Complete, Duplication-Aware Phylogenetic Trees in Vertebrates
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Prospects & Overviews Orthology Prediction Methods: a Quality Assessment Using Curated Protein Families
Prospects & Overviews Methods, Models & Techniques Orthology prediction methods: A quality assessment using curated protein families Kalliopi Trachana1), Tomas A. Larsson1)2), Sean Powell1), Wei-Hua Chen1), Tobias Doerks1), Jean Muller3)4) and Peer Bork1)5)Ã The increasing number of sequenced genomes has Introduction prompted the development of several automated orthology prediction methods. Tests to evaluate the accuracy of pre- The analysis of fully sequenced genomes offers valuable insights into the function and evolution of biological systems dictions and to explore biases caused by biological and [1]. The annotation of newly sequenced genomes, comparative technical factors are therefore required. We used 70 man- and functional genomics, and phylogenomics depend on ually curated families to analyze the performance of five reliable descriptions of the evolutionary relationships of public methods in Metazoa. We analyzed the strengths protein families. All the members within a protein family and weaknesses of the methods and quantified the impact are homologous and can be further separated into orthologs, of biological and technical challenges. From the latter part which are genes derived through speciation from a single ancestral sequence, and paralogs, which are genes resulting of the analysis, genome annotation emerged as the largest from duplication events before and after speciation (out- and single influencer, affecting up to 30% of the performance. in-paralogy, respectively) [2, 3]. The large number of fully Generally, most methods did well in assigning orthologous sequenced genomes and the fundamental role of orthology group but they failed to assign the exact number of genes in modern biology have led to the development of a plethora of forhalfofthegroups.Thepublicly available benchmark set methods (e.g. -
Complementary Symbiont Contributions to Plant Decomposition in a Fungus-Farming Termite
Complementary symbiont contributions to plant decomposition in a fungus-farming termite Michael Poulsena,1,2, Haofu Hub,1, Cai Lib,c, Zhensheng Chenb, Luohao Xub, Saria Otania, Sanne Nygaarda, Tania Nobred,3, Sylvia Klaubaufe, Philipp M. Schindlerf, Frank Hauserg, Hailin Panb, Zhikai Yangb, Anton S. M. Sonnenbergh, Z. Wilhelm de Beeri, Yong Zhangb, Michael J. Wingfieldi, Cornelis J. P. Grimmelikhuijzeng, Ronald P. de Vriese, Judith Korbf,4, Duur K. Aanend, Jun Wangb,j, Jacobus J. Boomsmaa, and Guojie Zhanga,b,2 aCentre for Social Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; bChina National Genebank, BGI-Shenzen, Shenzhen 518083, China; cCentre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark; dLaboratory of Genetics, Wageningen University, 6708 PB, Wageningen, The Netherlands; eFungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, Royal Netherlands Academy of Arts and Sciences, NL-3584 CT, Utrecht, The Netherlands; fBehavioral Biology, Fachbereich Biology/Chemistry, University of Osnabrück, D-49076 Osnabrück, Germany; gCenter for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; hDepartment of Plant Breeding, Wageningen University and Research Centre, NL-6708 PB, Wageningen, The Netherlands; iDepartment of Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria SA-0083, South Africa; and jDepartment of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark Edited by Ian T. Baldwin, Max Planck Institute for Chemical Ecology, Jena, Germany, and approved August 15, 2014 (received for review October 24, 2013) Termites normally rely on gut symbionts to decompose organic levels-of-selection conflicts that need to be regulated (12). -
Peregrine and Saker Falcon Genome Sequences Provide Insights Into Evolution of a Predatory Lifestyle
LETTERS OPEN Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle Xiangjiang Zhan1,7, Shengkai Pan2,7, Junyi Wang2,7, Andrew Dixon3, Jing He2, Margit G Muller4, Peixiang Ni2, Li Hu2, Yuan Liu2, Haolong Hou2, Yuanping Chen2, Jinquan Xia2, Qiong Luo2, Pengwei Xu2, Ying Chen2, Shengguang Liao2, Changchang Cao2, Shukun Gao2, Zhaobao Wang2, Zhen Yue2, Guoqing Li2, Ye Yin2, Nick C Fox3, Jun Wang5,6 & Michael W Bruford1 As top predators, falcons possess unique morphological, 16,263 genes were predicted for F. peregrines, and 16,204 were pre- physiological and behavioral adaptations that allow them to be dicted for F. cherrug (Supplementary Table 6 and Supplementary successful hunters: for example, the peregrine is renowned as Note). Approximately 92% of these genes were functionally annotated the world’s fastest animal. To examine the evolutionary basis of using homology-based methods (Supplementary Table 7). predatory adaptations, we sequenced the genomes of both the Comparative genome analysis was carried out to assess evolution peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and innovation within falcons using related genomes with comparable All rights reserved. and we present parallel, genome-wide evidence for evolutionary assembly quality (Supplementary Table 8). Orthologous genes were innovation and selection for a predatory lifestyle. The genomes, identified in the chicken, zebra finch, turkey, peregrine and saker assembled using Illumina deep sequencing with greater than using the program TreeFam3. For the five genome-enabled avian spe- 100-fold coverage, are both approximately 1.2 Gb in length, cies, a maximum-likelihood phylogeny using 861,014 4-fold degen- with transcriptome-assisted prediction of approximately 16,200 erate sites from 6,267 single-copy orthologs confirmed that chicken America, Inc. -
