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. 2022 Apr 25;25(5):104291.
doi: 10.1016/j.isci.2022.104291. eCollection 2022 May 20.

Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology

Yuguang Liu  1   2   3 , Patricio Jeraldo  1   2 , William Herbert  2   4 , Samantha McDonough  5 , Bruce Eckloff  5 , Dirk Schulze-Makuch  6   7   8   9 , Jean-Pierre de Vera  10 , Charles Cockell  11 , Thomas Leya  12 , Mickael Baqué  13 , Jin Jen  5 , Marina Walther-Antonio  1   2   14
Affiliations

Whole genome sequencing of cyanobacterium Nostoc sp. CCCryo 231-06 using microfluidic single cell technology

Yuguang Liu et al. iScience. .

Abstract

The Nostoc sp. strain CCCryo 231-06 is a cyanobacterial strain capable of surviving under extreme conditions and thus is of great interest for the astrobiology community. The knowledge of its complete genome sequence would serve as a guide for further studies. However, a major concern has been placed on the effects of contamination on the quality of sequencing data without a reference genome. Here, we report the use of microfluidic technology combined with single cell sequencing and de novo assembly to minimize the contamination and recover the complete genome of the Nostoc strain CCCryo 231-06 with high quality. 100% of the whole genome was recovered with all contaminants removed and a strongly supported phylogenetic tree. The data reported can be useful for comparative genomics for phylogenetic and taxonomic studies. The method used in this work can be applied to studies that require high-quality assemblies of genomes of unknown microorganisms.

Keywords: Astrobiology; Microbial genomics; Microbiology; Space sciences.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Optofluidic platform overview (A) An optofluidic platform consists of a microscope, laser tweezers and a microfluidic device consists of 4 identical reaction blocks for high-throughput SC-WGA. (B) The use of laser tweezers to trap single cells of Nostoc strain CCCryo 231-06. Laser trap A_1 was turned on and trapped a single cell in the sample suspension; laser trap B_1 was turned off.
Figure 2
Figure 2
An overview of the workflow of SC-WGS for Nostoc strain CCCryo 231-06
Figure 3
Figure 3
Quality control of the sequencing data (A) Raw data reads R1-based sequence quality. (B) Filtered reads R1-based sequence quality. (C) Raw data reads R2-based sequence quality. (D) Filtered reads R2-based sequence quality.
Figure 4
Figure 4
Representation of metagenome contigs for manual binning Highlighted is the bin for the Nostoc strain CCCryo 231-06. Other organisms are present in the sequence data, being members of the culture or environmental contaminants.
Figure 5
Figure 5
A COG usage bar chart shows the percent of predicted genes of Nostoc strain CCCryo 231-06 and four close relatives No significant differences in gene category usage were apparent among the genomes of these species.
Figure 6
Figure 6
A bar chart shows contaminants detected within amplified Nostoc sp. CCCryo 231-06 samples
Figure 7
Figure 7
A protein-based phylogenetic tree highlighting the position of the Nostoc strain CCCryo 231-06 relative to the neighboring species and other members of Nostoc. Cylindrospermum spp., Leptolyngbya spp., and Phormidium spp. are the outgroup genomes Bootstrap values are shown at each subtree.
Figure 8
Figure 8
Two putative prophages identified in the genome of Nostoc strain CCCryo 231-06 (A) A prophage similar to a putative prophage belonging to N. punctiforme PCC 73102 (91% BLAST identity). (B) A prophage similar to a putative prohage belonging to N. commune HK-02 (93% BLAST identity).
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