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  • SINGLe: Accurate detection of single nucleotide polymorphisms using nanopore sequencing in gene libraries
    bioRxiv. Genom. Pub Date : 2020-06-01
    Rocio Espada; Nikola Zarevski; Adele Drame-Maigne; Yannick Rondelez

    Nanopore sequencing is a powerful single molecule DNA sequencing technology which offers high throughput and long sequence reads. Nevertheless, its high native error rate limits the direct detection of point mutations in individual reads of amplicon libraries, as these mutations are difficult to distinguish from the sequencing noise. In this work, we developed SINGLe (SNPs In Nanopore reads of Gene

    更新日期:2020-06-01
  • Direct detection of RNA modifications and structure using single molecule nanopore sequencing
    bioRxiv. Genom. Pub Date : 2020-06-01
    William Stephenson; Roham Razaghi; Steven Busan; Kevin M. Weeks; Winston Timp; Peter Smibert

    Many methods exist to detect RNA modifications by short-read sequencing, relying on either antibody enrichment of transcripts bearing modified bases or mutational profiling approaches which require conversion to cDNA. Endogenous modifications are present on several major classes of RNA including tRNA, rRNA and mRNA and can modulate diverse biological processes such as genetic recoding, mRNA export

    更新日期:2020-06-01
  • TMEM106B and CPOX are genetic determinants of cerebrospinal fluid Alzheimer's disease biomarker levels
    bioRxiv. Genom. Pub Date : 2020-06-01
    Shengjun Hong; Valerija Dobricic; Isabelle Bos; Stephanie J. B. Vos; Dmitry Prokopenko; Betty M. Tijms; Ulf Andreasson; Kaj Blennow; Rik Vandenberghe; Silvy Gabel; Philip Scheltens; Charlotte E. Teunissen; Sebastiaan Engelborghs; Giovanni Frisoni; Olivier Blin; Jill C. Richardson; Regis Bordet; Alberto Lleo; Daniel Alcolea; Julius Popp; Christopher Clark; Gwendoline Peyratout; Pablo Martinez-Lage;

    Background: Neurofilament light (NF-L), chitinase-3-like protein 1 (YKL-40), and neurogranin (Ng) are utilized as biomarkers for Alzheimer's disease (AD), to monitor axonal damage, astroglial activation, and synaptic degeneration, respectively. Here we performed genome-wide association study (GWAS) analyses using all three biomarkers as outcome. Methods: DNA and cerebrospinal fluid (CSF) samples originated

    更新日期:2020-06-01
  • Peripheral blood microbial signatures in COPD
    bioRxiv. Genom. Pub Date : 2020-06-01
    Jarrett D Morrow; Peter J Castaldi; Robert P Chase; Jeong H Yun; Sool Lee; Yang-Yu Liu; Craig P Hersh; COPDGene Investigators

    Background: The human microbiome has a role in the development of human diseases. Individual microbiome profiles are highly personalized, though many species are shared. Understanding the relationship between the human microbiome and disease may inform future individualized treatments. Specifically, the blood microbiome, once believed sterile, may be a surrogate for some lung and gut microbial characteristics

    更新日期:2020-06-01
  • Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene
    bioRxiv. Genom. Pub Date : 2020-06-01
    Ildem Akerman; Miguel Angel Maestro; Vanessa Grau; Gerhard Mittler; Javier Garcia Hurtado; Philippe Ravassard; Lorenzo Piemonti; Jorge Ferrer

    Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their endogenous genomic location. This poses major limitations to understand the true consequences of causal regulatory variants. We focused on a cis-regulatory mutation (c.-331C>G) in the INS gene promoter that is recurrently mutated in unrelated patients with recessive

    更新日期:2020-06-01
  • LINE elements are a reservoir of regulatory potential in mammalian genomes
    bioRxiv. Genom. Pub Date : 2020-05-31
    Maša Roller; Ericca Stamper; Diego Villar; Osagie Izuogu; Fergal Martin; Aisling Redmond; Raghavendra Ramachanderan; Louise Harewood; Duncan T Odom; Paul Flicek

    To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in liver, brain, muscle, and testis from ten diverse mammals. The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching

    更新日期:2020-05-31
  • A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates
    bioRxiv. Genom. Pub Date : 2020-05-31
    Sofia Banu; Bani Jolly; Payel Mukherjee; Priya Singh; Shagufta Khan; Lamuk Zaveri; Sakshi Shambhavi; Namami Gaur; Rakesh K Mishra; Vinod Scaria; Divya Tej Sowpati

    From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed

    更新日期:2020-05-31
  • Interactions between the microbiome and mating influence the female's transcriptional profile in Drosophila melanogaster
    bioRxiv. Genom. Pub Date : 2020-05-31
    Sofie Y.N. Delbare; Yasir H Ahmed-Braimah; Mariana F. Wolfner; Andrew G. Clark

