Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research
While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and se...
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MDPI AG
2020-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/3/316 |
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| author | Yurui Wang Yaohan Jiang Yongqiang Liu Yuan Li Laura A. Katz Feng Gao Ying Yan |
| author_facet | Yurui Wang Yaohan Jiang Yongqiang Liu Yuan Li Laura A. Katz Feng Gao Ying Yan |
| author_sort | Yurui Wang |
| collection | DOAJ |
| description | While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 10<sup>4</sup> to 8.1 × 10<sup>5</sup>; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies. |
| first_indexed | 2024-12-22T05:51:00Z |
| format | Article |
| id | doaj.art-c04eb86e968f40faa5ce4b4466b8d8a0 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-12-22T05:51:00Z |
| publishDate | 2020-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-c04eb86e968f40faa5ce4b4466b8d8a02022-12-21T18:36:53ZengMDPI AGMicroorganisms2076-26072020-02-018331610.3390/microorganisms8030316microorganisms8030316Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological ResearchYurui Wang0Yaohan Jiang1Yongqiang Liu2Yuan Li3Laura A. Katz4Feng Gao5Ying Yan6Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaDepartment of Biological Sciences, Smith College, Northampton, MA 01063, USAInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaWhile nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 10<sup>4</sup> to 8.1 × 10<sup>5</sup>; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.https://www.mdpi.com/2076-2607/8/3/316ciliatesmtssu rdnanssu rdnacopy numberpolymorphismecology |
| spellingShingle | Yurui Wang Yaohan Jiang Yongqiang Liu Yuan Li Laura A. Katz Feng Gao Ying Yan Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research Microorganisms ciliates mtssu rdna nssu rdna copy number polymorphism ecology |
| title | Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research |
| title_full | Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research |
| title_fullStr | Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research |
| title_full_unstemmed | Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research |
| title_short | Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research |
| title_sort | comparative studies on the polymorphism and copy number variation of mtssu rdna in ciliates protista ciliophora implications for phylogenetic environmental and ecological research |
| topic | ciliates mtssu rdna nssu rdna copy number polymorphism ecology |
| url | https://www.mdpi.com/2076-2607/8/3/316 |
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