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
TL;DR: Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
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References
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Journal ArticleDOI
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The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
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Journal ArticleDOI
Comprehensive human genome amplification using multiple displacement amplification
Frank B. Dean,Seiyu Hosono,Linhua Fang,Xiaohong Wu,A. Fawad Faruqi,Patricia Bray-Ward,Zhenyu Sun,Qiuling Zong,Yuefen Du,Jing Du,Mark D. Driscoll,Wanmin Song,Stephen F. Kingsmore,Michael Egholm,Roger S. Lasken +14 more
TL;DR: MDA-based whole genome amplification by multiple displacement amplification is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage.
Journal ArticleDOI
Comparative Metagenomics of Microbial Communities
Susannah G. Tringe,Christian von Mering,Arthur Kobayashi,Asaf Salamov,Kevin Chen,Hwai W. Chang,Mircea Podar,Jay M. Short,Eric J. Mathur,John C. Detter,Peer Bork,Philip Hugenholtz,Edward M. Rubin +12 more
TL;DR: This work characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments.