Open AccessJournal Article
One Bacterial Cell, One Complete Genome
Reads0
Chats0
TLDR
In this article, the authors reported the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN, which is a polyploid species with genome copies ranging from approximately 200-900 per cell.Abstract:
While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.read more
Citations
More filters
Posted ContentDOI
Genome-reconstruction for eukaryotes from complex natural microbial communities
TL;DR: A kmer-based strategy for eukaryotic sequence identification is developed and applied to environmental samples to show that it enables genome recovery, genome completeness evaluation and prediction of metabolic potential and the broader utility of EukRep is demonstrated by reconstructing and evaluating relatively high quality fungal, protist, and rotifer genomes from complex environmental samples.
Journal ArticleDOI
Cytoplasmic incompatibility involving Cardinium and Wolbachia in the white-backed planthopper Sogatella furcifera (Hemiptera: Delphacidae)
TL;DR: This study was the first to document reproductive alteration by Cardinium in a diploid host species and it was found to cause a 76 % reduction in egg development, indicating thatcardinium induces CI and the dual infection raises the CI level.
Journal ArticleDOI
Act together-implications of symbioses in aquatic ciliates.
TL;DR: The current understanding of symbioses in aquatic ciliates is summarized to identify the many areas in which knowledge is lacking and to stimulate future research by providing an overview on new methodologies and by formulating a number of emerging questions in this field.
Journal ArticleDOI
Isolation of Optically Targeted Single Bacteria by Application of Fluidic Force Microscopy to Aerobic Anoxygenic Phototrophs from the Phyllosphere
TL;DR: The data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources.
Journal ArticleDOI
Modeling Microbial Community Structure and Functional Diversity Across Time And Space
TL;DR: It is shown that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways, and at both the very large and the very small scales at which microbial systems interact with their environments.
References
More filters
SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
Genome sequencing in microfabricated high-density picolitre reactors
Marcel Margulies,Michael Egholm,William E. Altman,Said Attiya,Joel S. Bader,Lisa A. Bemben,Jan Berka,Michael S. Braverman,Yi-Ju Chen,Zhoutao Chen,Scott Dewell,Lei Du,J. M. Fierro,Xavier V. Gomes,Brian C. Godwin,Wen He,Scott Edward Helgesen,Chun Heen Ho,Gerard P. Irzyk,Szilveszter C. Jando,Maria L. I. Alenquer,Thomas P. Jarvie,Kshama B. Jirage,Jong-Bum Kim,James R. Knight,Janna R. Lanza,John H. Leamon,Steven Lefkowitz,Ming Lei,Jing Li,Kenton Lohman,Hong Lu,Vinod Makhijani,Keith Mcdade,Michael P. McKenna,Eugene W. Myers,Elizabeth Nickerson,John Nobile,Ramona Plant,Bernard P. Puc,Michael T. Ronan,George T. Roth,Gary J. Sarkis,Jan Fredrik Simons,John Simpson,Maithreyan Srinivasan,Karrie R. Tartaro,Alexander Tomasz,Kari A. Vogt,Greg A. Volkmer,Shally H. Wang,Yong Wang,Michael P. Weiner,Pengguang Yu,Richard F. Begley,Jonathan M. Rothberg +55 more
TL;DR: A scalable, highly parallel sequencing system with raw throughput significantly greater than that of state-of-the-art capillary electrophoresis instruments with 96% coverage at 99.96% accuracy in one run of the machine is described.
Journal ArticleDOI
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Journal ArticleDOI
MEGAN analysis of metagenomic data
TL;DR: MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets, is introduced and provides graphical and statistical output for comparing different data sets.
Journal ArticleDOI
Metagenomics: Application of Genomics to Uncultured Microorganisms
TL;DR: Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community.