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  • A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations
    bioRxiv. Genom. Pub Date : 2021-01-22
    Diksha Sharma; Sylvie Hermann-Le Denmat; Nicholas J. Matzke; Katherine Hannan; Ross D. Hannan; Justin M. O'Sullivan; Austen R. D. Ganley

    Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs (rRNA) and in eukaryotic genomes are typically present as one or more arrays of tandem repeats. Species have characteristic rDNA copy numbers, ranging from tens to thousands of copies, with the number thought to be redundant for rRNA production. However, the tandem rDNA repeats are prone to recombination-mediated changes in copy number, resulting

    更新日期:2021-01-22
  • The landscape of alternative polyadenylation in single cells of the developing mouse embryo
    bioRxiv. Genom. Pub Date : 2021-01-22
    Vikram Agarwal; Sereno Lopez-Darwin; David R Kelley; Jay Shendure

    3' untranslated regions (3' UTRs) post-transcriptionally regulate mRNA stability, localization, and translation rate. While 3'-UTR isoforms have been globally quantified in limited cell types using bulk measurements, their differential usage among cell types during mammalian development remains poorly characterized. In this study, we examined a dataset comprising ~2 million cells spanning E9.5-E13

    更新日期:2021-01-22
  • Optimizing Sequencing Resources in Genotyped Livestock Populations Using Linear Programming
    bioRxiv. Genom. Pub Date : 2021-01-21
    Hao Cheng; Keyu Xu; Kuruvilla Joseph Abraham; Jinghui Li

    Low-cost genome-wide single-nucleotide polymorphisms (SNPs) are routinely used in animal breeding programs. Compared to SNP arrays, the use of whole-genome sequence data generated by the next-generation sequencing technologies (NGS) has great potential in livestock populations. However, a large number of animals are required to be sequenced to exploit the full potential of whole-genome sequence data

    更新日期:2021-01-22
  • Genome-wide discovery of lupus genetic risk variant allelic regulatory activity
    bioRxiv. Genom. Pub Date : 2021-01-21
    Xiaoming Lu; Xiaoting Chen; Carmy Forney; Omer Donmez; Daniel Miller; Sreeja Parameswaran; Ted Hong; Yongbo Huang; Mario Pujato; Tareian Cazares; Emily R Miraldi; John P Ray; Carl G de Boer; John B Harley; Matthew T Weirauch; Leah C Kottyan

    Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into

    更新日期:2021-01-22
  • Fixed single-cell RNA sequencing for understanding virus infection and host response
    bioRxiv. Genom. Pub Date : 2021-01-21
    Hoang Van Phan; Michiel van Gent; Nir Drayman; Anindita Basu; Michaela Gack; Savas Tay

    Single-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited because current high-throughput RNA sequencing methods are incompatible with paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq, a high-throughput method for droplet-based RNA sequencing

    更新日期:2021-01-22
  • Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions
    bioRxiv. Genom. Pub Date : 2021-01-21
    Mazdak Salavati; Shernae A. Woolley; Yennifer Cortes Araya; Michelle M. Halstead; Claire Stenhouse; Martin Johnsson; Cheryl J. Ashworth; Alan L. Archibald; Francesc X. Donadeu; Musa A. Hassan; Emily Louise Clark

    There is very little species-specific information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programmes. In order to address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We have optimised the ′Improved

    更新日期:2021-01-22
  • Single-cell deconvolution of 3,000 post-mortem brain samples for eQTL and GWAS dissection in mental disorders
    bioRxiv. Genom. Pub Date : 2021-01-21
    Yongjin P Park; Liang He; Jose Davila-Velderrain; Lei Hou; Shahin Mohammadi; Hansruedi Mathys; Zhuyu Peng; David Bennett; Li-Huei Tsai; Manolis Kellis

    Thousands of genetic variants acting in multiple cell types underlie complex disorders, yet most gene expression studies profile only bulk tissues, making it hard to resolve where genetic and non-genetic contributors act. This is particularly important for psychiatric and neurodegenerative disorders that impact multiple brain cell types with highly-distinct gene expression patterns and proportions

    更新日期:2021-01-22
  • Emergence of XDR high-risk Pseudomonas aeruginosa ST309 in South America: a global comparative genomic analysis
    bioRxiv. Genom. Pub Date : 2021-01-21
    Erica L Fonseca; Sergio Morgado; Raquel Caldart; Fernanda Freitas; Ana Carolina Vicente

    Pseudomonas aeruginosa has been considered one of the major nosocomial pathogens associated with elevated morbidity and mortality worldwide. Outbreaks have been associated with few high-risk pandemic P. aeruginosa lineages, presenting a remarkable antimicrobial resistance. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be

    更新日期:2021-01-22
  • Uncovering the Gene Regulatory Networks Underlying Macrophage Polarization Through Comparative Analysis of Bulk and Single-Cell Data
    bioRxiv. Genom. Pub Date : 2021-01-21
    Klebea Carvalho; Elisabeth Rebboah; Camden Jansen; Katherine Williams; Andrew Dowey; Cassandra Joan McGill; Ali Mortazavi