    Drosophila melanogaster females undergo a variety of post-mating changes that influence their activity, feeding behavior, metabolism, egg production and gene expression. These changes are induced either by mating itself or by sperm or seminal fluid proteins. In addition, studies have shown that axenic females (those lacking a microbiome) have altered fecundity compared to females with a microbiome

    更新日期:2020-05-31
  • A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina
    bioRxiv. Genom. Pub Date : 2020-05-31
    Guillermo Friis; Joel Vizueta; David R. Nelson; Basel Khraiwesh; Enas Qudeimat; Kourosh Salehi-Ashtiani; Alejandra Ortega; Alyssa Marshell; Carlos M. Duarte; John A. Burt

    The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied,

    更新日期:2020-05-31
  • Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver
    bioRxiv. Genom. Pub Date : 2020-05-31
    Ullas V. Chembazhi; Sushant Bangru; Mikel Hernaez; Auinash Kalsotra

    The adult liver has exceptional ability to regenerate, but how it sustains normal metabolic activities during regeneration remains unclear. Here, we use partial hepatectomy (PHx) in tandem with single-cell transcriptomics to track cellular transitions and heterogeneities of ~22,000 liver cells through the initiation, progression, and termination phases of mouse liver regeneration. Our results reveal

    更新日期:2020-05-31
  • Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators
    bioRxiv. Genom. Pub Date : 2020-05-31
    Cheng Sun; Jiaxing Huang; Yun Wang; Xiaomeng Zhao; Long Su; Gregg W.C. Thomas; Mengya Zhao; Xingtan Zhang; Irwin Jungreis; Manolis Kellis; Saverio Vicario; Igor V. Sharakhov; Semen M. Bondarenko; Martin Hasselmann; Chang N. Kim; Benedict Paten; Luca Penso-Dolfin; Li Wang; Yuxiao Chang; Qiang Gao; Ling Ma; Lina Ma; Zhang Zhang; Hongbo Zhang; Huahao Zhang; Livio Ruzzante; Hugh M. Robertson; Yihui Zhu;

    Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage

    更新日期:2020-05-31
  • The Caribbean-Hispanic Alzheimer's Brain Transcriptome Reveals Ancestry-Specific Disease Mechanisms
    bioRxiv. Genom. Pub Date : 2020-05-31
    Daniel Felsky; Sanjeev Sariya; Ismael Santa-Maria; Julie A Schneider; David A Bennett; Richard P Mayeux; Phillip L De Jager; Giuseppe Tosto

    Ethnicity impacts Alzheimer's disease risk, especially among Caribbean-Hispanics. We report the first RNA-sequencing analysis of brain tissue from 45 Alzheimer's disease and control Caribbean-Hispanics. Data were compared with two independent samples of non-Hispanic Caucasians (total n=729). By identifying and characterizing those genes with ancestry- and region-specific expression patterns in Alzheimer's

    更新日期:2020-05-31
  • Epigenome dysregulation resulting from NSD1 mutation in head and neck squamous cell carcinoma
    bioRxiv. Genom. Pub Date : 2020-05-31
    Nargess Farhangdoost; Cynthia Horth; Bo Hu; Eric Bareke; Xiao Chen; Yinglu Li; Mariel Coradin; Benjamin A. Garcia; Chao Lu; Jacek Majewski

    Epigenetic dysregulation has emerged as an important mechanism of oncogenesis. To develop targeted treatments, it is important to understand the epigenetic and transcriptomic consequences of mutations in epigenetic modifier genes. Recently, mutations in the histone methyltransferase gene NSD1 have been identified in a subset of head and neck squamous cell carcinomas (HNSCCs)-- one of the most common

    更新日期:2020-05-31
  • The genome sequence of Aloe vera reveals adaptive evolution of drought tolerance mechanisms
    bioRxiv. Genom. Pub Date : 2020-05-31
    Shubham K. Jaiswal; Abhisek Chakraborty; Shruti Mahajan; Sudhir Kumar; Vineet K Sharma

    Aloe vera is a species from Asphodelaceae plant family having unique characteristics such as drought resistance and also possesses numerous medicinal properties. However, the genetic basis of these phenotypes is yet unknown, primarily due to the unavailability of its genome sequence. In this study, we report the first Aloe vera draft genome sequence comprising of 13.83 Gbp and harboring 86,177 coding

    更新日期:2020-05-31
  • Multi-ancestry genome-wide gene-sleep interactions identify novel loci for blood pressure
    bioRxiv. Genom. Pub Date : 2020-05-31
    Heming Wang; Raymond Noordam; Brian E Cade; Karen Schwander; Thomas W Winkler; Jiwon Lee; Yun Ju Sung; Amy R Bentley; Alisa K Manning; Hugues Aschard; Tuomas O Kilpelainen; Marjan Ilkov; Michael R Brown; Andrea R Horimoto; Melissa Richard; Traci M Bartz; Dina Vojinovic; Elise Lim; Jovia L Nierenberg; Yongmei Liu; Kumaraswamynaidu Chitrala; Tuomo Rankinen; Solomon K Musani; Nora Franceschini; Rainer

