The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes
The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the exist...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2018.00533/full |
| _version_ | 1819267406794588160 |
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| author | Jia Li Yingjuan Su Yingjuan Su Ting Wang |
| author_facet | Jia Li Yingjuan Su Yingjuan Su Ting Wang |
| author_sort | Jia Li |
| collection | DOAJ |
| description | The plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed. Together with 39 GenBank sequence data, our taxon sampling covered all the extant gymnosperm orders. The repetitive elements and substitution rates of accD among 57 gymnosperm species were analyzed, the results show: (1) Reading frame length of accD gene in 18 cupressophytes species has also expanded. (2) Many repetitive elements were identified in accD gene of cupressophyte lineages. (3) The synonymous and non-synonymous substitution rates of accD were accelerated in cupressophytes. (4) accD was located in rearrangement endpoints. These results suggested that repetitive elements may mediate the chloroplast genome rearrangement and accelerated the substitution rates. |
| first_indexed | 2024-12-23T21:16:40Z |
| format | Article |
| id | doaj.art-41a08ed21fe64773bb433b7aabe43991 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-23T21:16:40Z |
| publishDate | 2018-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-41a08ed21fe64773bb433b7aabe439912022-12-21T17:30:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-04-01910.3389/fpls.2018.00533356885The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in CupressophytesJia Li0Yingjuan Su1Yingjuan Su2Ting Wang3Department of Life Sciences, Shaanxi Xueqian Normal University, Xi’an, ChinaSchool of Life Sciences, Sun Yat-sen University, Guangzhou, ChinaResearch Institute of Sun Yat-sen University, Shenzhen, ChinaCollege of Life Science, South China Agricultural University, Guangzhou, ChinaThe plastid accD gene encodes a subunit of the acetyl-CoA carboxylase (ACCase) enzyme. The length of accD gene has been supposed to expand in Cryptomeria japonica, Taiwania cryptomerioides, Cephalotaxus, Taxus chinensis, and Podocarpus lambertii, and the main reason for this phenomenon was the existence of tandemly repeated sequences. However, it is still unknown whether the accD gene length in other cupressophytes has expanded. Here, in order to investigate how widespread this phenomenon was, 18 accD sequences and its surrounding regions of cupressophyte were sequenced and analyzed. Together with 39 GenBank sequence data, our taxon sampling covered all the extant gymnosperm orders. The repetitive elements and substitution rates of accD among 57 gymnosperm species were analyzed, the results show: (1) Reading frame length of accD gene in 18 cupressophytes species has also expanded. (2) Many repetitive elements were identified in accD gene of cupressophyte lineages. (3) The synonymous and non-synonymous substitution rates of accD were accelerated in cupressophytes. (4) accD was located in rearrangement endpoints. These results suggested that repetitive elements may mediate the chloroplast genome rearrangement and accelerated the substitution rates.http://journal.frontiersin.org/article/10.3389/fpls.2018.00533/fullaccDrepeat sequencessubstitution ratesrearrangementcupressophytes |
| spellingShingle | Jia Li Yingjuan Su Yingjuan Su Ting Wang The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes Frontiers in Plant Science accD repeat sequences substitution rates rearrangement cupressophytes |
| title | The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes |
| title_full | The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes |
| title_fullStr | The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes |
| title_full_unstemmed | The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes |
| title_short | The Repeat Sequences and Elevated Substitution Rates of the Chloroplast accD Gene in Cupressophytes |
| title_sort | repeat sequences and elevated substitution rates of the chloroplast accd gene in cupressophytes |
| topic | accD repeat sequences substitution rates rearrangement cupressophytes |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2018.00533/full |
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