Supplemental Material for Aggregated Dendrograms for Visual Comparison Between Many Phylogenetic Trees
Supplemental Material for Aggregated Dendrograms for Visual Comparison Between Many Phylogenetic Trees Zipeng Liu, Shing Hei Zhan, and Tamara Munzner December 3, 2018 Contents S1 View coordination details2 S2 Cluster AD gradient coloring4 S3 Algorithm details5 S3.1 AD layout function parameters..........................5 S3.2 Front-end caching for rendering ADs.......................6 S4 Expert Interview Study8 S4.1 Participants....................................8 S4.2 Interview Questions................................8 S5 Full Screenshots of Usage Scenario 1: 1KP pilot study 10 S5.1 Sister group of land plants............................ 10 S5.2 Early diversification of land plants........................ 15 S6 Usage scenario 2: TreeFam 17 S6.1 PROTOSTOMIA and DEUTEROSTOMIA ..................... 17 S6.2 ECDYSOZOA and LOPHOTROZOA ........................ 22 S7 Screenshots of Information Density Comparison 24 S8 Case Studies 27 S8.1 Full Screenshots of Case Study 1......................... 27 S8.2 Full Screenshots of Case Study 2......................... 28 S8.3 Case Study 3................................... 28 S9 Screenshots of Dataset Upload 31 1 S1 View coordination details Table S1 documents the view coordination discussed in Section 6.6 of the main paper, showing which aspect of the data is visually encoded across all five levels of detail for each of the eight views. The table has six columns since we break out branches from leaves for clarity; both of these are the lowest level of detail. We duplicate Figure 7 and put it here for a quick reference showing all of these views, as Figure S1. 2 View Level of detail (LoD) Tree collection Subset of trees Individual Subtree Branch & Leaf node tree its attributes Reference color text label & whole view line & tooltip Dendrogram background black dot Tree Distribution row segment in row Cluster AD whole view one cluster line or Individual AD one AD block collapsed Pairwise butterfly color text label & consensus tree line & tooltip comparison layout background black dot t-SNE Tree Similarity dot scatterplot Ref. -
Strategic Plan 2011-2016
Strategic Plan 2011-2016 Wellcome Trust Sanger Institute Strategic Plan 2011-2016 Mission The Wellcome Trust Sanger Institute uses genome sequences to advance understanding of the biology of humans and pathogens in order to improve human health. -i- Wellcome Trust Sanger Institute Strategic Plan 2011-2016 - ii - Wellcome Trust Sanger Institute Strategic Plan 2011-2016 CONTENTS Foreword ....................................................................................................................................1 Overview .....................................................................................................................................2 1. History and philosophy ............................................................................................................ 5 2. Organisation of the science ..................................................................................................... 5 3. Developments in the scientific portfolio ................................................................................... 7 4. Summary of the Scientific Programmes 2011 – 2016 .............................................................. 8 4.1 Cancer Genetics and Genomics ................................................................................ 8 4.2 Human Genetics ...................................................................................................... 10 4.3 Pathogen Variation .................................................................................................. 13 4.4 Malaria -
Treefam: 2008 Update Jue Ruan1, Heng Li2, Zhongzhong Chen1, Avril Coghlan2, Lachlan James M