    Long and short sleep duration are associated with elevated blood pressure (BP), possibly through effects on molecular pathways that influence neuroendocrine and vascular systems. To gain new insights into the genetic basis of sleep-related BP variation, we performed genome-wide gene by short or long sleep duration interaction analyses on four BP traits (systolic BP, diastolic BP, mean arterial pressure

    更新日期:2020-05-31
  • Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph
    bioRxiv. Genom. Pub Date : 2020-05-31
    Rui Martiniano; Erik Garrison; Eppie R Jones; Andrea Manica; Richard Durbin

    During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less

    更新日期:2020-05-31
  • CREBBP and STAT6 co-mutation and 16p13 and 1p36 loss define the t(14;18)-negative diffuse variant of follicular lymphoma
    bioRxiv. Genom. Pub Date : 2020-05-31
    Rena R. Xian; Yi Xie; Lisa M. Haley; Raluca Yonescu; Aparna Pallavajjala; Stefania Pittaluga; Elaine S. Jaffe; Amy S. Duffield; Chad M McCall; Shereen M. F. Gheith; Christopher D. Gocke

    The diffuse variant of follicular lymphoma (dFL) is a rare variant of FL lacking t(14;18) that was first described in 2009. In this study, we use a comprehensive approach to define unifying pathologic and genetic features through gold-standard pathologic review, FISH, SNP-microarray and next-generation sequencing of 16 cases of dFL. We found unique morphologic features, including interstitial sclerosis

    更新日期:2020-05-31
  • Efficient Representations of Tumor Diversity with Paired DNA-RNA Anomalies
    bioRxiv. Genom. Pub Date : 2020-05-31
    Qian Ke; Wikum Dinalankara; Laurent Younes; Donald Geman; Luigi Marchionni

    Cancer cells display massive dysregulation of key regulatory pathways due to now well- catalogued mutations and other DNA-related aberrations. Moreover, enormous heterogeneity has been commonly observed in the identity, frequency, and location of these aberrations across individuals with the same cancer type or subtype, and this variation naturally propagates to the transcriptome, resulting in myriad

    更新日期:2020-05-31
  • High accuracy DNA sequencing on a small, scalable platform via electrical detection of single base incorporations
    bioRxiv. Genom. Pub Date : 2020-05-30
    Hesaam Esfandyarpour; Kosar B. Parizi; Meysam Rezaei Barmi; Hamid Rategh; Lisen Wang; Saurabh Paliwal; Hamid Reza Golnabi; Paul Kenney; Richard Reel; Frank Lee; Xavier Gomes; Seth Stern; Ashok Ramachandran; Subra Sankar; Solomon Doomson; Rick Ung; Maryam Jouzi; Ramya Akula Suresh Babu; Ali Nabi; Nestor Castillo; Raymond Lei; Mohammad Fallahi; Eric LoPrete; Austin Kemper; Srijeeta Bagchi; Robert Tarbox;

    High throughput DNA sequencing technologies have undergone tremendous development over the past decade. Although optical detection-based sequencing has constituted the majority of data output, it requires a large capital investment and aggregation of samples to achieve optimal cost per sample. We have developed a novel electronic detection-based platform capable of accurately detecting single base

    更新日期:2020-05-30
  • Single-cell Transcriptomics Identifies Gene Expression Networks Driving Differentiation and Tumorigenesis in the Human Fallopian Tube
    bioRxiv. Genom. Pub Date : 2020-05-30
    Huy Q Dinh; Xianzhi Lin; Forough Abbasi; Robbin Nameki; Marcela Haro; Claire Olingy; Heidi Chang; Lourdes Hernandez; Simon Gayther; Kelly N Wright; Paul-Joseph Aspuria; Beth Karlan; Rosario I Corona; Andrew Li; BJ Rimel; Matthew Siedhoff; Fabiola Medeiros; Kate Lawrenson

    The human fallopian tube harbors the cell-of-origin for the majority of high-grade serous ovarian cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly characterized. We performed single-cell transcriptomic profiling in 12 primary fallopian specimens from 8 patients, analyzing around 53,000 individual cells to map the major immune, fibroblastic and epithelial

    更新日期:2020-05-30
  • Genomic analysis of early SARS-CoV-2 strains introduced in Mexico
    bioRxiv. Genom. Pub Date : 2020-05-30
    Blanca Taboada; Joel A. Vázquez-Pérez; Jose Esteban Muñoz-Medina; Pilar Ramos-Cervantes; Marina Escalera-Zamudio; Celia Boukadida; Alejandro Sánchez-Flores; Isa Pavel; Edgar Mendieta-Condado; José A. Martínez-Orozco; Eduardo Becerril-Vargas; Jorge Salas-Hernández; Ricardo Grande; Carolina González-Torres; Francisco J. Gaytán-Cervantes; Gloria Vázquez; Francisco Pulido; Adnan Araiza-Rodríguez; Fabiola