    Gene regulatory networks (GRNs) provide a powerful framework for studying cellular differentiation. However, it is less clear how GRNs encode cellular responses to everyday microenvironmental cues. Macrophages can be polarized and potentially repolarized based on environmental signaling. In order to identify the GRNs that drive macrophage polarization and the heterogeneous single-cell subpopulations

    更新日期:2021-01-22
  • Comparative whole-genome analysis of a Thar desert strain Streptomyces sp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system
    bioRxiv. Genom. Pub Date : 2021-01-21
    Dharmesh Harwani; Jyotsna Begani; Jyoti Lakhani

    We sequenced the genome of Streptomyces sp. JB150, isolated from a unique site of the Thar desert in India. Genome mining of the JB150 genome revealed the presence of many interesting secondary metabolic biosynthetic gene clusters (BGCs). The encoded parvome of JB150 includes non-ribosomal peptides, polyketides including β-lactone, butyrolactone, ectoine, lantipeptides, lasso peptides, melanin, resorcinol

    更新日期:2021-01-21
  • Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics
    bioRxiv. Genom. Pub Date : 2021-01-21
    Lars Velten; Benjamin A. Story; Pablo Hernandez-Malmierca; Danie R Leonce; Jennifer Milbank; Malte Paulsen; Aykut Demir; Chelsea Szu-Tu; Robert Froemel; Christoph Lutz; Daniel Nowak; Johann-Christoph Jann; Caroline Pabst; Tobias Boch; Wolf-Karsten Hofmann; Carsten Mueller-Tidow; Simon Raffel; Andreas Trumpp; Simon Haas; Lars M Steinmetz

    Cancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with it the ability to eradicate cancer at its source. In acute myeloid leukemia (AML), leukemic stem cells (LSCs) underlie mortality but are difficult to isolate due to their low abundance and high similarity to healthy hematopoietic stem cells

    更新日期:2021-01-21
  • Polymorphic SNPs, short tandem repeats and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains
    bioRxiv. Genom. Pub Date : 2021-01-20
    Milad Mortazavi; Yangsu Ren; Shubham Saini; Danny Antaki; Celine St. Pierre; April Williams; Abhishek Sohni; Miles Wilkinson; Melissa Gymrek; Jonathan Sebat; Abraham A. Palmer

    Mouse substrains are an invaluable model for understanding disease. We compared C57BL/6J, which is the most commonly used inbred mouse strain, with several closely related substrains. We performed whole genome sequencing and RNA-sequencing analysis on 9 C57BL/6 and 5 C57BL/10 substrains. We identified 352,631 SNPs, 109,096 INDELs, 150,344 short tandem repeats (STRs), 3,425 structural variants (SVs)

    更新日期:2021-01-21
  • H2A.B is a cancer/testis factor involved in activation of ribosome biogenesis in Hodgkin Lymphoma
    bioRxiv. Genom. Pub Date : 2021-01-20
    David Tremethick; Jiang Xuanzhao; Jiayu JW Wen; Elizabeth Pavwer; Wu Yu-Huan; Gege Sun; Amanda Pullman; Jane E Dahlstrome; Tatiana Soboleva

    Testis-specific regulators of chromatin function are commonly ectopically expressed in human cancers, but their roles are poorly understood. Examination of 81 primary Hodgkin Lymphoma (HL) samples showed that the ectopic expression of the eutherian testis-specific histone variant H2A.B is an inherent feature of HL. Using two HL-derived cell lines derived from different subtypes of HL, H2A.B knockdown

    更新日期:2021-01-21
  • Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
    bioRxiv. Genom. Pub Date : 2021-01-20
    Daniel E Goszczynski; Michelle M Halstead; Alma D Islas-Trejo; Huaijun Zhou; PABLO J ROSS

    Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and contains a low number of transcripts in comparison to human

    更新日期:2021-01-21
  • Integrated analysis of glycan and RNA in single cells
    bioRxiv. Genom. Pub Date : 2021-01-20
    Fumi Minoshima; Haruka Ozaki; Haruki Odaka; Hiroaki Tateno

    Single-cell sequencing has emerged as an indispensable technology to dissect cellular heterogeneity but never been applied to the simultaneous analysis of glycan and RNA. Using oligonucleotide-labeled lectins, we first established lectin-based glycan profiling of single cells by sequencing (scGlycan-seq). We then combined the scGlycan-seq with single-cell transcriptome profiling (scRNA-seq) for joint

    更新日期:2021-01-21
  • Enhancer-associated H3K4 methylation safeguards in vitro germline competence
    bioRxiv. Genom. Pub Date : 2021-01-20
    Tore Bleckwehl; Giuliano Crispatzu; Kaitlin Schaaf; Patricia Respuela; Michaela Bartusel; Laura Benson; Stephen J. Clark; Kristel M. Dorighi; Antonio Barral; Magdalena Laugsch; Wilfred van IJcken; Miguel Manzanares; Joanna Wysocka; Wolf Reik; Alvaro Rada-Iglesias

