Data integration in microbial genomics ... - Jacobs University

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58 4. MIMARKS troducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages. A schematic overview of MIxS along with the MIxS environmental packages is shown in Figure 4.1. Figure 4.1: Schematic overview about the GSC MIxS standard (brown), including combination with specific environmental packages (blue). Shared descriptors apply to all MIxS checklists, however, each checklist has its own specific descriptors as well. Environmental packages can be applied to any of the checklists. EU, eukarya; BA, bacteria/archaea; PL, plasmid; VI, virus; ORG, organelle. 4.3 Development of MIMARKS and the environmental packages Over the past three decades, the 16S rRNA, 18S rRNA and internal transcribed spacer gene sequences (ITS) from Bacteria, Archaea and microbial Eukaryotes have provided deep insights into the topology of the tree of life [Ludwig and Schleifer, 2005, Ludwig et al., 1998] and the composition of communities of organisms that live in diverse environments, ranging from deep sea hydrothermal vents to ice sheets
4.3. Development of MIMARKS 59 in the Arctic [Giovannoni et al., 1990, Stahl et al., 1984, Ward et al., 1990,DeLong, 1992,Díez et al., 2001,Fuhrman et al., 1992,Hewson and Fuhrman, 2004, Huber et al., 2002, López-García et al., 2001, van der Staay et al., 2001,Pace, 1997,Rappé and Giovannoni, 2003]. Numerous other phylogenetic marker genes have proven useful, including RNA polymerase subunits (rpoB), DNA gyrases (gyrB), DNA recombination and repair proteins (recA) and heat shock proteins (HSP70) [Ludwig and Schleifer, 2005]. Marker genes can also reveal key metabolic functions rather than phylogeny; examples include nitrogen cycling (amoA, nifH, ntcA) [Francis et al., 2007, Zehr et al., 1998] sulfate reduction (dsrAB) [Minz et al., 1999] or phosphorus metabolism (phnA, phnI, phnJ) [Gilbert et al., 2009, Martinez et al., 2010]. In this paper we define all phylogenetic and functional genes (or gene fragments) used to profile natural genetic diversity as ‘marker genes’. MIMARKS (Table 4.1) complements the MIGS/MIMS checklists for genomes and metagenomes by adding two new checklists, a MIMARKS survey, for uncultured diversity marker gene surveys, and a MIMARKS specimen, for marker gene sequences obtained from any material identifiable by means of specimens. The MIMARKS extension adopts and incorporates the standards being developed by the Consortium for the Barcode of Life (CBOL) [Hanner, 2009]. Therefore, the checklist can be universally applied to any marker gene, from small subunit rRNA to cytochrome oxidase I (COI), to all taxa, and to studies ranging from single individuals to complex communities. Both MIMARKS and the environmental packages were developed by collating information from several sources and evaluating it in the framework of the existing MIGS/MIMS checklists. These include four independent community-led surveys, examination of the parameters reported in published studies, and examination of compliance with optional features in INSDC documents. The overall goal of these activities was to design the backbone of the MIMARKS checklist, which describes the most important aspects of marker gene contextual data. Results of community-led surveys Four online surveys about descriptors for marker genes have been conducted to determine researcher preferences for core descriptors. The Department of Energy Joint Genome Institute and SILVA [Pruesse
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Max Planck Institute for Marine Mic
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List of abbreviations BLAST Basic L
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Thesis abstract Deoxyribonucleic ac
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4.2 Introduction . . . . . . . . .
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2 1. Introduction syntax: data leve
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Page 110 and 111: 102 BIBLIOGRAPHY [Beynon-Davies, 20
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CHAPTER 9 ACKNOWLEDGEMENTS First, I
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