Published online 1 December 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D735–D740 doi:10.1093/nar/gkm1005 TreeFam: 2008 Update Jue Ruan1, Heng Li2, Zhongzhong Chen1, Avril Coghlan2, Lachlan James M. Coin3, Yiran Guo1, Jean-Karim He´ riche´ 2, Yafeng Hu1, Karsten Kristiansen4, Ruiqiang Li1,4, Tao Liu1, Alan Moses2, Junjie Qin1, Søren Vang5, Albert J. Vilella6, Abel Ureta-Vidal6, Lars Bolund1,7, Jun Wang1,4,7 and Richard Durbin2,* 1Beijing Institute of Genomics of the Chinese Academy of Sciences, Beijing Genomics Institute, Beijing 101300, China, 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, 3Department of Epidemiology & Public Health, Imperial College, St Mary’s Campus, Norfolk Place, London W2 1PG, UK, 4Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, 5Research Unit for Molecular Medicine, Aarhus University Hospital and Faculty of Health Sciences, University of Aarhus, DK-8200 Aarhus N, Denmark, 6EMBL-European Bioinformatics Institute, Hinxton, Cambridge, UK and 7Institute of Human Genetics, University of Aarhus, DK-8000 Aarhus C, Denmark Received September 14, 2007; Revised October 21, 2007; Accepted October 23, 2007 ABSTRACT In his original definition of orthology, Fitch defined orthologues in terms of a phylogenetic tree of a gene TreeFam (http://www.treefam.org) was developed family (1). It has now been well established that analysis of to provide curated phylogenetic trees for all animal phylogenetic trees is a very accurate way to determine gene families, as well as orthologue and paralogue orthology (2,3), which led us to develop the TreeFam assignments. Release 4.0 of TreeFam contains database and accompanying website in 2005 (4). -
Regulatory Evolution in Proteins by Turnover and Lineage-Specific Changes of Cyclin-Dependent Kinase Consensus Sites
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites Alan M. Moses*†, Muluye E. Liku‡, Joachim J. Li§, and Richard Durbin* *Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1HH, United Kingdom; and Departments of ‡Biochemistry and §Microbiology and Immunology, University of California, San Francisco, CA 94143 Edited by Philip P. Green, University of Washington School of Medicine, Seattle, WA, and approved September 25, 2007 (received for review February 6, 2007) Evolutionary change in gene regulation is a key mechanism un- after the initiation of DNA replication, to ensure that a single derlying the genetic component of organismal diversity. Here, we round of DNA replication occurs in each eukaryotic cell cycle, study evolution of regulation at the posttranslational level by a subset of the DNA replication machinery (the pre-RC) is examining the evolution of cyclin-dependent kinase (CDK) consen- directly inhibited by cyclin-dependent kinase (CDK) (17, 18). sus phosphorylation sites in the protein subunits of the pre- Here, we examine the evolution of regulation of the pre-RC replicative complex (RC). The pre-RC, an assembly of proteins by CDKs. Several features of this system make it attractive for formed during an early stage of DNA replication, is believed to be evolutionary analysis. First, the pre-RC proteins are found in regulated by CDKs throughout the animals and fungi. Interest- single copy in many animals and fungi (17), so it is relatively easy ingly, although orthologous pre-RC components often contain to identify their orthologs in most species. Also, human CDKs clusters of CDK consensus sites, the positions and numbers of sites have been shown to rescue yeast CDK mutations (19, 20), do not seem conserved. -
Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation. -
Endosomal PI(3)P Regulation by the COMMD/CCDC22/CCDC93
ARTICLE https://doi.org/10.1038/s41467-019-12221-6 OPEN Endosomal PI(3)P regulation by the COMMD/ CCDC22/CCDC93 (CCC) complex controls membrane protein recycling Amika Singla 1,5, Alina Fedoseienko2,5, Sai S.P. Giridharan3, Brittany L. Overlee2, Adam Lopez1, Da Jia 4, Jie Song1, Kayci Huff-Hardy1, Lois Weisman3, Ezra Burstein 1,6 & Daniel D. Billadeau2,6 1234567890():,; Protein recycling through the endolysosomal system relies on molecular assemblies that interact with cargo proteins, membranes, and effector molecules. Among them, the COMMD/CCDC22/CCDC93 (CCC) complex plays a critical role in recycling events. While CCC is closely associated with retriever, a cargo recognition complex, its mechanism of action remains unexplained. Herein we show that CCC and retriever are closely linked through sharing a common subunit (VPS35L), yet the integrity of CCC, but not retriever, is required to maintain normal endosomal levels of phosphatidylinositol-3-phosphate (PI(3)P). CCC complex depletion leads to elevated PI(3)P levels, enhanced recruitment and activation of WASH (an actin nucleation promoting factor), excess endosomal F-actin and trapping of internalized receptors. Mechanistically, we find that CCC regulates the phosphorylation and endosomal recruitment of the PI(3)P phosphatase MTMR2. Taken together, we show that the regulation of PI(3)P levels by the CCC complex is critical to protein recycling in the endosomal compartment. 1 Department of Internal Medicine, and Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 2 Division of Oncology Research and Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA. -
An Atlas of Cell Types in the Mouse Epididymis and Vas Deferens
