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
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
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.
Journal ArticleDOI
Single-cell genome sequencing: current state of the science
TL;DR: An overview of the current state of the field of single-cell genome sequencing is provided, focusing on the technical challenges of making measurements that start from a single molecule of DNA, and how some of these recent methodological advancements have enabled the discovery of unexpected new biology.
Journal ArticleDOI
Clonal evolution in breast cancer revealed by single nucleus genome sequencing
Yong Wang,Jill Waters,Marco L. Leung,Anna K. Unruh,Whijae Roh,Xiuqing Shi,Ken Chen,Paul Scheet,Selina Vattathil,Han Liang,Asha S. Multani,Hong Zhang,Rui Zhao,Franziska Michor,Funda Meric-Bernstam,Nicholas Navin +15 more
TL;DR: The data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded, which has important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
Journal ArticleDOI
Droplet microfluidics for high-throughput biological assays
TL;DR: Droplets allow sample volumes to be significantly reduced, leading to concomitant reductions in cost, and compartmentalization in droplets increases assay sensitivity by increasing the effective concentration of rare species and decreasing the time required to reach detection thresholds.
References
More filters
Journal ArticleDOI
Complete Genome Sequences of the Obligate Symbionts “Candidatus Sulcia muelleri” and “Ca. Nasuia deltocephalinicola” from the Pestiferous Leafhopper Macrosteles quadripunctulatus (Hemiptera: Cicadellidae)
TL;DR: Two bacterial symbionts of the European pest leafhopper, Macrosteles quadripunctulatus, were fully sequenced and are nearly identical to strains reported from the closely related host species, M. quadrilineatus.
Journal ArticleDOI
Capturing and cultivating single bacterial cells in gel microdroplets to obtain near-complete genomes
TL;DR: The method of cocultivation of single-captured bacterial cells in gel microdroplets (GMDs) to improve full genomic sequence recovery is adopted and modified and its efficacy on diverse bacterial species using human oral and gut microbiome samples is demonstrated.
Journal ArticleDOI
Intrahost Genetic Diversity of Bacterial Symbionts Exhibits Evidence of Mixed Infections and Recombinant Haplotypes.
TL;DR: The results strongly suggest that these variant haplotypes originated through recombination events, potentially during prior mixed infections or in the external environment, rather than as novel mutations within symbiont populations.
Journal ArticleDOI
Microbial single-cell omics: the crux of the matter.
TL;DR: This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies.
Journal ArticleDOI
Noninvasive prenatal screening by next-generation sequencing.
Anthony R. Gregg,Ignatia B Van den Veyver,Susan J. Gross,Rajeevi Madankumar,Britton D. Rink,Mary E. Norton +5 more
TL;DR: Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%.