well as quantitative RT-PCR measurement of tissue-specific mRNAs upon RNAi knockdown. The germline-specific RNAi strain shows no obvious deficiencies in reproduction, lipid accumulation, thermo-tolerance and life span compared to wild-type animals. By screening an RNAi sub-library of phosphatase genes, we identified novel regulators of thermo-tolerance. Together, we have created a useful tool that can facilitate the genetic analysis of germline-specific functions in C. elegans.

genetics↗

bioRxiv2018

The mitochondrial DNA content can not predict the embryo viability

ObjectiveTo investigate whether the mitochondrial DNA content could predict the embryo viability\n\nDesignRetrospective analysis.\n\nSettingReproductive genetics laboratory\n\nPatient(s)A total of 421 biopsied samples obtained from 129 patients\n\nIntervention(s)Embryo biopsies samples underwent whole genome amplification (WGA) and were tested by next generation sequencing (NGS) and array Comparative Genomic Hybridization (aCGH), 30 samples were selected randomly to undergo quantitative real-time polymerase chain reaction (qPCR).\n\nMain Outcome Measure(s)Those embryos which obtained the consistent chromosome status determined both aCGH and NGS platform were further classified. We investigated the relationship of mtDNA content with several factors including female patient age, embryo morphology, chromosome status, and live birth rate of both blastocysts and blastomeres.\n\nResult(s)A total of 386 (110 blastomeres and 276 blastocysts) out of 399 embryos showed consistent chromosome status outcome. We found no statistically difference was observed in aneuploid and euploid blastocysts (p=0.14), the same phenomenon was observed in aneuploid and euploid blastomeres (p=0.89). Similarly, the mtDNA content was independent of female patient age, embryo morphology and live birth rate.\n\nConclusion(s)The mtDNA content did not provide a reliable prediction of the viability of blastocysts to initiate a pregnancy.

ecology↗

bioRxiv2018

Metatranscriptome profiling of the dynamic transcription of mRNA and sRNA of a probiotic Lactobacillus strain in human gut

Metatranscriptomic sequencing has recently been applied to study how pathogens and probiotics affect human gastrointestinal (GI) tract microbiota, which provides new insights into their mechanisms of action. In this study, metatranscriptomic sequencing was applied to deduce the in vivo expression patterns of an ingested Lactobacillus casei strain, which was compared with its in vitro growth transcriptomes. Extraction of the strain-specific reads revealed that transcripts from the ingested L. casei were increased, while those from the resident L. paracasei strains remained unchanged. Mapping of all metatranscriptomic reads and transcriptomic reads to L. casei genome showed that gene expression in vitro and in vivo differed dramatically. About 39% (1163) mRNAs and 45% (93) sRNAs of L. casei well-expressed were repressed after ingested into human gut. Expression of ABC transporter genes and amino acid metabolism genes was induced at day-14 of ingestion; and genes for sugar and SCFA metabolisms were activated at day-28 of ingestion. Moreover, expression of sRNAs specific to the in vitro log phase was more likely to be activated in human gut. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in human gut; this sRNA repressed L. casei growth and lactic acid production in vitro. These findings implicate that the ingested L. casei might have to successfully change its transcription patterns to survive in human gut, and the time-dependent activation patterns indicate a highly dynamic cross-talk between the probiotic and human gut including its microbe community.\n\nImportanceProbiotic bacteria are important in food industry and as model microorganisms in understanding bacterial gene regulation. Although probiotic functions and mechanisms in human gastrointestinal tract are linked to the unique probiotic gene expression, it remains elusive how transcription of probiotic bacteria is dynamically regulated after being ingested. Previous study of probiotic gene expression in human fecal samples has been restricted due to its low abundance and the presence of of closely related species. In this study, we took the advantage of the good depth of metatranscriptomic sequencing reads and developed a strain-specific read analysis method to discriminate the transcription of the probiotic Lactobacillus casei and those of its resident relatives. This approach and additional bioinformatics analysis allowed the first study of the dynamic transcriptome profiles of probiotic L casei in vivo. The novel findings indicate a highly regulated repression and dynamic activation of probiotic genome in human GI tract.

