Discrimination Between Synechocystis Members (Cyanobacteria) Based on Heterogeneity of Their 16S rRNA and ITS Regions

Juteršek, Mojca; Klemenčič, Marina; Dolinar, Marko

doi:10.17344/acsi.2017.3262

Cited by 6 publications

(4 citation statements)

References 41 publications

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“…Divided cells may remain solitary or form small colonies in culture as Synechocystis (Jutersek et al. 2017), few celled rows as in Crocosphaera , large irregular colonies as in Microcystis (Harke et al. 2016) or colonies with unique radial ( Woronichinia ) or rectangular ( Merismopedia ) shapes.…”

Section: Resultsmentioning

confidence: 99%

“…Cells are generally 4-8 lm wide, (2) 4-8 lm long, spherical, oval, or cylindrical with widely rounded ends, with irregularly oriented stacks or rafts of thylakoids. Divided cells may remain solitary or form small colonies in culture as Synechocystis (Jutersek et al 2017), few celled rows as in Crocosphaera, large irregular colonies as in Microcystis (Harke et al 2016) or colonies with unique radial (Woronichinia) or rectangular (Merismopedia) shapes. Several genera can form macroscopic spherical or irregular gelatinous colonies spreading over a substrate (Gloeothece, Aphanothece).…”

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confidence: 99%

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An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

Strunecký

Ivanova

Mareš

2023

Journal of Phycology

125

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Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well‐described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

Strunecký

Ivanova

Mareš

2023

Journal of Phycology

125

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“…2011) and have been used for Synechocystis species (Juteršek et al. 2017). In Altericista spp., total ITS length is 508–543 bp (Table S3 in the Supporting Information) and within this region, two tRNAs are encoded: one for iso‐leucine and the other for alanine.…”

Section: Resultsmentioning

confidence: 99%

A new cyanobacterial genus Altericista and three species, A. lacusladogae sp. nov., A. violacea sp. nov., and A. variichlora sp. nov., described using a polyphasic approach

Averina

Polyakova

Senatskaya

et al. 2021

Journal of Phycology

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Several strains of unicellular cyanobacteria from the culture collection of St. Petersburg State University, St. Petersburg, Russia (CALU), which were preliminary identified as Synechocystis sp., are reclassified in the new genus Altericista. Three new species are proposed, A. lacusladogae, A. violacea, and A. variichlora. The last species produces accessory chlorophylls d and f in cultures illuminated by far‐red light, an attribute rarely observed in cyanobacteria, especially in unicellular strains. This genus is morphologically similar to Synechocysis having coccoid cells that divide in two successive planes at right angles, containing no sheath or capsule, and having the lamellar system represented by peripheral concentric thylakoids. Altericista shows ecological, biochemical, and physiological characters unlike those in Synechocystis and has the distinguishing phenotypic characters as follows: freshwater, non‐halotolerant ecotype; palmitate and α‐linoleate as major fatty acids; and the ability to photoacclimate, including several types of complementary chromatic adaptation. Genetic differences from Synechocystis sp. include 16S rRNA, rpoC1, and rbcL gene sequences, as well as sequence and folding of 16S‐23S ITS.

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“…NKBG15041c, which are unicellular strains that encode both a CrhR-like and RhlE-like helicase. Polyphyly has long been a known issue in the genera Synechococcus [ 56 ] and Synechocystis [ 57 ]. 16S rDNA and concatenated gene trees group Synechocystis sp.…”

Section: Resultsmentioning

confidence: 99%

Genera specific distribution of DEAD-box RNA helicases in cyanobacteria

2021

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Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli . The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales , Oscillatoriales and Synechococcales . Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus . In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.

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Discrimination Between Synechocystis Members (Cyanobacteria) Based on Heterogeneity of Their 16S rRNA and ITS Regions

Cited by 6 publications

References 41 publications

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

A new cyanobacterial genus Altericista and three species, A. lacusladogae sp. nov., A. violacea sp. nov., and A. variichlora sp. nov., described using a polyphasic approach

Genera specific distribution of DEAD-box RNA helicases in cyanobacteria

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