    Germline specification in mammals occurs through an inductive process whereby competent cells in the post-implantation epiblast differentiate into primordial germ cells (PGC). The intrinsic factors that endow epiblast cells with the competence to respond to germline inductive signals remain unknown. Single-cell RNA sequencing across multiple stages of an in vitro PGC-like cells (PGCLC) differentiation

    更新日期:2021-01-20
  • A scalable pipeline for local ancestry inference using tens of thousands of reference haplotypes
    bioRxiv. Genom. Pub Date : 2021-01-20
    Eric Y Durand; Chuong B Do; Peter R Wilton; Joanna L Mountain; Adam Auton; G David Poznik; J Michael Macpherson

    Ancestry deconvolution is the task of identifying the ancestral origins of chromosomal segments of admixed individuals. It has important applications, from mapping disease genes to identifying loci potentially under natural selection. However, most existing methods are limited to a small number of ancestral populations and are unsuitable for large-scale applications. In this article, we describe Ancestry

    更新日期:2021-01-20
  • Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments
    bioRxiv. Genom. Pub Date : 2021-01-19
    Luca Barbon; Victoria Offord; Elizabeth J. Radford; Adam P. Butler; Sebastian S. Gerety; David J. Adams; Matthew E. Hurles; Hong Kee Tan; Andrew J. Waters

    Motivation: Recent advances in CRISPR/Cas9 technology allow for the functional analysis of genetic variants at single nucleotide resolution whilst maintaining genomic context (Findlay et al., 2018). This approach, known as saturation genome editing (SGE), is a distinct type of deep mutational scanning (DMS) that systematically alters each position in a target region to explore its function. SGE experiments

    更新日期:2021-01-20
  • Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions
    bioRxiv. Genom. Pub Date : 2021-01-19
    Yue Wan; Siwy Ling Yang; Louis DeFalco; Danielle E Anderson; Yu Zhang; Ashley J Aw; Su Ying Lim; Xin Ni Lim; Kiat Yee Tan; Tong Zhang; Tanu Chawla; Yan Su; Alexander Lezhava; Paola de Sessions; Andres Merits; Lin-Fa Wang; Roland G Huber

    SARS-CoV-2 has emerged as a major threat to global public health, resulting in global societal and economic disruptions. Here, we investigate the intramolecular and intermolecular RNA interactions of wildtype (WT) and a mutant (Δ382) SARS-CoV-2 virus in cells using high throughput structure probing on Illumina and Nanopore platforms. We identified twelve potentially functional structural elements within

    更新日期:2021-01-20
  • The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions
    bioRxiv. Genom. Pub Date : 2021-01-19
    Chloé Suzanne Berger; Jérôme Laroche; Halim Maaroufi; Hélène Martin; Kyung-Mee Moon; Christian Landry; Leonard Foster; Nadia Aubin-Horth

    Manipulative parasites are thought to liberate molecules in their external environment acting as manipulation factors with biological functions implicated in their host's physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative

    更新日期:2021-01-20
  • Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
    bioRxiv. Genom. Pub Date : 2021-01-19
    Jakub Jankowski; Hye Kyung Lee; Julia Wilflingseder; Lothar Hennighausen

    Summary: Recently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show

    更新日期:2021-01-20
  • SARS-CoV-2 Genomic Surveillance in Costa Rica: Evidence of a Divergent Population and an Increased Detection of a Spike T1117I Mutation
    bioRxiv. Genom. Pub Date : 2021-01-19
    Jose Arturo Molina Mora; Estela Cordero-Laurent; Adriana Godinez; Melany Calderon-Osorno; Hebleen Brenes; Claudio Soto-Garita; Cristian Perez-Corrales; COINGESA-CR Consorcio Interinstitucional de Estudios Genomicos del SARS-CoV-2 Costa Rica; Jan Felix Drexler; Andres Moreira-Soto; Eugenia Corrales-Aguilar; Francisco Duarte-Martinez

    Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. Costa Rica was first exemplary for the region in its pandemic control, declaring a swift state of emergency on March 16th that led to a low quantity of cases, until measures

    更新日期:2021-01-20
  • Highly accurate barcode and UMI error correction using dual nucleotide dimer blocks allows direct single-cell nanopore transcriptome sequencing
    bioRxiv. Genom. Pub Date : 2021-01-19
    Martin Philpott; jonathan watson; Anjan Thakurta; Tom Brown; Tom Brown; Udo Oppermann; Adam P Cribbs

    Droplet-based single-cell sequencing techniques have provided unprecedented insight into cellular heterogeneities within tissues. However, these approaches only allow for the measurement of the distal parts of a transcript following short-read sequencing. Therefore, splicing and sequence diversity information is lost for the majority of the transcript. The application of long-read Nanopore sequencing