microbiology↗

bioRxiv2018

Cdc42 negatively regulates endocytosis during apical plasma membrane maintenance and development in mouse tubular organs in vivo

Lumen establishment and maintenance are fundamental for tubular organs physiological functions. Most of the studies investigating the mechanisms regulating this process have been carried out in cell cultures or in smaller organisms, whereas little has been done in mammalian model systems in vivo. Here we used the salivary glands of live mice to examine the role of the small GTPase Cdc42 in the regulation of the homeostasis of the intercellular canaliculi, a specialized apical domain of the acinar cells, where protein and fluid secretion occur. Depletion of Cdc42 in adult mice induced a significant expansion of the apical canaliculi, whereas depletion at late embryonic stages resulted in a complete inhibition of their post-natal formation. In addition, intravital subcellular microscopy revealed that reduced levels of Cdc42 affected membrane trafficking from and towards the plasma membrane, highlighting a novel role for Cdc42 in membrane remodeling through the negative regulation of selected endocytic pathways.

cell biology↗

bioRxiv2018

Opposing effects of prostaglandin receptor EP2 signaling in mouse immune cells and neurons after status epilepticus

A multidimensional inflammatory response ensues after status epilepticus (SE), driven partly by cyclooxygenase-2 mediated activation of prostaglandin EP2 receptors. Here we identify those effects of EP2 antagonism that are reproduced by conditional ablation of EP2 receptors in immune myeloid cells and forebrain neurons. Removal of myeloid cell EP2 dampened induction of hippocampal IL-6, prevented erosion of the blood-brain barrier, accelerated weight regain, and relieved ptosis following SE. Elimination of EP2 receptor from neurons enhanced neuronal injury, elevated hippocampal induction of the pro-inflammatory cytokines, TNF and Ccl2, promoted deterioration of the blood-brain barrier, delayed weight recovery, and worsened animal posture and activity. Taken together these data highlight the complexities in neuroinflammatory signaling, wherein activation of EP2 receptors in innate immune cells is deleterious but neuronal EP2 signaling is protective. Effective treatments targeting brain prostaglandin signaling pathways should be cell targeted to be optimally effective.\n\nSignificance StatementSeizures reduce quality of life, promote the development of epilepsy, and can be fatal. We previously identified inflammation, via prostaglandin receptor EP2 activation, as a driver of undesirable seizure-induced effects. However, the relevant EP2-expressing cell types remain unclear. We identify innate immune cells as a driver of the EP2-related negative consequences of seizures, whereas neuronal EP2 signaling is protective. Genetic removal of EP2 from immune cells was beneficial, accelerating weight gain and limiting behavioral deficits. Elimination of EP2 from neurons was harmful, worsening behavioral deficits and promoting neuronal damage. These findings enhance our understanding of the complex inflammatory processes engaged after seizures and will assist in the development of beneficial therapies to enhance quality of life in individuals susceptible to seizures.

neuroscience↗

bioRxiv2018

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation

BackgroundInvestigating cell fate decision and subpopulation specification in the context of the neural lineage is fundamental to understanding neurogenesis and neurodegenerative diseases. The differentiation process of neural-tube-like rosettes in vitro is representative of neural tube structures, which are composed of radially organized, columnar epithelial cells and give rise to functional neural cells. However, the underlying regulatory network of cell fate commitment during early neural differentiation remains elusive.\n\nResultsIn this study, we investigated the genome-wide transcriptome profile of single cells from six consecutive reprogramming and neural differentiation time points and identified cellular subpopulations present at each differentiation stage. Based on the inferred reconstructed trajectory and the characteristics of subpopulations contributing the most towards commitment to the central nervous system (CNS) lineage at each stage during differentiation, we identified putative novel transcription factors in regulating neural differentiation. In addition, we dissected the dynamics of chromatin accessibility at the neural differentiation stages and revealed active c/s-regulatory elements for transcription factors known to have a key role in neural differentiation as well as for those that we suggest are also involved. Further, communication network analysis demonstrated that cellular interactions most frequently occurred among embryoid body (EB) stage and each cell subpopulation possessed a distinctive spectrum of ligands and receptors associated with neural differentiation which could reflect the identity of each subpopulation.\n\nConclusionsOur study provides a comprehensive and integrative study of the transcriptomics and epigenetics of human early neural differentiation, which paves the way for a deeper understanding of the regulatory mechanisms driving the differentiation of the neural lineage.

