Reference Genome Sequence of the Model Plant Setaria
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Reproductive Phasirna Loci and DICER-LIKE5, but Not Microrna
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.25.061721; this version posted April 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Reproductive phasiRNA loci and DICER‐LIKE5, but not microRNA loci, diversified in monocotyledonous plants Parth Patel2§, Sandra M. Mathioni1§, Reza Hammond2, Alex E. Harkess1, Atul Kakrana2, Siwaret Arikit3, Ayush Dusia2, and Blake C. Meyers1,2,4* 1Donald Danforth Plant Science Center, Saint Louis, Missouri 63132 2Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19716 3Department of Agronomy, Kamphaeng Saen and Rice Science Center, Kasetsart University, Nakhon Pathom 73140, Thailand 4Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 §These authors contributed equally to this work. *Corresponding author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.04.25.061721; this version posted April 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract (200 words) 2 In monocots other than maize and rice, the repertoire and diversity of microRNAs (miRNAs) and 3 the populations of phased, secondary, small interfering RNAs (phasiRNAs) are poorly 4 characterized. To remedy this, we sequenced small RNAs from vegetative and dissected 5 inflorescence tissue in 28 phylogenetically diverse monocots and from several early‐diverging 6 angiosperm lineages, as well as publicly available data from 10 additional monocot species. -
Y Chromosome Dynamics in Drosophila
Y chromosome dynamics in Drosophila Amanda Larracuente Department of Biology Sex chromosomes X X X Y J. Graves Sex chromosome evolution Proto-sex Autosomes chromosomes Sex Suppressed determining recombination Differentiation X Y Reviewed in Rice 1996, Charlesworth 1996 Y chromosomes • Male-restricted • Non-recombining • Degenerate • Heterochromatic Image from Willard 2003 Drosophila Y chromosome D. melanogaster Cen Hoskins et al. 2015 ~40 Mb • ~20 genes • Acquired from autosomes • Heterochromatic: Ø 80% is simple satellite DNA Photo: A. Karwath Lohe et al. 1993 Satellite DNA • Tandem repeats • Heterochromatin • Centromeres, telomeres, Y chromosomes Yunis and Yasmineh 1970 http://www.chrombios.com Y chromosome assembly challenges • Repeats are difficult to sequence • Underrepresented • Difficult to assemble Genome Sequence read: Short read lengths cannot span repeats Single molecule real-time sequencing • Pacific Biosciences • Average read length ~15 kb • Long reads span repeats • Better genome assemblies Zero mode waveguide Eid et al. 2009 Comparative Y chromosome evolution in Drosophila I. Y chromosome assemblies II. Evolution of Y-linked genes Drosophila genomes 2 Mya 0.24 Mya Photo: A. Karwath P6C4 ~115X ~120X ~85X ~95X De novo genome assembly • Assemble genome Iterative assembly: Canu, Hybrid, Quickmerge • Polish reference Quiver x 2; Pilon 2L 2R 3L 3R 4 X Y Assembled genome Mahul Chakraborty, Ching-Ho Chang 2L 2R 3L 3R 4 X Y Y X/A heterochromatin De novo genome assembly species Total bp # contigs NG50 D. simulans 154,317,203 161 21,495729 -
The Bacteria Genome Pipeline (BAGEP): an Automated, Scalable Workflow for Bacteria Genomes with Snakemake
The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake Idowu B. Olawoye1,2, Simon D.W. Frost3,4 and Christian T. Happi1,2 1 Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria 2 African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria 3 Microsoft Research, Redmond, WA, USA 4 London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom ABSTRACT Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across -
Lawrence Berkeley National Laboratory Recent Work
Lawrence Berkeley National Laboratory Recent Work Title 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Permalink https://escholarship.org/uc/item/7cx5710p Journal Nature biotechnology, 35(7) ISSN 1087-0156 Authors Mukherjee, Supratim Seshadri, Rekha Varghese, Neha J et al. Publication Date 2017-07-01 DOI 10.1038/nbt.3886 Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESOU r CE OPEN 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life Supratim Mukherjee1,10, Rekha Seshadri1,10, Neha J Varghese1, Emiley A Eloe-Fadrosh1, Jan P Meier-Kolthoff2 , Markus Göker2 , R Cameron Coates1,9, Michalis Hadjithomas1, Georgios A Pavlopoulos1 , David Paez-Espino1 , Yasuo Yoshikuni1, Axel Visel1 , William B Whitman3, George M Garrity4,5, Jonathan A Eisen6, Philip Hugenholtz7 , Amrita Pati1,9, Natalia N Ivanova1, Tanja Woyke1, Hans-Peter Klenk8 & Nikos C Kyrpides1 We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. -
