Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria

Abstract

Microsatellites (simple sequence repeats, SSRs) are ubiquitously distributed in almost all known genomes. Here, the first investigation was designed to examine the SSRs and compound microsatellites (CSSRs) in genomes of Leptolyngbya-like strains. The results disclosed diversified patterns of distribution, abundance, density, and diversity of SSRs and CSSRs in genomes, indicating that they may be subject to rapid evolutionary change. The numbers of SSRs and CSSRs were extremely unevenly distributed among genomes, ranging from 11,086 to 24,000 and from 580 to 1865, respectively. Dinucleotide SSRs were the most abundant category in 31 genomes, while the other 15 genomes followed the pattern: mono- > di- > trinucleotide SSRs. The patterns related to SSRs and CSSRs showed differences among phylogenetic groups. Both SSRs and CSSRs were overwhelmingly distributed in coding regions. The numbers of SSRs and CSSRs were significantly positively correlated with genome size (p < 0.01) and negatively correlated with GC content (p < 0.05). Moreover, the motif (A/C)n and (AG)n was predominant in mononucleotide and dinucleotide SSRs, and unique motifs of CSSRs were identified in 39 genomes. This study provides the first insight into SSRs and CSSRs in genomes of Leptolyngbya-like strains and will be useful to understanding their distribution, predicting their function, and tracking their evolution. Additionally, the identified SSRs may provide an evolutionary advantage of fast adaptation to environmental changes and may play an important role in the cosmopolitan distribution of Leptolyngbya strains to globally diverse niches.

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

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Characterization of Molecular Diversity and Organization of Phycobilisomes in Thermophilic Cyanobacteria

“…Maximum-likelihood (ML) phylogenetic analyses were carried out using PhyML v3.0 [ 66 ], and the substitution models were automatically selected by the model selection function implemented in PhyML [ 67 ] under Bayesian information criterion (BIC). Parameter settings in PhyML and bootstrap analysis of phylogenies were followed as described [ 68 ].…”

Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae

“…Consequently, establishing new genera as references will benefit the reallocation of numerous taxonomically ambiguous strains. For instance, Leptolyngbya -like strains have been scattered across phylogenies based on 16S rRNA or multi-locus sequence analysis within or even beyond family Leptolyngbyaceae ( Sciuto and Moro, 2016 ; Yao et al, 2021 ). As the taxonomic delineation of isolates through systematic identification, numerous Leptolyngbya -like strains were assigned to new genus or species, such as Allonema , Enugrolinea , and Thermoleptolyngbya ( Sciuto and Moro, 2016 ; Walter et al, 2017 ).…”