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. 2021 Oct 11;28(6):dsab024.
doi: 10.1093/dnares/dsab024.

Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade

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Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade

Yuu Hirose et al. DNA Res. .

Abstract

Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.

Keywords: Cyanobacteria; culture collection; genome; heterocyst; taxonomy.

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Figures

Figure 1
Figure 1
The number of genome assemblies of Cyanobacteria deposited in the International Nucleotide Sequence Database Collaboration (INSDC) databases (DDBJ, European Nucleotide Archive, and GenBank). The total number of released Cyanobacteria genomes per year is plotted. The composition of the assembly levels of each genome are shown as stacked line graphs: contig (light yellow), scaffold (light orange), chromosome (light green), and complete genome (light red). The fraction of metagenome-derived assemblies is shown as dashed line graph (black).
Figure 2
Figure 2
The number of Cyanobacteria genome assemblies in the RefSeq database. (A) The total number of assemblies (upper) and distribution of the genome size (lower) are plotted for each Cyanobacteria section. The box plots show first and third quartiles. The middle line in the box shows median genome size. The upper and lower whiskers show maximum and minimum genome size, which extended no more than 1.5-folds of distance between the first and third quartiles. The violin plots show the distribution of genome size of each assembly. (B) The composition of the assembly levels from this study was plotted for each Cyanobacteria section. We did not include assemblies with unassigned sections.
Figure 3
Figure 3
The phylogenetic position of the sequenced NIES strains from this study in the RefSeq database. The phylogenetic relationships among the 31 sequenced strains from the NIES collection are shown within the context of all 855 Cyanobacteria genomes in the RefSeq database. The phylogenetic tree was estimated with the ML method based on the conserved marker genes using PhyloPhlAn (see Supplementary Fig. S2 for the entire tree). Clades 1, 2, and 3, which contain the 31 sequenced NIES strains from this study (red), are enlarged here. The morphological classifications of each strain are shown as coloured circles at the tips of the phylogenetic tree: Sections of I (yellow), II (orange), III (green), IV (red), V (blue), and unassigned (purple). The assembly levels of each genome are shown as coloured stripes: contig (light yellow), scaffold (light orange), chromosome (light green), and complete genome (light red). Major subclades made up of a single genus (solid black lines) and multiple genera (dashed black lines) are shown. The distribution of members of the genera Nostoc, Anabaena, Trichormus, Tolypothrix, Calothrix, and Scytonema are shown (filled black squares). Bootstrap values of >80% in the 100 replications are shown with a black circle.
Figure 4
Figure 4
A phylogenetic tree for 1,709 strains of Cyanobacteria based on their 16S rRNA gene sequences in the SILVA database. The phylogenetic tree was estimated based on 1,709 sequences from the SILVA database for Cyanobacteria 16S rRNA genes clustered at 97% identity. Section- and family-level assignments of the sequences based on the SILVA taxonomy are shown. The number of sequences in each cluster is indicated by the circle sizes. Clusters containing RefSeq assemblies are colored in red. The fraction of uncultured strains was estimated from the taxonomic assignments in SILVA (e.g. taxonomy containing ‘Uncultured’) and is plotted on the tree (black/white gradient).

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