Telomere-To-Telomere Assembly of a Complete Human X Chromosome W
https://doi.org/10.1038/s41586-020-2547-7 Accelerated Article Preview Telomere-to-telomere assembly of a W complete human X chromosome E VI Received: 30 July 2019 Karen H. Miga, Sergey Koren, Arang Rhie, Mitchell R. Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, GlennisE A. Logsdon, Accepted: 29 May 2020 Valerie A. Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Accelerated Article Preview Published Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki,R Christopher Markovic, online 14 July 2020 Valerie Maduro, Amalia Dutra, Gerard G. Bouffard, Alexander M. Chang, Nancy F. Hansen, Amy B. Wilfert, Françoise Thibaud-Nissen, Anthony D. Schmitt,P Jon-Matthew Belton, Cite this article as: Miga, K. H. et al. Siddarth Selvaraj, Megan Y. Dennis, Daniela C. Soto, Ruta Sahasrabudhe, Gulhan Kaya, Telomere-to-telomere assembly of a com- Josh Quick, Nicholas J. Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, plete human X chromosome. Nature Rosa ana Risques, Tina A. Graves Lindsay, RobertE Fulton, Ira Hall, Benedict Paten, https://doi.org/10.1038/s41586-020-2547-7 Kerstin Howe, Winston Timp, Alice Young, James C. Mullikin, Pavel A. Pevzner, (2020). Jennifer L. Gerton, Beth A. Sullivan, EvanL E. Eichler & Adam M. Phillippy C This is a PDF fle of a peer-reviewedI paper that has been accepted for publication. Although unedited, the Tcontent has been subjected to preliminary formatting. Nature is providing this early version of the typeset paper as a service to our authors and readers. The text andR fgures will undergo copyediting and a proof review before the paper is published in its fnal form. -
The Setaria Viridis Genome and Diversity Panel Enables Discovery of a Novel
bioRxiv preprint doi: https://doi.org/10.1101/744557; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene Authors: Pu Huang1,5, Sujan Mamidi2, Adam Healey2, Jane Grimwood2, Jerry Jenkins2, Kerrie Barry3, Avinash Sreedasyam2, Shengqiang Shu3, Maximilian Feldman1,6, Jinxia Wu1,7, Yunqing Yu1, Cindy Chen3, Jenifer Johnson3, Hitoshi Sakakibara4,8, Takatoshi Kiba4,9, Tetsuya Sakurai4,9, Daniel Rokhsar3, Ivan Baxter1, Jeremy Schmutz2,3, Thomas P. Brutnell1,7, Elizabeth A. Kellogg1,* 1 Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA 2 HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA 3 Department of Energy Joint Genome Institute, Walnut Creek, California, USA 4 RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan 5 present address: BASF Corporation, 26 Davis Dr., Durham, NC 27709, USA 6 present address: USDA-ARS Temperate Tree Fruit and Vegetable Research Unit, 24106 N. Bunn Rd., Prosser, WA 99350, USA 7 Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China 8 present address: Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan 1 bioRxiv preprint doi: https://doi.org/10.1101/744557; this version posted August 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Foxtail Millet (Setaria Italica), Grain | Feedipedia
Foxtail millet (Setaria italica), grain | Feedipedia Animal feed resources Feedipedia information system Home About Feedipedia Team Partners Get involved Contact us Foxtail millet (Setaria italica), grain Automatic translation Description Nutritional aspects Nutritional tables References Sélectionner une langue ▼ Click on the "Nutritional aspects" tab for recommendations for ruminants, pigs, poultry, rabbits, horses, fish and crustaceans Feed categories All feeds Forage plants Cereal and grass forages Legume forages Forage trees Aquatic plants Common names Other forage plants Plant products/by-products Foxtail millet, dwarf setaria, foxtail bristle grass, German millet, giant setaria, green bristle grass, green foxtail, green foxtail Cereal grains and by-products millet, Hungarian millet, Italian millet, wild foxtail millet, nunbank setaria [English]; mijo, mijo de Italia, mijo menor, moha, moha Legume seeds and by-products de Alemania, moha de Hungria, panizo común, almorejo [Spanish]; painço, milho painço, milho painço de Itália [Portuguese]; Oil plants and by-products millet d'Italie, millet des oiseaux, petit