    更新日期:2021-01-20
  • Molecular programs of fibrotic change in aging human lung
    bioRxiv. Genom. Pub Date : 2021-01-19
    Jasmine Lee; Mohammad Naimul Islam; Kaveh Boostanpour; Dvir Aran; Stephanie Christenson; Michael A Matthay; Walter Eckalbar; Daryle J. DePianto; Joseph R. Arron; Liam Magee; Sunita Bhattacharya; Rei Matsumoto; Masaru Kubota; Donna L. Farber; Jahar Bhattacharya; Paul J. Wolters; Mallar Bhattacharya

    Aging is associated with both overt and subclinical lung fibrosis, which increases risk for mortality from viruses and other respiratory pathogens. The molecular programs that induce fibrosis in the aging lung are not well understood. To overcome this knowledge gap, we undertook multimodal profiling of distal lung samples from healthy human donors across the lifespan. Telomere shortening, a cause of

    更新日期:2021-01-20
  • Simultaneous single cell measurements of intranuclear proteins and gene expression
    bioRxiv. Genom. Pub Date : 2021-01-19
    Hattie Chung; Christopher Parkhurst; Emma M Magee; Devan Phillips; Ehsan Habibi; Fei Chen; Bertrand Yeung; Julia A Waldman; David Artis; Aviv Regev

    Identifying gene regulatory targets of nuclear proteins in tissues remains a challenge. Here we describe intranuclear Cellular Indexing of Transcriptomes and Epitopes (inCITE-seq), a scalable method for measuring multiplexed intranuclear protein levels and the transcriptome in parallel in thousands of cells, enabling joint analysis of TF levels and gene expression in vivo. We apply inCITE-seq to characterize

    更新日期:2021-01-20
  • A Chromosome-scale draft genome sequence of horsegram (Macrotyloma uniflorum)
    bioRxiv. Genom. Pub Date : 2021-01-19
    Kenta Shirasawa; Rakesh Chahota; Hideki Hirakawa; Soichiro Nagano; Hideki Nagasaki; Tilak R Sharma; Sachiko Isobe

    Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] is an underutilized warm season diploid legume (2n=20, 22), It is consumed as a food legume in India, and animal feed and fodder in Africa and Australia. Because of its ability to grow under water-deficient and marginal soil conditions, horsegram is a preferred choice in the era of the global climatic change. In recognition of its potential as a crop

    更新日期:2021-01-20
  • Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio
    bioRxiv. Genom. Pub Date : 2021-01-19
    Huolin Tu; Matthew R Avenarius; Laura Kubatko; Matthew Hunt; Xiaokang Pan; Peng Ru; Jason Garee; Keelie Thomas; Peter Mohler; Preeti Pancholi; Dan Jones

    Following the worldwide emergence of the p.Asp614Gly shift in the Spike (S) gene of SARS-CoV-2, there have been few recurring pathogenic shifts occurring during 2020, as assessed by genomic sequencing. This situation has evolved in the last several months with the emergence of several distinct variants (first identified in the United Kingdom and South Africa, respectively) that illustrate multiple

    更新日期:2021-01-20
  • Germline ERBB3 mutation in familial non-small cell lung carcinoma: expanding the role of the ErbB family in oncogenesis.
    bioRxiv. Genom. Pub Date : 2021-01-19
    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

    Background: 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 somatic mutations in EGFR/ErbB1 and ERBB2. Methods: Germline exome sequencing was performed in a multi-generation

    更新日期:2021-01-19
  • Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States
    bioRxiv. Genom. Pub Date : 2021-01-19
    Adrian A Pater; Michael S Bosmeny; Christopher L Barkau; Katy N Ovington; Ramdevi Chilamkurthy; Mansi Parasrampuria; Seth B Eddington; Abadat O Yinusa; Adam A White; Paige E Metz; Rourke J Sylvain; Madison M Hebert; Scott W Benzinger; Koushik T Sinha; Keith T Gagnon

    Genomic surveillance can lead to early identification of novel viral variants and inform pandemic response. Using this approach, we identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.). The earliest sequenced genomes of this variant, referred to as 20C-US, can be traced to Texas in late May of 2020. This variant circulated in the U.S. uncharacterized for months

    更新日期:2021-01-19
  • In vivo structure and dynamics of the RNA genome of SARS-Cov-2
    bioRxiv. Genom. Pub Date : 2021-01-19
    Yan Zhang; Kun Huang; Dejian Xie; Jian You Lau; Wenlong Shen; Ping Li; Dong Wang; Zhong Zou; Shu Shi; Hongguang Ren; Meilin Jin; Grzegorz Kudla; Zhihu Zhao

    The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3'-UTR and 5'-UTR, frameshifting element (FSE) pseudoknot and genome cyclization

    更新日期:2021-01-19
  • A region-based method for causal mediation analysis of DNA methylation data
    bioRxiv. Genom. Pub Date : 2021-01-18
    Qi Yan; Erick Forno; Juan Celedon; Wei Chen

