Complete genome sequence of Candidatus Ruthia magnifica

Roeselers, Guus; Newton, Irene L.  G.; Woyke, Tanja; Auchtung, Thomas A.; Dilly, Geoffrey F.; Dutton, Rachel J.; Fisher, Meredith C.; Fontanez, Kristina M.; Lau, Evan; Stewart, Frank J.; Richardson, Paul M.; Barry, Kerrie W.; Saunders, Elizabeth; Detter, John C.; Wu, Dongying; Eisen, Jonathan A.; Cavanaugh, Colleen M.

doi:10.4056/sigs.1103048

Complete genome sequence of Candidatus Ruthia magnifica

Journal Article · Wed Oct 27 00:00:00 EDT 2010 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1103048· OSTI ID:1628649

Roeselers, Guus ^[1]; Newton, Irene L. G. ^[2]; Woyke, Tanja ^[3]; Auchtung, Thomas A. ^[4]; Dilly, Geoffrey F. ^[4]; Dutton, Rachel J. ^[5]; Fisher, Meredith C. ^[4]; Fontanez, Kristina M. ^[4]; Lau, Evan ^[4]; Stewart, Frank J. ^[4]; Richardson, Paul M. ^[3]; Barry, Kerrie W. ^[3]; Saunders, Elizabeth ^[3]; Detter, John C. ^[3]; Wu, Dongying ^[6]; Eisen, Jonathan A. ^[6]; Cavanaugh, Colleen M. ^[4]

Harvard Univ., Cambridge, MA (United States). Dept. of Organismic and Evolutionary Biology; Radboud Univ., Nijmegen (Netherlands). Dept. of Microbiology; DOE/OSTI
Harvard Univ., Cambridge, MA (United States). Dept. of Organismic and Evolutionary Biology; Wellesley College, Wellesley, MA (United States). Dept. of Biological Sciences
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Harvard Univ., Cambridge, MA (United States). Dept. of Organismic and Evolutionary Biology
Harvard Medical School, Boston, MA (United States). Dept. of Microbiology and Molecular Genetics
Univ. of California, Davis, CA (United States). Davis Genome Center, Genome and Biomedical Sciences Facility

The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628649

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 2 Vol. 3; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Draft Genome Sequence of the Endosymbiont “ Candidatus Ruthia magnifica” UCD-CM (Phylum Proteobacteria ) Lee, Ruth D.; Jospin, Guillaume; Coil, David A. Genome Announcements, Vol. 2, Issue 4 https://doi.org/10.1128/genomea.00717-14	journal	August 2014
A new genus Turneroconcha (Bivalvia: Vesicomyidae: Pliocardiinae) for the giant hydrothermal vent clam ‘Calyptogena’ magnifica Krylova, Elena M.; Sahling, Heiko Zootaxa, Vol. 4808, Issue 1 https://doi.org/10.11646/zootaxa.4808.1.4	journal	July 2020
Small genomes and the difficulty to define minimal translation and metabolic machineries Gil, Rosario; Peretó, Juli Frontiers in Ecology and Evolution, Vol. 3 https://doi.org/10.3389/fevo.2015.00123	journal	October 2015
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Diversity and Transcriptional Levels of RuBisCO Form II of Sulfur-Oxidizing γ-Proteobacteria in Coastal-Upwelling Waters with Seasonal Anoxia Léniz, Bárbara; Murillo, Alejandro A.; Ramírez-Flandes, Salvador Frontiers in Marine Science, Vol. 4 https://doi.org/10.3389/fmars.2017.00213	journal	July 2017
On the evolutionary ecology of symbioses between chemosynthetic bacteria and bivalves Roeselers, Guus; Newton, Irene L. G. Applied Microbiology and Biotechnology, Vol. 94, Issue 1 https://doi.org/10.1007/s00253-011-3819-9	journal	February 2012
Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species Lim, Shen Jean; Davis, Brenton G.; Gill, Danielle E. The ISME Journal, Vol. 13, Issue 4 https://doi.org/10.1038/s41396-018-0318-3	journal	December 2018
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Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi McCuaig, Bonita; Pena-Castillo, Lourdes; Dufour, Suzanne C. Animal Microbiome https://doi.org/10.1101/330373	journal	May 2018
Metagenomic analysis suggests broad metabolic potential in extracellular symbionts of the bivalve Thyasira cf. gouldi McCuaig, Bonita; Peña-Castillo, Lourdes; Dufour, Suzanne C. Animal Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/s42523-020-00025-9	journal	March 2020

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Clam
Genetics & Heredity
Hydrotheral vent
Microbiology
chemosynthesis
vesicomyidae
sulfur
symbiosis

Complete genome sequence of Candidatus Ruthia magnifica

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