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Nakamurella Multipartita Type Strain (Y-104) Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Nakamurella multipartita type strain (Y-104). Permalink https://escholarship.org/uc/item/85k2g84g Journal Standards in genomic sciences, 2(2) ISSN 1944-3277 Authors Tice, Hope Mayilraj, Shanmugam Sims, David et al. Publication Date 2010 DOI 10.4056/sigs.721316 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:168-175 DOI:10.4056/sigs.721316 Complete genome sequence of Nakamurella multipartita type strain (Y-104T) Hope Tice1, Shanmugam Mayilraj2,3, David Sims4, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Tijana Glavina Del Rio1, Alex Copeland1, Jan-Fang Cheng1, Linda Meincke4, David Bruce1,4, Lynne Goodwin1,4, Sam Pitluck1, Natalia Ivanova1, Konstantinos Mavromatis1, Galina Ovchinnikova1, Amrita Pati1, Amy Chen5, Krishna Palaniappan5, Miriam Land1,6, Loren Hauser1,6, Yun-Juan Chang1,6, Cynthia D. Jeffries1,6, John C. Detter1,4, Thomas Brettin1,4, Manfred Rohde7, Markus Göker2, Jim Bristow1, Jonathan A. Eisen1,8, Victor Markowitz4, Philip Hugenholtz1, Nikos C. Kyrpides1, Hans-Peter Klenk2*, and Feng Chen1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 MTCC - Microbial Type Culture Collection, Institute of Microbial Technology, Chandigarh, India 4 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: polysaccharide-accumulating, septa-forming, nonmotile, Gram-positive, MK-8 (H4), ‘Microsphaeraceae’, Frankineae, GEBA. Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the mo- nospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome se- quence and annotation. This is the first complete genome sequence of a member of the fami- ly Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein- coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain Y-104T [1] (DSM 44233 = ATCC 700099 = Nomenclature of Bacteria (1990 Revision) recom- JCM 9533) is the type strain of the species Naka- mends avoiding the use of names which might murella multipartita, which is the sole member cause confusion and therefore grants priority of and type species of the genus Nakamurella [2], the the fungal genus Microsphaera in the family Erysi- type genus of the family Nacamurellaceae [2]. N. phaceae [4], Stackebrandt et al. maintained the multipartita was first described in 1996 by Yo- illegitimate name when creating the likewise ille- shimi et al. as polysaccharide-accumulating ‘Mi- gitimate family ‘Microsphaeraceae’ in 1997 [5]. In crosphaera multipartita’ and type species of the 2004 Tao et al. replaced the illegitimate genus and genus ‘Microsphaera’ [1]. Unfortunately, Yoshimi family names with the legitimate and validly pub- et al. [1] overlooked the priority of the named fun- lished names Nakamurella and Nakamurellaceae, gal genus Microsphaera described 145 years earli- respectively, in honor of the Japanese microbiolo- er [3]. Principle 1(2) of the International Code of gist Kazonuri Nakamura, who also discovered The Genomic Standards Consortium Nakamurella multipartita type strain (Y-104T) strain Y-104T [2]. Here we present a summary 96.6% sequence identity (EF632902). None of the classification and a set of features for N. multipar- sequences generated from large scale environ- tita strain Y-104T, together with the description of mental samplings and genome surveys surpassed the complete genomic sequencing and annotation. 93% sequence identity and were thereby signifi- cantly less similar to strain Y-104T than the closest Classification and features of organism related type strain, DS-52 T of Humicoccus flavidus The environmental diversity of the members of (95.9%) [7] (status November 2009). the species N. multipartita appears to be limited. Figure 1 shows the phylogenetic neighborhood of Only one 16S rRNA gene sequence from a Finish N. multipartita strain Y-104T in a 16S rRNA based indoor isolate (BF0001B070, 96.2% sequence tree. The sequences of the two identical 16S rRNA identity) is reported in Genbank [6], as well as two gene copies differ by one nucleotide (C- Finish indoor phylotypes (FM872655, 98.2%; homopolymer close to 3’-end) from the previously FM873571, 96.2%) by Taubel et al., and a phylo- published 16S rRNA sequence generated from JCM type from fresh water sediment of the high alti- 9543 (Y08541). tude Andean Altiplano (northern Chile) with Figure 1. Phylogenetic tree highlighting the position of N. multipartita Y-104T relative to the other type strains within the Frankineae. The tree was inferred from 1362 aligned characters [8,9] of the 16S rRNA gene sequence under the maximum likelihood criterion [10] and rooted with the type strain of the order. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Lineages with type strain genome sequencing projects regis- tered in GOLD [11] such as the GEBA organism Geodermatophilus obscurus [12] are shown in blue. Important non-type strains are shown in green [13], and published genomes in bold. N. multipartita strain Y-104T is aerobic and che- septa, were frequently observed during the late moorganotrophic. Cells are non-motile, non-spore log phase of the growth cycle [1]. The doubling forming, Gram-positive (Table 1) and coccus- time was reported to be approximately 11 hours shaped [1]. The cells are 0.8 to 3.0 µm in diameter; in a liquid medium at pH 7.0 and at 25°C [1]. Colo- depending on the growth stage. They occur as nies on agar plates are circular, smooth, convex singles, in pairs or in small irregular clusters (Fig- and white at the early stage of growth and cream- ure 2). A rod-coccus cycle was not observed at any colored at later stage of growth. The polysaccha- stage of the growth. Strain Y-104T has a characte- ride content of the cells is very high, sometimes ristic cell division in which a cell wall-like struc- more than 50% (wt/wt) depending on the culture ture occurs in the middle of each cell during their conditions. Growth of strain Y-104T occurs at a early growth phase. Such structures, also called temperature range of 10-35 °C and a pH range of 169 Standards in Genomic Sciences Tice et al. 5.0 to 9.0 and in the presence of up to 6% NaCl. N. aranine, glutamate, glutamine and histidine as multipartita is positive for catalase production carbon and energy sources [1]. The strain cannot and negative for oxidase activity [1]. It is capable utilize acetate, malate, succinate, arginine, aspara- of utilizing glucose, fructose, mannose, galactose, gine, methanol or glycogen as carbon and energy xylose, sucrose, maltose, lactose, mannitol, sorbi- sources [1]. Strain Y-104T is able to accumulate tol, ethanol, propanol, glycerol, starch, pyruvate, large amounts of polysaccharides in its cells [1]. Figure 2. Scanning electron micrograph of N. multipartita strain Y-104T Chemotaxonomy The murein of N. multipartita strain Y-104T con- isolated from 1-1.5 g of cell paste using Qiagen tains meso-diaminopimelic acid as the diagnostic Genomic 500 DNA Kit (Qiagen, Hilden, Germany) diamino acid [1]. The fatty acid pattern of Y-104T following the manufacturer's instructions with is dominated by iso-C16:0 (19.7%), iso-C15:0 (15.7%) modification st/FT for cell lysis according to Wu and C18:1 (14.0%) and substantial amounts of C16:0 et al. [20]. (10.3%), anteiso-C15:0 (9.2%), iso-C17:0 (8.5%) and anteiso-C (5.2%) were detected [1]. The pre- 17:0 Genome sequencing and assembly dominant menaquinones are MK-8 (H ), approx- 4 The genome was sequenced using Sanger se- imately 97.0%, and minor amounts of MK-7 (H ), 4 quencing platform. All general aspects of library MK-8 (H ) and MK-9 (H ) were present [1]. Mycol- 2 4 construction and sequencing can be found on the ic acids are absent [1]. JGI website. Optimal raft assembly was produced using Arachne assembler. Finishing assemblies Genome sequencing and annotation were made using the parallel phrap assembler Genome project history (High Performance Software, LLC). Possible mis- This organism was selected for sequencing on assemblies were corrected with Dupfinisher [21] the basis of each phylogenetic position, and is or transposon bombing of bridging clones (Epi- part of the Genomic Encyclopedia of Bacteria and centre Biotechnologies, Madison, WI). Gaps be- Archaea project. The genome project is depo- tween contigs were closed by editing in Consed, sited in the Genome OnLine Database [14] and custom primer walk or PCR amplification. A total the complete genome sequence is deposited in of 2,596 Sanger finishing reads were produced to GenBank. Sequencing, finishing and annotation close gaps, to resolve repetitive regions, and to were performed by the DOE Joint Genome Insti- raise the quality of the finished sequence. The tute (JGI). A summary of the project information error rate of the completed genome sequence is is shown in Table 2. less than 1 in 100,000. Together all Sanger reads Growth conditions and DNA isolation provided 15.4× coverage of the genome. The final assembly contains 118,931 Sanger reads.
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