Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing
Microcystis is one of the most common and dominant bloom-forming cyanobacteria in freshwater worldwide. The method for genotype detection based on traditional molecular cloning is expensive and time consuming and generates a limited number of sequences. In this study, a high-throughput sequencing (H...
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| Format: | Article |
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Frontiers Media S.A.
2018-05-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00971/full |
| _version_ | 1818672610599239680 |
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| author | Da Huo Da Huo Youxin Chen Tao Zheng Xiang Liu Xinyue Zhang Gongliang Yu Zhiyi Qiao Renhui Li |
| author_facet | Da Huo Da Huo Youxin Chen Tao Zheng Xiang Liu Xinyue Zhang Gongliang Yu Zhiyi Qiao Renhui Li |
| author_sort | Da Huo |
| collection | DOAJ |
| description | Microcystis is one of the most common and dominant bloom-forming cyanobacteria in freshwater worldwide. The method for genotype detection based on traditional molecular cloning is expensive and time consuming and generates a limited number of sequences. In this study, a high-throughput sequencing (HTS) method was developed to detect the internal transcribed spacer (ITS) regions between 16S and 23S rRNA region of Microcystis populations along a typical water system in Yuqiao Reservoir–Haihe River in Tianjin, northern China. A total of 629,341 reads were obtained and clustered into 2005 operational taxonomic units (OTUs). Analysis of alpha diversity indices showed that the Haihe River is more diverse than Yuqiao Reservoir. In general, the two water areas exhibit a clear differentiation pattern in OTU abundance, sharing genotypes from a small part of Yuqiao Reservoir with those in the Haihe River. Phylogenetic analysis further indicated the possible flexible evolution of Microcystis genotypes occurring in the research areas. This study provides the first exhaustive description of HTS method for detection of ITS region to evaluate Microcystis intra-species diversity and relationship. |
| first_indexed | 2024-12-17T07:42:38Z |
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| id | doaj.art-c53843da351e4a88b6f1447de5ec7d54 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-17T07:42:38Z |
| publishDate | 2018-05-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-c53843da351e4a88b6f1447de5ec7d542022-12-21T21:58:06ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-05-01910.3389/fmicb.2018.00971329518Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation SequencingDa Huo0Da Huo1Youxin Chen2Tao Zheng3Xiang Liu4Xinyue Zhang5Gongliang Yu6Zhiyi Qiao7Renhui Li8National Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, ChinaKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaNational Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, ChinaKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaNational Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, ChinaKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaNational Demonstration Center for Experimental Aqua-ecology and Aquaculture Education, Department of Fisheries Sciences, Tianjin Agricultural University, Tianjin, ChinaKey Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, ChinaMicrocystis is one of the most common and dominant bloom-forming cyanobacteria in freshwater worldwide. The method for genotype detection based on traditional molecular cloning is expensive and time consuming and generates a limited number of sequences. In this study, a high-throughput sequencing (HTS) method was developed to detect the internal transcribed spacer (ITS) regions between 16S and 23S rRNA region of Microcystis populations along a typical water system in Yuqiao Reservoir–Haihe River in Tianjin, northern China. A total of 629,341 reads were obtained and clustered into 2005 operational taxonomic units (OTUs). Analysis of alpha diversity indices showed that the Haihe River is more diverse than Yuqiao Reservoir. In general, the two water areas exhibit a clear differentiation pattern in OTU abundance, sharing genotypes from a small part of Yuqiao Reservoir with those in the Haihe River. Phylogenetic analysis further indicated the possible flexible evolution of Microcystis genotypes occurring in the research areas. This study provides the first exhaustive description of HTS method for detection of ITS region to evaluate Microcystis intra-species diversity and relationship.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00971/fullcyanobacteriaYuqiao reservoirHaihe Riverhigh throughput sequencingITS region |
| spellingShingle | Da Huo Da Huo Youxin Chen Tao Zheng Xiang Liu Xinyue Zhang Gongliang Yu Zhiyi Qiao Renhui Li Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing Frontiers in Microbiology cyanobacteria Yuqiao reservoir Haihe River high throughput sequencing ITS region |
| title | Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing |
| title_full | Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing |
| title_fullStr | Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing |
| title_full_unstemmed | Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing |
| title_short | Characterization of Microcystis (Cyanobacteria) Genotypes Based on the Internal Transcribed Spacer Region of rRNA by Next-Generation Sequencing |
| title_sort | characterization of microcystis cyanobacteria genotypes based on the internal transcribed spacer region of rrna by next generation sequencing |
| topic | cyanobacteria Yuqiao reservoir Haihe River high throughput sequencing ITS region |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00971/full |
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