TOOLS AND RESOURCES An atlas of cell types in the mouse epididymis and vas deferens Vera D Rinaldi1†, Elisa Donnard2†, Kyle Gellatly2, Morten Rasmussen1‡, Alper Kucukural2, Onur Yukselen2, Manuel Garber2,3, Upasna Sharma4, Oliver J Rando1* 1Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States; 2Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States; 3Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States; 4Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States Abstract Following testicular spermatogenesis, mammalian sperm continue to mature in a long epithelial tube known as the epididymis, which plays key roles in remodeling sperm protein, lipid, and RNA composition. To understand the roles for the epididymis in reproductive biology, we generated a single-cell atlas of the murine epididymis and vas deferens. We recovered key epithelial cell types including principal cells, clear cells, and basal cells, along with associated *For correspondence: support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. [email protected] Moreover, our data illuminate extensive regional specialization of principal cell populations across †These authors contributed the length of the epididymis. In addition to region-specific specialization of principal cells, we find equally to this work evidence for functionally specialized subpopulations of stromal cells, and, most notably, two ‡ distinct populations of clear cells. Our dataset extends on existing knowledge of epididymal Present address: Department of Virus and Microbiological biology, and provides a wealth of information on potential regulatory and signaling factors that Special Diagnostics, Statens bear future investigation. -
A New Entrez Database Transitioning from Locuslink to Entrez
NCBI News National Center for Biotechnology Information National Library of Medicine National Institutes of Health Spring 2004 Department of Health and Human Services Transitioning from LocusLink to Entrez Gene Cancer Chromosomes: a New Entrez Database A gene-based view of annotated The Entrez Gene help document genomes is essential to capitalize on provides tips to ease the transition Three databases, the NCI/NCBI the increase in the sequencing and for LocusLink users to the current SKY (Spectral Karyotyping)/M- analysis of model genomes. The Entrez Gene database. FISH (Multiplex-FISH) and CGH Entrez Gene database has been (Comparative Genomic The default display format for developed to supply key connections Hybridization) Database, the NCI Entrez Gene is the graphics display between maps, sequences, expression Mitelman Database of Chromosome shown in Figure 1 for BMP7, which profiles, structure, function, homolo- Aberrations in Cancer, and the NCI resembles the traditional view of a gy data, and the scientific literature. Recurrent Chromosome Aberrations LocusLink record. The array of col- Unique identifiers are assigned to in Cancer databases are now integrat- ored boxes at the head of LocusLink genes with defining sequence, genes ed into NCBI’s Entrez system as the reports that provide links to gene- with known map positions, and “Cancer Chromosomes” database. related resources is replaced by the genes inferred from phenotypic Cancer Chromosomes supports “Links” menu in Gene, which information. These gene identifiers searches for cytogenetic, clinical, or includes additional links, such as are tracked, and functional informa- reference information using the flexi- those to Books, GEO, UniSTS, and tion is added when available. -
Treefam V9: a New Website, More Species and Orthology-On-The-Fly Fabian Schreiber1,2,*, Mateus Patricio2, Matthieu Muffato2, Miguel Pignatelli2 and Alex Bateman2
D922–D925 Nucleic Acids Research, 2014, Vol. 42, Database issue Published online 4 November 2013 doi:10.1093/nar/gkt1055 TreeFam v9: a new website, more species and orthology-on-the-fly Fabian Schreiber1,2,*, Mateus Patricio2, Matthieu Muffato2, Miguel Pignatelli2 and Alex Bateman2 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and 2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received September 12, 2013; Accepted October 11, 2013 ABSTRACT often used to find these corresponding genes and to allow transfer of annotation from the known to the TreeFam (http://www.treefam.org) is a database of unknown gene. phylogenetic trees inferred from animal genomes. The original orthology definition of Fitch used a phylo- For every TreeFam family we provide homology genetic tree to determine orthology (1). Some of the predictions together with the evolutionary history orthology databases available today follow the same prin- of the genes. Here we describe an update of the ciple and predict orthology/paralogy relationships based TreeFam database. The TreeFam project was resur- on phylogenetic trees reconstructed from alignments of rected in 2012 and has seen two releases since. homologous sequences. One of these databases is The latest release (TreeFam 9) was made available TreeFam, which aims at providing comprehensive gene in March 2013. It has orthology predictions and evolution information and orthology assignments for gene trees for 109 species in 15 736 families animal gene families (2,3). Other tree-based databases that differ either in taxonomic scope and/or tools used covering 2.2 million sequences.