    Exposure to environmental factors can affect DNA methylation at a CpG site or a genomic region, which can then affect an outcome. In other words, environmental effects on an outcome could be mediated by DNA methylation. To date, single CpG site-based mediation analysis has been employed extensively. More recently, however, there has been considerable interest on studying differentially methylated regions

    更新日期:2021-01-19
  • PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome
    bioRxiv. Genom. Pub Date : 2021-01-18
    Siqi Liang; Matthew Mort; Peter D Stenson; David N Cooper; Haiyuan Yu

    Variants of uncertain significance (VUS) have posed an increasingly prominent challenge to clinicians due to their growing numbers and difficulties in making clinical responses to them. Currently there are no existing methods that leverage the spatial relationship of known disease mutations and genomic properties for prioritizing variants of uncertain significance. More importantly, disease genes often

    更新日期:2021-01-19
  • Geographical and environmental contributions to genomic divergence in mangrove forests
    bioRxiv. Genom. Pub Date : 2021-01-18
    Michele Fernandes da Silva; Mariana Vargas Cruz; João de Deus Vidal Júnior; Maria Imaculada Zucchi; Gustavo Maruyama Mori; Anete Pereira de Souza

    Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves

    更新日期:2021-01-19
  • AsmMix: A pipeline for high quality diploid de novo assembly
    bioRxiv. Genom. Pub Date : 2021-01-18
    Pei Wu; Chao Liu; Ou Wang; Zhao Xia; Fang Chen; XiaoFang Chen; Hongmei Zhu

    In this paper, we report a pipeline, AsmMix, which is capable of producing both contiguous and high-quality diploid genomes. The pipeline consists of two steps. In the first step, two sets of assemblies are generated: one is based on co-barcoded reads, which are highly accurate and haplotype-resolved but contain many gaps, the other assembly is based on single-molecule sequencing reads, which is contiguous

    更新日期:2021-01-18
  • Mutation rate variations in the human genome are encoded in DNA shape
    bioRxiv. Genom. Pub Date : 2021-01-18
    Zian Liu; Md Abul Hassan Samee

    Single nucleotide mutation rates have critical implications for human evolution and genetic diseases. Accurate modeling of these mutation rates has long remained an open problem since the rates vary substantially across the human genome. A recent model, however, explained much of the variation by considering higher order nucleotide interactions in the local (7-mer) sequence context around mutated nucleotides

    更新日期:2021-01-18
  • NyuWa Genome Resource: Deep Whole Genome Sequencing Based Chinese Population Variation Profile and Reference Panel
    bioRxiv. Genom. Pub Date : 2021-01-18
    Peng Zhang; Huaxia Luo; Yanyan Li; You Wang; Jiajia Wang; Yu Zheng; Yiwei Niu; Yirong Shi; Honghong Zhou; Tingrui Song; Quan Kang; Tao Xu; Shunmin He

    The lack of Chinese population specific haplotype reference panel and whole genome sequencing resources has greatly hindered the genetics studies in the world's largest population. Here we presented the NyuWa genome resource of 71.1M SNPs and 8.2M indels based on deep (26.2X) sequencing of 2,999 Chinese individuals, and constructed NyuWa reference panel of 5,804 haplotypes and 19.3M variants, which

    更新日期:2021-01-18
  • Cross-tissue single-cell transcriptomics reveals organizing principles of fibroblasts in health and disease
    bioRxiv. Genom. Pub Date : 2021-01-17
    Matthew B Buechler; Rachana N Pradhan; Aslihan Karabacak Calviello; Soren Muller; Richard Bourgon; Shannon J Turley

    Fibroblasts are non-hematopoietic structural cells that define the architecture of organs, support the homeostasis of tissue-resident cells and play key roles in fibrosis, cancer, autoimmunity and wound healing. Recent studies have described fibroblast heterogeneity within individual tissues. However, the field lacks a definition of fibroblasts at single-cell resolution across tissues in healthy and

    更新日期:2021-01-18
  • Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
    bioRxiv. Genom. Pub Date : 2021-01-17
    Audald Lloret-Villas; Meenu Bhati; Naveen Kumar Kadri; Ruedi Fries; Hubert Pausch

    Background: Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of

    更新日期:2021-01-18
  • High trait variability in optimal polygenic prediction strategy within multiple-ancestry cohorts
    bioRxiv. Genom. Pub Date : 2021-01-17
    Brieuc CL Lehmann; Maxine Mackintosh; Gil McVean; Chris C Holmes

    Polygenic scores (PGS) are individual-level measures that quantify the genetic contribution to a given trait. PGS have predominantly been developed using European ancestry samples and recent studies have shown that the predictive performance of European ancestry-derived PGS is lower in non-European ancestry samples, reflecting differences in linkage disequilibrium, variant frequencies, and variant