mil, sétaire verte, sétaire d'Italie [French]; Kolbenhirse, Italienische Borstenhirse ذيل الثعلب اإيطالي ;[Fruits and by-products [German]; jawawut, sekoi [Indonesian]; setária-verde [Italian]; juwawut, otèk [Javanese]; setariya [Kinyarwanda Roots, tubers and by-products [Arabic]; 粟 [Chinese]; 조 [Korean]; [Hindi]; アワ [Japanese]; [Kannada]; [Malayalam]; Sugar processing by-products [Nepali]; Щети́ нник италья́нский [Russian]; [Tamil]; [Telugu]; ขาวฟ้ ่ างหางหมา [Thai] Plant oils and fats Other plant by-products Species Feeds of animal origin Animal by-products Setaria italica (L.) P. Beauv. [Poaceae] Dairy products/by-products Animal fats and oils Synonyms Insects Other feeds Chaetochloa italica (L.) Scribn., Chaetochloa viridis (L.) Scribn., Chamaeraphis viridis (L.) Millsp., Panicum italicum L., Minerals Panicum pachystachys Franch. -
Human Genome Reference Program (HGRP)
Frequently Asked Questions – Human Genome Reference Program (HGRP) Funding Announcements • RFA-HG-19-002: High Quality Human Reference Genomes (HQRG) • RFA-HG-19-003: Research and Development for Genome Reference Representations (GRR) • RFA-HG-19-004: Human Genome Reference Center (HGRC) • NOT-HG-19-011: Emphasizing Opportunity for Developing Comprehensive Human Genome Sequencing Methodologies Concept Clearance Slides https://www.genome.gov/pages/about/nachgr/september2018agendadocuments/sept2018council_hg _reference_program.pdf. *Note that this presentation includes a Concept for a fifth HGRP component seeking development of informatics tools for the pan-genome. Eligibility Questions 1. Are for-profit entities eligible to apply? a. Only higher education institutes, governments, and non-profits are eligible to apply for the HGRC (RFA-HG-19-004). b. For-profit entities are eligible to apply for HQRG and GRR (RFA-HG-19-002 and 003), and for the Notice for Comprehensive Human Genome Sequencing Methodologies (NOT-HG- 19-011). The Notice also allows SBIR applications. 2. Can foreign institutions apply or receive subcontracts? a. Foreign institutions are eligible to apply to the HQRG and GRR announcements, and Developing Comprehensive Sequencing Methodologies Notice. b. Foreign institutions, including non-domestic (U.S.) components of U.S. organizations, are not eligible for HGRC. However, the FOA does allow foreign components. c. For more information, please see the NIH Grants Policy Statement. 3. Will applications with multiple sites be considered? Yes, applications with multiple sites, providing they are eligible institutions, will be considered. Application Questions 1. How much funding is available for this program? NHGRI has set aside ~$10M total costs per year for the Human Genome Reference Program. -
De Novo Genome Assembly Versus Mapping to a Reference Genome
De novo genome assembly versus mapping to a reference genome Beat Wolf PhD. Student in Computer Science University of Würzburg, Germany University of Applied Sciences Western Switzerland [email protected] 1 Outline ● Genetic variations ● De novo sequence assembly ● Reference based mapping/alignment ● Variant calling ● Comparison ● Conclusion 2 What are variants? ● Difference between a sample (patient) DNA and a reference (another sample or a population consensus) ● Sum of all variations in a patient determine his genotype and phenotype 3 Variation types ● Small variations ( < 50bp) – SNV (Single nucleotide variation) – Indel (insertion/deletion) 4 Structural variations 5 Sequencing technologies ● Sequencing produces small overlapping sequences 6 Sequencing technologies ● Difference read lengths, 36 – 10'000bp (150-500bp is typical) ● Different sequencing technologies produce different data And different kinds of errors – Substitutions (Base replaced by other) – Homopolymers (3 or more repeated bases) ● AAAAA might be read as AAAA or AAAAAA – Insertion (Non existent base has been read) – Deletion (Base has been skipped) – Duplication (cloned sequences during PCR) – Somatic cells sequenced 7 Sequencing technologies ● Standardized output format: FASTQ – Contains the read sequence and a quality for every base http://en.wikipedia.org/wiki/FASTQ_format 8 Recreating the genome ● The problem: – Recreate the original patient genome from the sequenced reads ● For which we dont know where they came from and are noisy ● Solution: – Recreate the genome -
Literature Cited Robert W. Kiger, Editor This Is a Consolidated List Of
