Open AccessJournal Article
One Bacterial Cell, One Complete Genome
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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
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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).
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers,Nikos C. Kyrpides,Ramunas Stepanauskas,Miranda Harmon-Smith,Devin F. R. Doud,T. B. K. Reddy,Frederik Schulz,Jessica K. Jarett,Adam R. Rivers,Adam R. Rivers,Emiley A. Eloe-Fadrosh,Susannah G. Tringe,Susannah G. Tringe,Natalia Ivanova,Alex Copeland,Alicia Clum,Eric D. Becraft,Rex R. Malmstrom,Bruce W. Birren,Mircea Podar,Peer Bork,George M. Weinstock,George M. Garrity,Jeremy A. Dodsworth,Shibu Yooseph,Granger G. Sutton,Frank Oliver Gloeckner,Jack A. Gilbert,William C. Nelson,Steven J. Hallam,Sean P. Jungbluth,Sean P. Jungbluth,Thijs J. G. Ettema,Scott Tighe,Konstantinos T. Konstantinidis,Wen Tso Liu,Brett J. Baker,Thomas Rattei,Jonathan A. Eisen,Brian P. Hedlund,Katherine D. McMahon,Noah Fierer,Rob Knight,Robert D. Finn,Guy Cochrane,Ilene Karsch-Mizrachi,Gene W. Tyson,Christian Rinke,Alla Lapidus,Folker Meyer,Pelin Yilmaz,Donovan H. Parks,A. M. Eren,Lynn M. Schriml,Jillian F. Banfield,Philip Hugenholtz,Tanja Woyke +56 more
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References
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Journal ArticleDOI
Development of a targeted metagenomic approach to study a genomic region involved in light harvesting in marine Synechococcus
Florian Humily,Florian Humily,Gregory K. Farrant,Gregory K. Farrant,Dominique Marie,Dominique Marie,Frédéric Partensky,Frédéric Partensky,Sophie Mazard,Sophie Mazard,Morgan Perennou,Karine Labadie,Jean-Marc Aury,Patrick Wincker,Audrey Nicolas Segui,Audrey Nicolas Segui,David J. Scanlan,Laurence Garczarek,Laurence Garczarek +18 more
TL;DR: Novel insights are provided into Synechococcus community structure and pigment type diversity at a representative coastal station of the English Channel with known dominance of these clades in temperate coastal waters.
Journal ArticleDOI
Draft Genome Sequence of Rickettsia sp. Strain MEAM1, Isolated from the Whitefly Bemisia tabaci
TL;DR: The draft genome sequence of the Rickettsia sp.
Journal ArticleDOI
Proceedings of the 2014 A.S.P.E.N. Research Workshop The Interface Between Nutrition and the Gut Microbiome: Implications and Applications for Human Health
John C. Alverdy,Jack A. Gilbert,Jack A. Gilbert,Jennifer R. DeFazio,Michael J. Sadowsky,Eugene B. Chang,Michael J. Morowitz,Daniel H. Teitelbaum +7 more
TL;DR: This report highlights some of the topics of an A.S.P.E.N.N.-sponsored symposium held during Clinical Nutrition Week in 2013 that address the importance of the human microbiome to human health and disease.
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Single-virus genomics and beyond.
TL;DR: The history of single-virus genomics is provided, how this emergent method has facilitated advances in virus ecology and its current limitations and future potential are discussed, and how this method may synergistically intersect with other single-Virus and single-cell approaches are addressed.
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Overlapping genes in bacterial and bacteriophage genomes
D V Shcherbakov,M B Garber +1 more