    The COVID-19 pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to implement effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational

    更新日期:2020-05-30
  • GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases
    bioRxiv. Genom. Pub Date : 2020-05-30
    Phillip A Richmond; Tamar V Av-Shalom; Oriol Fornes; Bhavi Modi; Wyeth W Wasserman

    Mendelian rare genetic diseases affect 5-10% of the population, and with over 5,300 genes responsible for ~7,000 different diseases, they are challenging to diagnose. The use of whole genome sequencing (WGS) for patients and families affected by rare diseases has bolstered the diagnosis rate significantly. Effective use of WGS in this setting relies on the ability to identify the ″broken″ gene responsible

    更新日期:2020-05-30
  • Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
    bioRxiv. Genom. Pub Date : 2020-05-30
    Diego Garrido-Martín; Beatrice Borsari; Miquel Calvo; Ferran Reverter; Roderic Guigó

    We have developed an efficient and reproducible pipeline for the discovery of genetic variants affecting splicing (sQTLs), based on an approach that captures the intrinsically multivariate nature of this phenomenon. We employed it to analyze the multi-tissue transcriptome GTEx dataset, generating a comprehensive catalogue of sQTLs in the human genome. A core set of these sQTLs is shared across multiple

    更新日期:2020-05-30
  • Lineage tracing of human embryonic development and foetal haematopoiesis through somatic mutations
    bioRxiv. Genom. Pub Date : 2020-05-30
    Michael Spencer Chapman; Anna Maria Ranzoni; Brynelle Myers; Nick Williams; Tim Coorens; Emily Mitchell; Timothy Butler; Kevin J Dawson; Yvette Hooks; Luiza Moore; Jyoti Nangalia; Philip S Robinson; Elizabeth Hook; Peter J Campbell; Ana Cvejic

    To date, ontogeny of the human haematopoietic system during foetal development has been characterized mainly through careful microscopic observations. Here we used whole-genome sequencing (WGS) of 511 single-cell derived haematopoietic colonies from healthy human foetuses of 8 and 18 post-conception weeks (pcw) coupled with deep targeted sequencing of tissues of known embryonic origin to reconstruct

    更新日期:2020-05-30
  • The genome of the nonphotosynthetic diatom, Nitzschia sp.: Insights into the metabolic shift to heterotrophy and the rarity of loss of photosynthesis in diatoms
    bioRxiv. Genom. Pub Date : 2020-05-30
    Anastasiia Pendergrass; Wade R Roberts; Elizabeth C Ruck; Jeffrey A Lewis; Andrew J Alverson

    Although most of the tens of thousands of diatom species are obligate photoautotrophs, many mixotrophic species can also use extracellular organic carbon for growth, and a small number of obligate heterotrophs have lost photosynthesis entirely. We sequenced the genome of a nonphotosynthetic diatom, Nitzschia sp. strain Nitz4, to determine how carbon metabolism was altered in the wake of this rare and

    更新日期:2020-05-30
  • Verification of CRISPR editing by XdropTM Indirect Sequence Capture followed by short- and long- read sequencing
    bioRxiv. Genom. Pub Date : 2020-05-30
    Thorarinn Blondal; Cristina Gamba; Camille M Johnston; Eva M Riising; Marie J Mikkelsen; Peter Mouritzen

    Validation of CRISPR-Cas9 editing typically explore the immediate vicinity of the target site and distal off-target sequences, which have led to the conclusion that CRISPR-Cas9 editing is very specific. However, an increasing number of studies suggest that on-target unintended editing events like deletions and insertions are relatively frequent but unfortunately often missed in the validation of CRISPR-Cas9

    更新日期:2020-05-30
  • Understanding the diversity of DNA methylation in Mycobacterium tuberculosis
    bioRxiv. Genom. Pub Date : 2020-05-30
    Victor Ndhlovu; Anmol Kiran; Derek J Sloan; Wilson Mandala; Marriott Nliwasa; Dean B Everett; Mphatso Mwapasa; Konstantina Kontogianni; Mercy Kamdolozi; Elizabeth L Corbett; Maxine Caws; Gerry Davies

    Although Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized. We completed methylomes of 18 Mycobacterium tuberculosis (Mtb)

    更新日期:2020-05-30
  • Germline ERBB3 mutation in familial non-small cell lung carcinoma: expanding the role of the ErbB family in oncogenesis.
    bioRxiv. Genom. Pub Date : 2020-05-30
    Aideen M McInerney-Leo; Hui Yi Chew; Po-Ling Inglis; Paul J. Leo; Shannon R. Joseph; Caroline L. Cooper; Satomi Okano; Tim Hassall; Lisa Anderson; Rayleen V. Bowman; Michael Gattas; Jessica E. Harris; Mhairi S. Marshall; Janet G. Shaw; Lawrie Wheeler; Ian A. Yang; Matthew A. Brown; Kwun M. Fong; Fiona Simpson; Emma L Duncan