    更新日期:2021-01-18
  • AlleleShift: An R package to predict and visualize population-level changes in allele frequencies in response to climate change
    bioRxiv. Genom. Pub Date : 2021-01-17
    Roeland Kindt

    Background: At any particular location, frequencies of alleles in organisms that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients

    更新日期:2021-01-18
  • Evolution of cytokine production capacity in ancient and modern European populations
    bioRxiv. Genom. Pub Date : 2021-01-17
    Jorge Domínguez-Andrés; Yunus Kuijpers; Olivier B. Bakker; Martin Jaeger; Cheng-Jian Xu; Jos WM van der Meer; Mattias Jakobsson; Jaume Bertranpetit; Leo AB Joosten; Yang Li; Mihai G. Netea

    As our ancestors migrated throughout the different continents, natural selection increased the presence of alleles advantageous in the new environments. Heritable variations that alter the susceptibility to diseases vary with the historical period, the virulence of the infections, and their geographical spread. In this study we built polygenic scores for heritable traits influencing the genetic adaptation

    更新日期:2021-01-18
  • Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs
    bioRxiv. Genom. Pub Date : 2021-01-16
    Christine N Goldfarb; David J Waxman

    While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for lncRNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions

    更新日期:2021-01-18
  • Genetic Control of Pluripotency Epigenome Determines Differentiation Bias in Mouse Embryonic Stem Cells
    bioRxiv. Genom. Pub Date : 2021-01-16
    Candice Byers; Catrina Spruce; Haley J Fortin; Anne Czechanski; Steve C Munger; Laura G Reinholdt; Daniel A Skelly; Christopher L Baker

    Genetically diverse pluripotent stem cells (PSCs) display varied, heritable responses to differentiation cues in the culture environment. By harnessing these disparities through derivation of embryonic stem cells (ESCs) from the BXD mouse genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, we demonstrate genetically determined biases in lineage commitment and identify

    更新日期:2021-01-18
  • De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
    bioRxiv. Genom. Pub Date : 2021-01-16
    Matthew B Hufford; Arun S Seetharam; Margaret R Woodhouse; Kapeel M. Chougule; Shujun Ou; JIANING LIU; William A Ricci; Tingting Guo; Andrew Olson; Yinjie Qiu; Rafael Della Coletta; Silas Tittes; Asher I Hudson; Alexandre P. Marand; Sharon Wei; Zhenyuan Lu; Bo Wang; Marcela K Tello-Ruiz; Rebecca D Piri; Na Wang; Dong won Kim; Yibing Zeng; Christine H O'Connor; Xianran Li; Amanda M Gilbert; Erin Baggs;

    We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete

    更新日期:2021-01-18
  • Insights into the genomic evolution of insects from cricket genomes
    bioRxiv. Genom. Pub Date : 2021-01-15
    Guillem Ylla; Taro Nakamura; Takehiko Itoh; Rei Kajitani; Atsushi Toyoda; Sayuri Tomonari; Tetsuya Bando; Yoshiyasu Ishimaru; Takahito Watanabe; Masao Fuketa; Yuji Matsuoka; Austen Barnett; Sumihare Noji; Taro Mito; Cassandra G. Extavour

    Most of our knowledge of insect genomes comes from Holometabolous species, which undergo the complete metamorphosis and have genomes under 2Gb with little signs of DNA methylation. In contrast, Hemiemetabolous insects undergo the ancestral incomplete metamorphosis and have larger genomes with high levels of DNA methylation. Hemimetabolous species from the Orthopteran order (grasshoppers and crickets)

    更新日期:2021-01-18
  • Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis
    bioRxiv. Genom. Pub Date : 2021-01-15
    Hemakumar M Reddy; Rupa Bhattacharya; Zeenath Jehan; Kankadeb Mishra; Pranatharthi Annapurna; Shrish Tiwari; Nissankararao Mary Praveena; Jomini Liza Alex; Vishnu M Dhople; Lalji Singh; Mahadevan Sivaramakrishnan; Anurag Chaturvedi; Nandini Rangaraj; Thomas Michael Shiju; Badanapuram Sridevi; Sachin Kumar; Ram Reddy Dereddi; Sunayana Rayabandla; Rachel A Jesudasan

    Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which shows unprecedented number of splice variants in testis. Further, Pirmy transcript

    更新日期:2021-01-18
  • Single-cell analysis of colonic epithelium reveals unexpected shifts in cellular composition and molecular phenotype in treatment-naïve adult Crohn’s disease
    bioRxiv. Genom. Pub Date : 2021-01-15
    Matt Kanke; Meaghan M. Kennedy; Sean Connelly; Matthew Schaner; Michael T. Shanahan; Elisabeth A. Wolber; Caroline Beasley; Grace Lian; Animesh Jain; Millie D. Long; Edward L. Barnes; Hans H. Herfarth; Kim L. Isaacs; Jonathan J. Hansen; Muneera Kapadia; José Gaston Guillem; Terrence S. Furey; Shehzad Z. Sheikh; Praveen Sethupathy