RWKiger 26 Jul 18 Literature Cited Robert W. Kiger, Editor This is a consolidated list of all works cited in volumes 24 and 25. In citations of articles, the titles of serials are rendered in the forms recommended in G. D. R. Bridson and E. R. Smith (1991). When those forms are abbreviated, as most are, cross references to the corresponding full serial titles are interpolated here alphabetically by abbreviated form. Two or more works published in the same year by the same author or group of coauthors will be distinguished uniquely and consistently throughout all volumes of Flora of North America by lower-case letters (b, c, d, ...) suffixed to the date for the second and subsequent works in the set. The suffixes are assigned in order of editorial encounter and do not reflect chronological sequence of publication. The first work by any particular author or group from any given year carries the implicit date suffix "a"; thus, the sequence of explicit suffixes begins with "b". Works missing from any suffixed sequence here are ones cited elsewhere in the Flora that are not pertinent in these volumes. Aares, E., M. Nurminiemi, and C. Brochmann. 2000. Incongruent phylogeographies in spite of similar morphology, ecology, and distribution: Phippsia algida and P. concinna (Poaceae) in the North Atlantic region. Pl. Syst. Evol. 220: 241–261. Abh. Senckenberg. Naturf. Ges. = Abhandlungen herausgegeben von der Senckenbergischen naturforschenden Gesellschaft. Acta Biol. Cracov., Ser. Bot. = Acta Biologica Cracoviensia. Series Botanica. Acta Horti Bot. Prag. = Acta Horti Botanici Pragensis. Acta Phytotax. Geobot. = Acta Phytotaxonomica et Geobotanica. [Shokubutsu Bunrui Chiri.] Acta Phytotax. -
Practical Guideline for Whole Genome Sequencing Disclosure
Practical Guideline for Whole Genome Sequencing Disclosure Kwangsik Nho Assistant Professor Center for Neuroimaging Department of Radiology and Imaging Sciences Center for Computational Biology and Bioinformatics Indiana University School of Medicine • Kwangsik Nho discloses that he has no relationships with commercial interests. What You Will Learn Today • Basic File Formats in WGS • Practical WGS Analysis Pipeline • WGS Association Analysis Methods Whole Genome Sequencing File Formats WGS Sequencer Base calling FASTQ: raw NGS reads Aligning SAM: aligned NGS reads BAM Variant Calling VCF: Genomic Variation How have BIG data problems been solved in next generation sequencing? gkno.me Whole Genome Sequencing File Formats • FASTQ: text-based format for storing both a DNA sequence and its corresponding quality scores (File sizes are huge (raw text) ~300GB per sample) @HS2000-306_201:6:1204:19922:79127/1 ACGTCTGGCCTAAAGCACTTTTTCTGAATTCCACCCCAGTCTGCCCTTCCTGAGTGCCTGGGCAGGGCCCTTGGGGAGCTGCTGGTGGGGCTCTGAATGT + BC@DFDFFHHHHHJJJIJJJJJJJJJJJJJJJJJJJJJHGGIGHJJJJJIJEGJHGIIJJIGGIIJHEHFBECEC@@D@BDDDDD<<?DB@BDDCDCDDC @HS2000-306_201:6:1204:19922:79127/2 GGGTAAAAGGTGTCCTCAGCTAATTCTCATTTCCTGGCTCTTGGCTAATTCTCATTCCCTGGGGGCTGGCAGAAGCCCCTCAAGGAAGATGGCTGGGGTC + BCCDFDFFHGHGHIJJJJJJJJJJJGJJJIIJCHIIJJIJIJJJJIJCHEHHIJJJJJJIHGBGIIHHHFFFDEEDED?B>BCCDDCBBDACDD8<?B09 @HS2000-306_201:4:1106:6297:92330/1 CACCATCCCGCGGAGCTGCCAGATTCTCGAGGTCACGGCTTACACTGCGGAGGGCCGGCAACCCCGCCTTTAATCTGCCTACCCAGGGAAGGAAAGCCTC + CCCFFFFFHGHHHJIJJJJJJJJIJJIIIGIJHIHHIJIGHHHHGEFFFDDDDDDDDDDD@ADBDDDDDDDDDDDDEDDDDDABCDDB?BDDBDCDDDDD -
Y Chromosome
G C A T T A C G G C A T genes Article An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome Matthew J. Jevit 1 , Brian W. Davis 1 , Caitlin Castaneda 1 , Andrew Hillhouse 2 , Rytis Juras 1 , Vladimir A. Trifonov 3 , Ahmed Tibary 4, Jorge C. Pereira 5, Malcolm A. Ferguson-Smith 5 and Terje Raudsepp 1,* 1 Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458, USA; [email protected] (M.J.J.); [email protected] (B.W.D.); [email protected] (C.C.); [email protected] (R.J.) 2 Molecular Genomics Workplace, Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843-4458, USA; [email protected] 3 Laboratory of Comparative Genomics, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; [email protected] 4 Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-6610, USA; [email protected] 5 Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; [email protected] (J.C.P.); [email protected] (M.A.F.-S.) * Correspondence: [email protected] Abstract: The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y.