Reevaluation of Parasynechococcus-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites

Abstract

Morphologically similar to Synechococcus, a large number of Parasynechococcus strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 Synechococcus-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as Parasynechococcus-like strains and showing considerably intragenus genetic divergence among the subclades identified. Further, bioinformatics analysis disclosed diversified patterns of distribution, abundance, density, and diversity of microsatellites (SSRs) and compound microsatellites (CSSRs) in genomes of these Parasynechococcus-like strains. Variations of SSRs and CSSRs were observed amongst phylotypes and subclades. Both SSRs and CSSRs were in particular unequally distributed among genomes. Dinucleotide SSRs were the most widespread, while the genomes showed two patterns in the second most abundant repeat type (mononucleotide or trinucleotide SSRs). Both SSRs and CSSRs were predominantly observed in coding regions. These two types of microsatellites showed positive correlation with genome size (p < 0.01) but negative correlation with GC content (p < 0.05). Additionally, the motif (A)n, (AG)n and (AGC)n was a major one in the corresponding category. Meanwhile, distinctive motifs of CSSRs were found in 39 genomes. This study characterizes SSRs and CSSRs in genomes of Parasynechococcus-like strains and will be useful as a prerequisite for future studies regarding their distribution, function, and evolution. Moreover, the identified SSRs may facilitate fast acclimation of Parasynechococcus-like strains to fluctuating environments and contribute to the extensive distribution of Parasynechococcus species in global marine environments.

Genome-scale identification and comparative analysis of transcription factors in thermophilic cyanobacteria

“…Instead, a high similarity (98.2%) was observed between C9 and Gloeomargarita lithophora Alchichica-D10 from family Gloeomargaritaceae, suggesting that C9 was not a member of family Synechococcaceae. Both assignments of the two strains are consistent with previous studies that the actual taxonomy of Leptolyngbya JSC-1 and Synechococcus C9 has not been validated yet [ 44 , 45 ]. In addition, Thermosynechococcus sp.…”

Characterization of Molecular Diversity and Organization of Phycobilisomes in Thermophilic Cyanobacteria

“…No such distributions are noticed in the thermophiles. It is not surprising that freshwater Synechococcus C9 shows a distinct distribution pattern to marine Synechococcus strains, since the latter are phylogenetically divergent from the former [ 46 ]; recently, a revision of its name to Parasynechococcus has been proposed.…”

Characterization of a novel thermophilic cyanobacterium within Trichocoleusaceae, Trichothermofontia sichuanensis gen. et sp. nov., and its CO2-concentrating mechanism

“…Protein sequences of genes ccmK , -L , -M , -N , -O , and -P encoding carboxysome shell proteins were also collected for phylogenetic reconstruction. All the phylogenetic analyses were performed using Maximum-Likelihood (ML) algorithm as previously described ( Tang et al, 2022c ).…”

“…As a result, the diversity of thermophilic cyanobacterial genera might be severely underestimated, and community efforts are being made to rectify it. Synechococcus -like strains ( Tang et al, 2022c ) and Leptolyngbya -like strains ( Mai et al, 2018 ; Yao et al, 2021 ) have undergone an extensive reevaluation based on multi-locus sequence analysis and genomic data, providing new insights into genetic diversity of the two genera. Furthermore, polyphasic taxonomic classification approaches have been widely utilized for cyanobacterial identification, particularly for understudied or unresolved polyphyletic families/genera/species and identification of novel families and genera ( Raabova et al, 2019 ; Shalygin et al, 2020 ).…”