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.

scholarly journals High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

2018 ◽  
Vol 6 (19) ◽  
pp. e00383-18 ◽  
Author(s):  
David K. Ngugi ◽  
Ulrich Stingl
Keyword(s):  
Single Cell ◽  
Lake Sediments ◽  
Red Sea ◽  
Genome Sequence ◽  
Soda Lake ◽  
Genome Sequences ◽  
High Quality ◽  
Candidate Division ◽  
Cell Genome ◽  
Single Cell Genome

ABSTRACT Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

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 Resolving within-host malaria parasite diversity using single-cell sequencing

2018 ◽  
Author(s):  
Standwell C. Nkhoma ◽  
Simon G. Trevino ◽  
Karla M. Gorena ◽  
Shalini Nair ◽  
Stanley Khoswe ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Single Cell Analysis ◽  
Sequence Data ◽  
Host Population ◽  
Parasite Diversity ◽  
Genomic Analyses ◽  
Cell Genome ◽  
Diversity Transmission ◽  
Single Cell Genome

Malaria patients can carry one or more clonal lineage of the parasite, Plasmodium falciparum, but the composition of these infections cannot be directly inferred from bulk sequence data. Well-defined, complete haplotypes at single-cell resolution are ideal for describing within-host population structure and unambiguously determining parasite diversity, transmission dynamics and recent ancestry but have not been analyzed on a large scale. We generated 485 near-complete single-cell genome sequences isolated from fifteen P. falciparum patients from Chikhwawa, Malawi, an area of intense malaria transmission. Matched single-cell and bulk genomic analyses revealed patients harbored up to seventeen unique lineages. Estimation of parasite relatedness within patients suggests superinfection by repeated mosquito bites is rarer than co-transmission of parasites from a single mosquito. Our single-cell analysis indicates strong barriers to establishment of new infections in malaria-infected patients and allows high resolution dissection of intra-host variation in malaria parasites.

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 Three Draft Single-Cell Genome Sequences of Novel SAR324 Strains Isolated from the Abyssopelagic Southern Ocean

2021 ◽  
Vol 10 (39) ◽  
Author(s):  
Diego J. Castillo ◽  
Marc W. Van Goethem ◽  
Thulani P. Makhalanyane
Keyword(s):  
Southern Ocean ◽  
Single Cell ◽  
Marine Environments ◽  
Genome Sequences ◽  
Content Type ◽  
Cell Genome ◽  
Indian Sector ◽  
Single Cell Genome

SAR324 is a ubiquitous and phylogenetically distinct clade of Deltaproteobacteria in marine environments. Here, we present three single-cell amplified genome sequences from the SAR324 lineage, obtained from the abyssopelagic zone of the Indian sector of the Southern Ocean.

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