    Introduction: Lung cancer is the commonest cause of cancer deaths worldwide. Although strongly associated with smoking, predisposition to lung cancer is also heritable with multiple common risk variants identified. Rarely, dominantly-inherited non-small-cell lung cancer (NSCLC) has been reported, due to mutations in EGFR/ErbB1 and ERBB2. Methods: Germline exome sequencing was performed in a multi-generation

    更新日期:2020-05-30
  • Long read sequencing and de novo assembly of Hepatitis B Virus identifies 5mCpG in CpG islands
    bioRxiv. Genom. Pub Date : 2020-05-30
    Chloe Desiree Goldsmith; Damien Cohen; Anaelle Dubois; Maria-Guadaloupe Martinez; Kilian Petitjean; Anne Corlu; Hector Hernandez-Vargas; Isabelle Chemin

    Methylation of viral DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we

    更新日期:2020-05-30
  • Single-molecule long-read sequencing reveals a conserved selection mechanism determining intact long RNA and miRNA profiles in sperm
    bioRxiv. Genom. Pub Date : 2020-05-30
    Xin Li; Yu H Sun; Anqi Wang; Chi Song; Rajesh Srivastava; Kin Fai Au

    Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to be shaped by paternal environments and impact offspring phenotypes, we know little about long RNAs in sperm, including mRNAs and long non-coding RNAs. Here, by integrating PacBio single-molecule long reads with Illumina short reads, we found 2,778 sperm intact long transcript (SpILT) species in mouse. The SpILTs

    更新日期:2020-05-30
  • A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum (Hausmann) (Hemiptera: Aphididae)
    bioRxiv. Genom. Pub Date : 2020-05-30
    Roberto Biello; Archana Singh; Cindayniah J. Godfrey; Felicidad Fernández Fernández; Sam T. Mugford; Glen Powell; Saskia A. Hogenhout; Thomas C. Mathers

    Woolly apple aphid (WAA, Eriosoma lanigerum Hausmann) (Hemiptera: Aphididae), is a major pest of apple trees (Malus domestica, order Rosales) and is critical to the economics of the apple industry in most parts of the world. Here, we generated a chromosome-level genome assembly of WAA - representing the first genome sequence from the aphid subfamily Eriosomatinae - using a combination of 10X Genomics

    更新日期:2020-05-30
  • An analog to digital converter controls bistable transfer competence of a widespread integrative and conjugative element
    bioRxiv. Genom. Pub Date : 2020-05-30
    Jan Roelof van der Meer; Nicolas Carraro; Xavier Richard; Sandra Sulser; Francois Delavat; Christian Mazza

    Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3-5% of individual cells. The mechanisms controlling this bistable switch between non active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida

    更新日期:2020-05-30
  • Human Endogenous Retrovirus K Rec forms a regulatory loop with MITF that opposes the progression of melanoma to an invasive stage
    bioRxiv. Genom. Pub Date : 2020-05-30
    Manvendra Singh; Cai Huiqiang; Mario Bunse; Cedric Feschotte; Zsuzsanna Izsvak

    In the human genome, HERV-K(HML2) is the most recently endogenized retrovirus (ERV). While HERV-K(HML2) transcription is observed in normal tissues, both retroviral and the envelope (Env)-derived endogenized accessory products (e.g. Np9 and Rec) are upregulated in various cancer. Still, it is not clear whether the different HERV-K-derived genes contribute to a disease or are simple by-products. Here

    更新日期:2020-05-30
  • An atlas of robust microbiome associations with phenotypic traits based on large-scale cohorts from two continents
    bioRxiv. Genom. Pub Date : 2020-05-30
    Daphna Rothschild; Sigal Leviatan; Ariel Hanemann; Yossi Cohen; Omer Weissbrod; Eran Segal

    Numerous human conditions are associated with the microbiome, yet studies are inconsistent as to the magnitude of the associations and the bacteria involved, likely reflecting insufficiently employed sample sizes. Here, we collected diverse phenotypes and gut microbiota from 34,057 individuals from Israel and the U.S.. Analyzing these data using a much-expanded microbial genomes set, we derive an atlas

    更新日期:2020-05-30
  • Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence
    bioRxiv. Genom. Pub Date : 2020-05-30
    Nadia Kamal; Terry Mun; Dugald Reid; Jie-shun Lin; Turgut Yigit Akyol; Niels Sandal; Torben Asp; Hideki Hirakawa; Jens Stougaard; Klaus F X Mayer; Shusei Sato; Stig U. Andersen

    Lotus japonicus is a herbaceous perennial legume that has been used extensively as a genetically tractable model system for deciphering the molecular genetics of symbiotic nitrogen fixation. So far, the L. japonicus reference genome assembly has been based on Sanger and Illumina sequencing reads from the L. japonicus accession MG-20 and contained a large fraction of unanchored contigs. Here, we use

    更新日期:2020-05-30
  • Distinctive indel mutational signature in tumors carrying TOP2A p.K743N
    bioRxiv. Genom. Pub Date : 2020-05-30
    Arnoud Boot; Steven G Rozen

