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

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.

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

“…On the other hand, Ralstonia pickettii , Paracoccus yeei , and Bacillus oceanisediminis are typically found in nature environments including soil, brines, rivers, lakes, and marine environments ( Coenye et al., 2003 ; Koskinen et al., 2017 ; Zhang et al., 2010 ) and thus are more likely to be sourced from the original culture or exist in the extracellular polysaccharide matrix of the Nostoc strain ( Huo et al., 2021 ). Overall, because this platform provides visual confirmation of single cell prior to cell lysis and DNA amplification, the contamination rate is significantly lowered compared with the sequencing of colonies of Nostoc species (contamination rate ranging from 80% to <5%)( Huo et al., 2021 ; Hirose et al., 2021 ). In this work, identified contaminants were removed from the sequenced reads prior to the genome sequence assembly of Nostoc strain CCCryo 231-06.…”

Compensatory Transcriptional Response of Fischerella thermalis to Thermal Damage of the Photosynthetic Electron Transfer Chain

“…As most of the 48 Fischerella genomes were fragmented, we focused on the only F. thermalis closed genome (strain NIES-3754, GCF_001548455.1 [ 49 ]), which showed that F. thermalis has three G4- psb A copies ( Table S1 ). In contrast, the only complete genome from a mesophilic Fischerella (strain NIES-4106, GCF_002368315.1 [ 50 ]) has five copies of G4- psb A ( Table S1 ). Differences in the G4- psb A copy number between F. thermalis and the mesophilic Fischerella were also observed in the high-quality open genomes of the genus Fischerella ( Table S1 ), supporting that F. thermalis has fewer copies of G4- psb A than mesophilic Fischerella .…”

Thermosynechococcus switches the direction of phototaxis by a c-di-GMP-dependent process with high spatial resolution

“…Genomic DNA of WT_N strain was prepared from a 40-ml culture with an optical density of ~2.0 with a Genomic-tip 20/G kit (Qiagen). Preparation of the paired-end DNA libraries and sequencing on the Illumina MiSeq platform were performed as described previously ( Hirose et al, 2021 ). Raw sequence reads were deposited in the DDBJ Sequence Read Archive under accession number DRA013349.…”