    The intestinal epithelial barrier is comprised of a monolayer of specialized intestinal epithelial cells (IECs) that are critical in maintaining gut mucosal homeostasis. Dysfunction within various IEC fractions can increase intestinal permeability, resulting in a chronic and debilitating condition known as Crohn’s disease (CD). Defining the molecular changes in each IEC type in CD will contribute to

    更新日期:2021-01-18
  • Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent global expansion
    bioRxiv. Genom. Pub Date : 2021-01-15
    Yan Chen; Shiyong Li; Wei Wu; Shuaipeng Geng; Mao Mao

    A novel coronavirus, SARS-CoV-2, has caused over 85 million cases and over 1.8 million deaths worldwide since it occurred twelve months ago in Wuhan, China. Here we conceptualized the time-series evolutionary and expansion dynamics of SARS-CoV-2 by taking a series of cross-sectional view of viral genomes from early outbreak in January in Wuhan to early phase of global ignition in early April, and finally

    更新日期:2021-01-16
  • Comparative analysis of whole genome sequences of Leptospira spp. from RefSeq database provide interspecific divergence and repertoire of virulence factors
    bioRxiv. Genom. Pub Date : 2021-01-15
    Mohd Abdullah; Mohammad Kadivella; Rolee Sharma; Mirza S Baig; Syed M Faisal; Sarwar Azam

    Leptospirosis is an emerging zoonotic and neglected disease across the world causing huge loss of life and economy. The disease is caused by Leptospira of which 605 sequenced genomes representing 72 species are available in RefSeq database. A comparative genomics approach based on Average Amino acid Identity (AAI), Average Nucleotide Identity (ANI), and Insilco DNA-DNA hybridization provide insight

    更新日期:2021-01-16
  • The Contributions from the Progenitor Genomes of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible
    bioRxiv. Genom. Pub Date : 2021-01-15
    Yue Hao; Makenzie E. Mabry; Patrick Edger; Michael Freeling; Chunfang Zheng; Lingling Jin; Robert VanBuren; Marivi Colle; Hong An; R. Shawn Abrahams; Jacob D. Washburn; Xinshuai Qi; Kerrie Barry; Christopher Daum; Shengqiang Shu; Jeremy Schmutz; David Sankoff; Michael S. Barker; Eric Lyons; J. Chris Pires; Gavin C. Conant

    The members of the tribe Brassiceae share an ancient whole genome triplication (WGT), and plants in this tribe display extraordinarily high within-species morphological diversity. One proposed model for the formation of these mesohexaploid Brassiceae is that they result from a "two-step" pair of hybridizations. However, evidence supporting this model of formation is still incomplete; meanwhile, the

    更新日期:2021-01-16
  • Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic
    bioRxiv. Genom. Pub Date : 2021-01-14
    Muhammad Shakeel; Muhammad Irfan; Zaibun Nisa; Muhammad Rashid; Sabeeta Kanwal Ansari; Ishtiaq Ahmad Khan

    Surveillance of genetic diversity in the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we monitored mutational events in the SARS-CoV-2 genome through whole genome sequencing. The samples (n=48) were collected from the hot spot regions of the metropolitan city Karachi, Pakistan during the four months (May 2020 to August

    更新日期:2021-01-16
  • The genetic architecture of human cortical folding
    bioRxiv. Genom. Pub Date : 2021-01-14
    Dennis van der Meer; Tobias Kaufmann; Alexey A Shadrin; Carolina Makowski; Oleksandr Frei; Daniel Roelfs; Jennifer Monereo Sanchez; David EJ Linden; Jaroslav Rokicki; Christiaan de Leeuw; Wesley K Thompson; Robert J Loughnan; Chun Chieh Fan; Lars T Westlye; Ole A Andreassen; Anders M Dale

    The folding of the human cerebral cortex is a highly genetically regulated process that allows for a much larger surface area to fit into the cranial vault and optimizes functional organization. Sulcal depth is a robust, yet understudied measure of localized folding, previously associated with a range of neurodevelopmental disorders. Here, we report the first genome-wide association study of sulcal

    更新日期:2021-01-14
  • Functional annotation of human long noncoding RNAs using chromatin conformation data
    bioRxiv. Genom. Pub Date : 2021-01-14
    Saumya Agrawal; Tanvir Alam; Masaru Koido; Ivan V Kulakovskiy; Jessica Severin; Imad Abugessaisa; Andrey Buyan; Josée Dostie; Masayoshi Itoh; Naoto Kondo; Yunjing Li; Mickaël Mendez; Jordan A. Ramilowski; Ken Yagi; Kayoko Yasuzawa; Chi Wai Yip; Yasushi Okazaki; Michael M. Hoffman; Lisa Strug; Chung-Chau Hon; Chikashi Terao; Takeya Kasukawa; Vsevolod J. Makeev; Jay W Shin; Piero Carninci; Michiel Jan