    Topoisomerases are essential for genome stability. Here we link a rare recurrent hotspot mutation, p.K743N, in topoisomerase TOP2A to a unique pattern of small insertions and deletions (indels) in human cancers. This pattern consists mainly of duplications of 2 to 4 base pairs and deletions of 6 to 8 base pairs. These resemble indel mutational signatures ID17 and ID8, which until now had unknown causes

    更新日期:2020-05-30
  • Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin
    bioRxiv. Genom. Pub Date : 2020-05-30
    Ezequiel Miron; Roel Oldenkamp; Jill M Brown; David MS Pinto; C. Shan Xu; Anna R Faria; Haitham A Shaban; James DP Rhodes; Cassandravictoria Innocent; Sara de Ornellas; Harald Hess; Veronica Buckle; Lothar Schermelleh

    Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ~200-300-nm-wide

    更新日期:2020-05-30
  • Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen
    bioRxiv. Genom. Pub Date : 2020-05-29
    Damien Richard; Olivier Pruvost; François Balloux; Claudine Boyer; Adrien Rieux; Pierre Lefeuvre

    The reconstruction of the evolutionary histories of pathogen populations in space and time often improves our understanding of their epidemiology. However, analyses are usually restricted to the non-recombining genomic regions and, thus, fail to inform on the dynamics of the accessory genome. Yet, horizontal gene transfer is of striking importance to the evolution of bacteria as it can redistribute

    更新日期:2020-05-29
  • SARS-CoV-2 transmission chains from genetic data: a Danish case study
    bioRxiv. Genom. Pub Date : 2020-05-29
    Andreas Bluhm; Matthias Christandl; Fulvio Gesmundo; Frederik Ravn Klausen; Laura Mancinska; Vincent Steffan; Daniel Stilck Franca; Albert Werner

    Background: The Covid-19 pandemic caused by the SARS-CoV-2 virus started in China in December and has since spread globally. Many countries have instated measures to slow the spread of the virus. Information about the introduction of the virus to a country and its further spread can inform the gradual opening of a country and the avoidance of a second wave of infections. Denmark has seen first cases

    更新日期:2020-05-29
  • Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding
    bioRxiv. Genom. Pub Date : 2020-05-29
    Nikki E Freed; Markéta Vlková Muhammad B Faisal; Olin K Silander

    Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit

    更新日期:2020-05-29
  • Temporal evolution and adaptation of SARS-COV 2 codon usage
    bioRxiv. Genom. Pub Date : 2020-05-29
    Maddalena Dilucca; Sergio Forcelloni; Andrea Giansanti; Alexandros Georgakilas; Athanasia Pavlopoulou

    The outbreak of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. In this study, we compared 15,259 SARS-CoV-2 genomes isolated from 60 countries since the outbreak

    更新日期:2020-05-29
  • CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals
    bioRxiv. Genom. Pub Date : 2020-05-29
    Clarisse Ganier; Xinyi Du-Harpur; Nasrat Harun; Bo Wan; Callum Arthurs; Nicholas M Luscombe; Fiona M. Watt; Magnus D. Lynch

    Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a wide range of systemic manifestations. Several observations support a role for vascular endothelial dysfunction in the pathogenesis including an increased incidence of thrombotic events and coagulopathy and the presence of vascular risk factors as an independent predictor

    更新日期:2020-05-29
  • A Reference Genome from the symbiotic hydrozoan, Hydra viridissima
    bioRxiv. Genom. Pub Date : 2020-05-29
    Mayuko Hamada; Noriyuki Satoh; Konstantin Khalturin

    Cnidarians are one of the oldest eumetazoan taxa, and are thought to be a sister group to all bilaterians. In spite of comparatively simple morphology, cnidarians exhibit diverse body forms and life histories. In addition, many cnidarian species establish symbiotic relationships with microalgae. Various Hydra species have been employed as model organisms since the 18th century. Introduction of transgenic

    更新日期:2020-05-29
  • Shared SARS-CoV-2 diversity suggests localised transmission of minority variants
    bioRxiv. Genom. Pub Date : 2020-05-29
    Katrina A Lythgoe; Matthew David Hall; Luca Ferretti; Mariateresa de Cesare; George MacIntyre-Cockett; Amy Trebes; Monique Andersson; Newton Otecko; Emma L Wise; Nathan Moore; Jessica Lynch; Stephen Kidd; Nicholas Cortes; Matilde Mori; Anita Justice; Angie Green; M Azim Ansari; Lucie Abeler-Dorner; Catrin E Moore; Tim E.A. Peto; Robert Shaw; Peter Simmonds; David Buck; John A Todd; David Bonsall; Christophe

    SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019 causing a global pandemic, with the United Kingdom (UK) one of the hardest hit countries. Rapid sequencing and publication of consensus genomes have enabled phylogenetic analysis of the virus, demonstrating SARS-CoV-2 evolves relatively slowly, but with multiple sites in the genome that appear inconsistent with the overall consensus