developmental biology↗

bioRxiv2018

NudCL2 is an Hsp90 cochaperone to regulate sister chromatid cohesion by stabilizing cohesin subunits

Sister chromatid cohesion plays a key role in ensuring precise chromosome segregation during mitosis, which is mediated by the multisubunit complex cohesin. However, the molecular regulation of cohesin subunits stability remains unclear. Here, we show that NudCL2 (NudC-like protein 2) is essential for the stability of cohesin subunits by regulating Hsp90 ATPase activity in mammalian cells. Depletion of NudCL2 induces mitotic defects and premature sister chromatid separation and destabilizes cohesin subunits that interact with NudCL2. Similar defects are also observed upon inhibition of Hsp90 ATPase activity. Interestingly, ectopic expression of Hsp90 efficiently rescues the protein instability and functional deficiency of cohesin induced by NudCL2 depletion, but not vice versa. Moreover, NudCL2 not only binds to Hsp90, but also significantly modulates Hsp90 ATPase activity and promotes the chaperone function of Hsp90. Taken together, these data suggest that NudCL2 is a previously undescribed Hsp90 cochaperone to modulate sister chromatid cohesion by stabilizing cohesin subunits, providing a hitherto unrecognized mechanism that is crucial for faithful chromosome segregation during mitosis.

cell biology↗

bioRxiv2018

Genome-wide CNV study and functional evaluation identified CTDSPL as tumour suppressor gene for cervical cancer

We have investigated copy number variations (CNVs) in relation to cervical cancer by analyzing 731,422 single-nucleotide polymorphisms (SNPs) in 1,034 cervical cancer cases and 3,948 controls, followed by replication in 1,396 cases and 1,057 controls. We found that a 6367bp deletion in intron 1 of the CTD small phosphatase like gene (CTDSPL) was associated with 2.54-fold increased risk of cervical cancer (odds ratio =2.54, 95% confidence interval =2.08-3.12, P=2.0x10-19). This CNV is one of the strongest genetic risk variants identified so far for cervical cancer. The deletion removes the binding sites of zinc finger protein 263, binding protein 2 and interferon regulatory factor 1, and hence downregulates the transcription of CTDSPL. HeLa cells expressing CTDSPL showed a significant decrease in colony-forming ability. Compared with control groups, mice injected with HeLa cells expressing CTDSPL exhibited a significant reduction in tumour volume. Furthermore, CTDSPL-depleted immortalized End1/E6E7 could form tumours in NOD-SCID mice.

cancer biology↗

bioRxiv2018

Co-outbreak of ST37 and a novel ST3006 Klebsiella pneumoniae from multi-site infection in a neonatal intensive care unit, Fuzhou, China