    Transcription of the human genome yields mostly long non-coding RNAs (lncRNAs). Systematic functional annotation of lncRNAs is challenging due to their low expression level, cell type-specific occurrence, poor sequence conservation between orthologs, and lack of information about RNA domains. Currently, 95% of human lncRNAs have no functional characterization. Using chromatin conformation and Cap Analysis

    更新日期:2021-01-14
  • Mutational impact and signature of ionizing radiation
    bioRxiv. Genom. Pub Date : 2021-01-13
    Jeonghwan Youk; Hyun Woo Kwon; Joonoh Lim; Eunji Kim; Ryul Kim; Seongyeol Park; Kijong Yi; Sara Jeon; Jinwook Choi; Hyelin Na; Eun-Seok Lee; Young-Won Cho; Dong-Wook Min; Hyojin Kim; Yeong-Rok Kang; Si Ho Choi; Min Ji Bae; Chang Geun Lee; Joon-Goon Kim; Young Seo Kim; Dong Soo Lee; Tae You Kim; Taeyun Ku; Su Yeon Kim; Joo-Hyeon Lee; Bon-Kyoung Koo; Hyunsook Lee; On Vox Yi; Eon Chul Han; Ji Hyun Chang;

    Whole-genome sequencing (WGS) of human tumors and normal cells exposed to various carcinogens has revealed distinct mutational patterns that provide deep insights into the DNA damage and repair processes. Although ionizing radiation (IR) is conventionally known as a strong carcinogen, its genome-wide mutational impacts have not been comprehensively investigated at the single-nucleotide level. Here

    更新日期:2021-01-14
  • Ultra-conserved sequences in the genomes of highly diverse Anopheles mosquitoes, with implications for malaria vector control.
    bioRxiv. Genom. Pub Date : 2021-01-13
    Samantha M O'Loughlin; Austin Burt; Tony Nolan; Silke Fuchs; Andrea Crisanti; Tania Dottorini; Annie J Forster

    DNA sequences that are exactly conserved over long evolutionary time scales have been observed in a variety of taxa. Such sequences are likely under strong functional constraint and they have been useful in the field of comparative genomics for identifying genome regions with regulatory function. A potential new application for these ultra-conserved elements has emerged in the development of gene drives

    更新日期:2021-01-14
  • Peroxisome import stress impairs ribosome biogenesis and induces integrative stress response through eIF2α phosphorylation
    bioRxiv. Genom. Pub Date : 2021-01-13
    Hua Bai; Kerui Huang; Jinoh Kim; Pham Vo; Ting Miao

    Peroxisome biogenesis diseases (PBDs) are characterized by global defects in peroxisomal function and can result in severe brain, liver, kidney, and bone malfunctions. PBDs are due to mutations in peroxisome biogenesis factors (PEX genes) that are responsible for peroxisome assembly and function. Increasing evidence suggests that peroxisome import functions decline during aging. However, the transcriptome

    更新日期:2021-01-14
  • Phylogenomics of plant-associated Botryosphaeriaceae species
    bioRxiv. Genom. Pub Date : 2021-01-13
    Jadran Garcia; Daniel P Laurence; Abraham Morales-Cruz; Renaud Travadon; Andrea Minio; Rufina Hernadez-Martinez; Philippe E Rolshausen; Kendra Baumgartner; Dario Cantu

    The Botryosphaeriaceae is a fungal family that includes many destructive vascular pathogens of woody plants (e.g., Botryosphaeria dieback of grape, Panicle blight of pistachio). Species in the genera Botryosphaeria, Diplodia, Dothiorella, Lasiodiplodia, Neofusicoccum, and Neoscytalidium attack a range of horticultural crops, but they vary in virulence and in their abilities to infect their hosts via

    更新日期:2021-01-14
  • Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1
    bioRxiv. Genom. Pub Date : 2021-01-13
    Shuang Li; Yuanyuan Li; Blake R Rushing; Susan L McRitchie; Janice C Jones; Susan J Sumner; Henrik G Dohlman

    G proteins were originally discovered through efforts to understand the effects of hormones, such as glucagon and epinephrine, on glucose metabolism. On the other hand, many cellular metabolites, including glucose, serve as ligands for G protein-coupled receptors. Here we investigate the consequences of glucose-mediated receptor signaling, and in particular the role of a Gα subunit Gpa2 and a non-canonical

    更新日期:2021-01-14
  • Novel CHD8 genomic targets identified in fetal mouse brain by in vivo Targeted DamID
    bioRxiv. Genom. Pub Date : 2021-01-13
    A. Ayanna Wade; Jelle van den Ameele; Seth W Cheetham; Rebecca Yakob; Andrea H Brand; Alex S Nord

    Genetic studies of autism spectrum disorder (ASD) have revealed a causal role for mutations in chromatin remodeling genes. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with one of the highest de novo mutation rates in sporadic ASD. However, the relationship between CHD8 genomic function a