scholarly journals Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microbiome

2020 ◽  
Author(s):  
Yohei Nishikawa ◽  
Masato Kogawa ◽  
Masahito Hosokawa ◽  
Katsuhiko Mineta ◽  
Kai Takahashi ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Single Cells ◽  
Gene Clusters ◽  
Sequencing Platform ◽  
High Resolution Analysis ◽  
Resolution Analysis ◽  
Single Cell Isolation ◽  
Cell Genome ◽  
Single Cell Genome

AbstractTo improve our understanding of the environmental microbiome, we developed a single-cell genome sequencing platform, named SAG-gel, which utilizes gel beads for single-cell isolation, cell lysis, and whole genome amplification (WGA) for sequencing. SAG-gel enables serial, parallel and independent reactions of > 100,000 single cells in a single tube, delivering high-quality genome recovery with storable randomized single-cell genome libraries. From soil and marine environmental sources, we acquired 734 partial genomes that are recapitulated in 231 species, 35% of which were assigned as high-to-medium qualities. We found that each genome to be almost unique and 98.7% of them were newly identified, implying the complex genetic diversities across 44 phyla. The various metabolic capabilities including virulence factors and biosynthetic gene clusters were found across the lineages at single-cell resolution. This technology will accelerate the accumulation of reference genomes of uncharacterized environmental microbes and provide us new insights for their roles.

scholarly journals Construction of thousands of single cell genome sequencing libraries using combinatorial indexing

2016 ◽  
Author(s):  
Sarah A. Vitak ◽  
Kristof A. Torkenczy ◽  
Jimi L. Rosenkrantz ◽  
Andrew J. Fields ◽  
Lena Christiansen ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Copy Number ◽  
Low Cost ◽  
Single Cells ◽  
Copy Number Variant ◽  
Tumor Evolution ◽  
Somatic Variation ◽  
Cell Genome ◽  
Single Cell Genome

AbstractSingle cell genome sequencing has proven to be a valuable tool for the detection of somatic variation, particularly in the context of tumor evolution and neuronal heterogeneity. Current technologies suffer from high per-cell library construction costs which restrict the number of cells that can be assessed, thus imposing limitations on the ability to quantitatively measure genomic heterogeneity within a tissue. Here, we present Single cell Combinatorial Indexed Sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single cell libraries for the purpose of somatic copy number variant detection. In total, we constructed libraries for 16,698 single cells from a combination of cultured cell lines, frontal cortex tissue from Macaca mulatta, and two human adenocarcinomas. This novel technology provides the opportunity for low-cost, deep characterization of somatic copy number variation in single cells, providing a foundational knowledge across both healthy and diseased tissues.

scholarly journals Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

2018 ◽  
Author(s):  
Emma Laks ◽  
Hans Zahn ◽  
Daniel Lai ◽  
Andrew McPherson ◽  
Adi Steif ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Large Scale ◽  
Single Cells ◽  
Genome Structure ◽  
Cancer Tissue ◽  
Genome Replication ◽  
Wide Range ◽  
Cell Genome ◽  
Single Cell Genome

SummaryEssential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.

Characterization of Neonatal Lung Cells Through Single Cell Genome Sequencing

2019 ◽  
Author(s):  
S. Bhattacharya ◽  
J. Lillis ◽  
C. Baker ◽  
M. Guo ◽  
J.R. Myers ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Lung Cells ◽  
Neonatal Lung ◽  
Cell Genome ◽  
Single Cell Genome

scholarly journals High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani

2021 ◽  
Author(s):  
Gabriel H. Negreira ◽  
Pieter Monsieurs ◽  
Hideo Imamura ◽  
Ilse Maes ◽  
Nada Kuk ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
High Throughput ◽  
Early Stage ◽  
Population Expansion ◽  
Cellular Heterogeneity ◽  
Small Subset ◽  
Cell Genome ◽  
Mosaic Aneuploidy ◽  
Single Cell Genome

Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA) might have important evolutionary and functional implications, but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two Leishmania clonal populations representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations. MA usually affected a defined subset of chromosomes, of which some display enrichment in snoRNA genes which could represent an adaptative benefit to the amplification of these chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.

scholarly journals Analysis of single-cell genome sequences of bacteria and archaea

2017 ◽  
Vol 1 (3) ◽  
pp. 249-255 ◽  
Author(s):  
Robert M. Bowers ◽  
Devin F.R. Doud ◽  
Tanja Woyke
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Sequence Data ◽  
Bacterial Cells ◽  
Genome Sequences ◽  
Genetic Makeup ◽  
Cell Genome ◽  
Uncultured Microorganisms ◽  
Single Cell Genome

Single-cell genome sequencing of individual archaeal and bacterial cells is a vital approach to decipher the genetic makeup of uncultured microorganisms. With this review, we describe single-cell genome analysis with a focus on the unique properties of single-cell sequence data and with emphasis on quality assessment and assurance.

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