BackgroundThe outbreak of carbapenems resistant Klebsiella pneumoniae (K. pneumoniae) is a serious public health problem, especially in the neonatal intensive care unit (NICU).\n\nMethodsFifteen strains of K. pneumoniae were isolated from seven neonates during June 3-28, 2017 in a NICU. Antimicrobial susceptibility was determined by the Vitek 2 system and micro-broth dilution method. Multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were used to analyse the genetic relatedness of isolates. Genome sequencing and gene function analyses were performed for investigating pathogenicity and drug resistance and screening genomic islands.\n\nFindingsTwo K. pneumoniae clones were identified from seven neonates, one ST37 strain and another new sequence type ST3006. The ST37 strain exhibited multi-drug resistance genes and resistance to carbapenem. MLST and PFGE showed that 15 strains were divided into three groups, with a high level of homology. Gene sequencing and analysis indicated that KPN1343 harboured 12 resistance genes, 15 genomic islands and 205 reduced virulence genes. KPN1344 harboured four resistance genes, 19 genomic islands and 209 reduced virulence genes.\n\nConclusionCo-outbreak of K. pneumoniae involved two clones, ST36 and ST3006, causing multi-site infection. Genome sequencing and analysis is an effective method for studying bacterial resistance genes and their functions.

microbiology↗

bioRxiv2018

Native tau structure is disrupted by disease-associated mutations that promote aggregation

Tauopathies are neurodegenerative diseases characterized by intracellular amyloid deposits of tau protein. Missense mutations in the tau gene (MAPT) correlate with aggregation propensity and cause dominantly inherited tauopathies, but their biophysical mechanism driving amyloid formation is poorly understood. Many disease-associated mutations localize within taus repeat domain at inter-repeat interfaces proximal to amyloidogenic sequences, such as 306VQIVYK311. Using cross-linking mass spectrometry, intramolecular FRET, recombinant protein and synthetic peptide systems, in silico modeling, and cell models, we conclude that the aggregation prone 306VQIVYK311 motif forms metastable compact structures with the upstream sequence that modulates aggregation propensity. Disease-associated mutations, isomerization of a critical proline, or alternative splicing are all sufficient to destabilize this local structure and trigger spontaneous aggregation. These findings provide a biophysical framework to explain the basis of early conformational changes that may underlie genetic and sporadic tau pathogenesis.

biophysics↗

bioRxiv2018

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

Integrative analysis of multi-omics layers at single cell level is critical for accurate dissection of cell-to-cell variation within certain cell populations. Here we report scCAT-seq, a technique for simultaneously assaying chromatin accessibility and the transcriptome within the same single cell. We show that the combined single cell signatures enable accurate construction of regulatory relationships between cis-regulatory elements and the target genes at single-cell resolution, providing a new dimension of features that helps direct discovery of regulatory patterns specific to distinct cell identities. Moreover, we generated the first single cell integrated maps of chromatin accessibility and transcriptome in human pre-implantation embryos and demonstrated the robustness of scCAT-seq in the precise dissection of master transcription factors in cells of distinct states during embryo development. The ability to obtain these two layers of omics data will help provide more accurate definitions of \"single cell state\" and enable the deconvolution of regulatory heterogeneity from complex cell populations.

genomics↗

bioRxiv2018

Single tube bead-based DNA co-barcoding for cost effective and accurate sequencing, haplotyping, and assembly

Obtaining accurate sequences from long DNA molecules is very important for genome assembly and other applications. Here we describe single tube long fragment read (stLFR), a technology that enables this a low cost. It is based on adding the same barcode sequence to sub-fragments of the original long DNA molecule (DNA co-barcoding). To achieve this efficiently, stLFR uses the surface of microbeads to create millions of miniaturized barcoding reactions in a single tube. Using a combinatorial process up to 3.6 billion unique barcode sequences were generated on beads, enabling practically non-redundant co-barcoding with 50 million barcodes per sample. Using stLFR, we demonstrate efficient unique co-barcoding of over 8 million 20-300 kb genomic DNA fragments. Analysis of the genome of the human genome NA12878 with stLFR demonstrated high quality variant calling and phasing into contigs up to N50 34 Mb. We also demonstrate detection of complex structural variants and complete diploid de novo assembly of NA12878. These analyses were all performed using single stLFR libraries and their construction did not significantly add to the time or cost of whole genome sequencing (WGS) library preparation. stLFR represents an easily automatable solution that enables high quality sequencing, phasing, SV detection, scaffolding, cost-effective diploid de novo genome assembly, and other long DNA sequencing applications.

genomics↗