    更新日期:2020-05-29
  • Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration
    bioRxiv. Genom. Pub Date : 2020-05-29
    Joshua G Medina-Feliciano; Stacy Pirro; José E García-Arrarás; Vladimir Mashanov; Joseph F Ryan

    Regeneration is one of the most fascinating and yet least understood processes of animals. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Amongst echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The

    更新日期:2020-05-29
  • Advancing the genetic utility of pre-clinical species through a high-quality assembly of the cynomolgus monkey (Macaca fascicularis) genome
    bioRxiv. Genom. Pub Date : 2020-05-29
    Elias M Oziolor; Shawn Sullivan; Hayley Mangelson; Stephen M Eacker; Michael Agostino; Laurence Oliver Whiteley; Jon Cook; Petra Koza-Taylor

    The cynomolgus macaque is a non-human primate model, heavily used in biomedical research, but with outdated genomic resources. Here we have used the latest long-read sequencing technologies in order to assemble a fully phased, chromosome-level assembly for the cynomolgus macaque. We have built a hybrid assembly with PacBio, 10x Genomics, and HiC technologies, resulting in a diploid assembly that spans

    更新日期:2020-05-29
  • An embryonic stem cell-specific heterochromatin state allows core histone exchange in the absence of DNA accessibility
    bioRxiv. Genom. Pub Date : 2020-05-29
    Carmen Navarro; Simon J Elsasser

    Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. In our current understanding, nucleosome turnover is universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently intracisternal-A

    更新日期:2020-05-29
  • Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes
    bioRxiv. Genom. Pub Date : 2020-05-28
    Frédéric Bigey; Diego Segond; Anne Friedrich; Stephane Guezenec; Aurélie Bourgais; Lucie Huyghe; Nicolas Agier; Thibault Nidelet; Delphine Sicard

    Despite bread being one of the most historically and culturally important fermented products, its history and influence on the evolution of associated microbial species remains largely unknown. The first evidence of leavened bread dates to the second millenium BCE in Egypt and since, the art of bread-making developed and spread worldwide. Nowadays, leavened bread is made either by using a pure commercial

    更新日期:2020-05-28
  • Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states
    bioRxiv. Genom. Pub Date : 2020-05-28
    Bornali Bhattacharjee; Bhaswati Pandit

    The first Indian cases of COVID-19 caused by SARS-Cov-2 were reported in February 29, 2020 with a history of travel from Wuhan, China and so far above 4500 deaths have been attributed to this pandemic. The objectives of this study were to characterize Indian SARS-CoV-2 genome-wide nucleotide variations, trace ancestries using phylogenetic networks and correlate state-wise distribution of viral haplotypes

    更新日期:2020-05-28
  • LincRNA sequences are biased to counteract their translation
    bioRxiv. Genom. Pub Date : 2020-05-28
    Anneke Brümmer; René Dreos; Ana C Marques; Sven Bergmann

    Long intergenic non-coding RNAs (lincRNAs) represent a large fraction of transcribed loci in the human genome. Although classified as non-coding, the vast majority of lincRNAs contain putative open reading frames (pORFs), and the molecular mechanisms hindering their translation are currently unclear. Here, we analysed the sequences of lincRNAs in six species, ranging from human to fission yeast. We

    更新日期:2020-05-28
  • An open-sourced bioinformatic pipeline for the processing of Next-Generation Sequencing derived nucleotide reads: Identification and authentication of ancient metagenomic DNA
    bioRxiv. Genom. Pub Date : 2020-05-28
    Thomas C Collin; Konstantina Drosou; Jeremiah Daniel O'Riordan; Tengiz Meshveliani; Ron Pinhasi; Robin N.M. Feeney

    Bioinformatic pipelines optimised for the processing and assessment of metagenomic ancient DNA (aDNA) are needed for studies that do not make use of high yielding DNA capture techniques. These bioinformatic pipelines are traditionally optimised for broad aDNA purposes, are contingent on selection biases and are associated with high costs. Here we present a bioinformatic pipeline optimised for the identification

    更新日期:2020-05-28
  • Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates
    bioRxiv. Genom. Pub Date : 2020-05-28
    Rylan Shearn; Alison Wright; Sylvain Mousset; Corinne Regis; Simon Penel; Jean Francois Lemaitre; Guillaume Douay; Brigitte Crouau-Roy; Emilie Lecompte; Gabriel Marais

    Sex chromosomes are typically comprised of a non-recombining region and a recombining pseudoautosomal region. Accurately quantifying the relative size of these regions is critical for sex chromosome biology both from a functional (i.e. number of sex-linked genes) and evolutionary perspective (i.e. extent of Y degeneration and X-Y heteromorphy). The evolution of the pseudoautosomal boundary (PAB) -

    更新日期:2020-05-28
  • A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing
    bioRxiv. Genom. Pub Date : 2020-05-28
    Alexandra J Noble; John F Pearson; Joseph M Boden; L John Horwood; Neil J Gemmell; Martin A Kennedy; Amy J Osborne

