Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites
Morphologically similar to <i>Synechococcus</i>, a large number of <i>Parasynechococcus</i> strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 <i>Synechococcus</i>-like strains were reevaluated using a co...
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| Format: | Article |
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MDPI AG
2022-04-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/11/8/1060 |
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| author | Jie Tang Dan Yao Huizhen Zhou Lianming Du Maurycy Daroch |
| author_facet | Jie Tang Dan Yao Huizhen Zhou Lianming Du Maurycy Daroch |
| author_sort | Jie Tang |
| collection | DOAJ |
| description | Morphologically similar to <i>Synechococcus</i>, a large number of <i>Parasynechococcus</i> strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 <i>Synechococcus</i>-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as <i>Parasynechococcus</i>-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 <i>Parasynechococcus</i>-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 (<i>p</i> < 0.01) but negative correlation with GC content (<i>p</i> < 0.05). Additionally, the motif (A)<sub>n</sub>, (AG)<sub>n</sub> and (AGC)<sub>n</sub> 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 <i>Parasynechococcus</i>-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 <i>Parasynechococcus</i>-like strains to fluctuating environments and contribute to the extensive distribution of <i>Parasynechococcus</i> species in global marine environments. |
| first_indexed | 2024-03-09T13:07:47Z |
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| language | English |
| last_indexed | 2024-03-09T13:07:47Z |
| publishDate | 2022-04-01 |
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| series | Plants |
| spelling | doaj.art-88abc6bbf44646118f661d56e9baf05b2023-11-30T21:46:31ZengMDPI AGPlants2223-77472022-04-01118106010.3390/plants11081060Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound MicrosatellitesJie Tang0Dan Yao1Huizhen Zhou2Lianming Du3Maurycy Daroch4School of Food and Bioengineering, Chengdu University, Chengdu 610106, ChinaSchool of Food and Bioengineering, Chengdu University, Chengdu 610106, ChinaSchool of Food and Bioengineering, Chengdu University, Chengdu 610106, ChinaSchool of Food and Bioengineering, Chengdu University, Chengdu 610106, ChinaSchool of Environment and Energy, Peking University Shenzhen Graduate School, 2199 Lishui Road, Shenzhen 518055, ChinaMorphologically similar to <i>Synechococcus</i>, a large number of <i>Parasynechococcus</i> strains were misclassified, resulting in extreme underestimation of their genetic diversity. In this study, 80 <i>Synechococcus</i>-like strains were reevaluated using a combination of 16S rRNA phylogeny and genomic approach, identifying 54 strains as <i>Parasynechococcus</i>-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 <i>Parasynechococcus</i>-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 (<i>p</i> < 0.01) but negative correlation with GC content (<i>p</i> < 0.05). Additionally, the motif (A)<sub>n</sub>, (AG)<sub>n</sub> and (AGC)<sub>n</sub> 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 <i>Parasynechococcus</i>-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 <i>Parasynechococcus</i>-like strains to fluctuating environments and contribute to the extensive distribution of <i>Parasynechococcus</i> species in global marine environments.https://www.mdpi.com/2223-7747/11/8/1060<i>Parasynechococcus</i>microsatellitesSSRcompound microsatellitesgenetic diversity |
| spellingShingle | Jie Tang Dan Yao Huizhen Zhou Lianming Du Maurycy Daroch Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites Plants <i>Parasynechococcus</i> microsatellites SSR compound microsatellites genetic diversity |
| title | Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites |
| title_full | Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites |
| title_fullStr | Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites |
| title_full_unstemmed | Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites |
| title_short | Reevaluation of <i>Parasynechococcus</i>-like Strains and Genomic Analysis of Their Microsatellites and Compound Microsatellites |
| title_sort | reevaluation of i parasynechococcus i like strains and genomic analysis of their microsatellites and compound microsatellites |
| topic | <i>Parasynechococcus</i> microsatellites SSR compound microsatellites genetic diversity |
| url | https://www.mdpi.com/2223-7747/11/8/1060 |
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