    The Illumina Infinium MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. Due to their genome-wide nature, and their relatively high cost per sample, EPIC arrays are often used for hypothesis generation or pilot studies, the natural conclusion to which is to validate the most promising

    更新日期:2020-05-28
  • DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis
    bioRxiv. Genom. Pub Date : 2020-05-28
    Pierre Bourguet; Leticia López-González; Ángeles Gómez-Zambrano; Thierry Pélissier; Amy Hesketh; Magdalena E Potok; Marie-Noëlle Pouch-Pélissier; Magali Perez; Olivier Da Ines; David Latrasse; Charles I White; Steven E Jacobsen; Moussa Benhamed; Olivier Mathieu

    Chromatin organizes the DNA molecule and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases

    更新日期:2020-05-28
  • Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms
    bioRxiv. Genom. Pub Date : 2020-05-28
    R. Rebecca Love; Marco Pombi; Moussa W. Guelbeogo; Nathan R. Campbell; Melissa T. Stephens; Roch K. Dabire; Carlo Costantini; Alessandra della Torre; Nora J. Besansky

    Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling

    更新日期:2020-05-28
  • Freshwater diatom biomonitoring through benthic kick-net metabarcoding
    bioRxiv. Genom. Pub Date : 2020-05-28
    Victoria Carley Maitland; Chloe Victoria Robinson; Teresita M Porter; Mehrdad Hajibabaei

    Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater

    更新日期:2020-05-28
  • Reference genome and demographic history of the most endangered marine mammal, the vaquita
    bioRxiv. Genom. Pub Date : 2020-05-28
    Phillip A. Morin; Frederick I Archer; Catherine D Avila; Jennifer R Balacco; Yury V Bukhman; William Chow; Olivier Fedrigo; Giulio Formenti; Julie A Fronczek; Arkarachai Fungtammasan; Frances M. D. Gulland; Bettina Haase; Mads Peter Heide-Jørgensen; Marlys Houck; Kerstin Howe; Ann C Misuraca; Jacquelyn Mountcastle; Whitney Musser; Sadye Paez; Sarah Pelan; Adam M. Phillippy; Arang Rhie; Jacqueline A

    The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding

    更新日期:2020-05-28
  • High-resolution population-specific recombination rates and their effect on phasing and genotype imputation
    bioRxiv. Genom. Pub Date : 2020-05-28
    Shabbeer Hassan; Ida Surakka; Marja-Riita Taskinen; Veikko Salomaa; Aarno Palotie; Maija Wessman; Taru Tukiainen; Matti Pirinen; Priit Palta; Samuli Ripatti

    Founder population size, demographic changes (eg. population bottlenecks or rapid expansion) can lead to variation in recombination rates across different populations. Previous research has shown that using population-specific reference panels has a significant effect on downstream population genomic analysis like haplotype phasing, genotype imputation and association, especially in the context of

    更新日期:2020-05-28
  • Developmentally Delayed Epigenetic Reprogramming Underlying the Pathogenesis of Preeclampsia
    bioRxiv. Genom. Pub Date : 2020-05-28
    Wei He; Yuan Wei; Xiaoli Gong; Luyuan Chang; Wan Jin; Ke Liu; Xinghuan Wang; Yu Xiao; Wenjing Zhang; Qiong Chen; Kai Wu; Lili Liang; Jia Liu; Yawen Chen; Huanhuan Guo; Xiaojuan Li; Wenhao Chen; Jiexia Yang; Yiming Qi; Wei Dong; Meng Fu; Jiusi Liu; Yi Zhang; Aihua Yin

    Preeclampsia, a life-threatening pregnancy complication characterized by hypertension and multiorgan damage, affects 2-5% of pregnancies and causes 76,000 deaths per year. Most preeclampsia associated syndromes immediately dispel after removal of placenta, indicating a casual role of placenta in the pathogenesis. Failed transformation of spiral artery due to insufficient invasion and excessive apoptosis

    更新日期:2020-05-28
  • LESR2 is a lymphatic endothelial-specific lncRNA that governs cell proliferation and migration through KLF4 and SEMA3C
    bioRxiv. Genom. Pub Date : 2020-05-27
    Luca Ducoli; Saumya Agrawal; Eliane Sibler; Tsukasa Kouno; Carlotta Tacconi; Chung-Chau Hon; Simone D. Berger; Daniela Muellhaupt; Yuliang He; Marco D'Addio; Lothar Dieterich; Piero Carninci; Michiel J.L. de Hoon; Jay W. Shin; Michael Detmar

    Recent studies have revealed the importance of long noncoding RNAs (lncRNAs) as tissue-specific regulators of gene expression. There is ample evidence that distinct types of vasculature undergo tight transcriptional control to preserve their structure, identity, and functions. We determined, for the first time, the global lineage-specific lncRNAome of human dermal blood and lymphatic endothelial cells

    更新日期:2020-05-27
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