| 引用本文: | 沈宗芳, 陆添权, 张志荣, 蔡传涛, 田 波.槲蕨属叶绿体基因组密码子偏好性分析[J].广西植物,2021,41(2):266-273.[点击复制] |
| SHEN Zongfang, LU Tianquan, ZHANG Zhirong, CAI Chuantao, TIAN Bo.Condon preference of chloroplast genome of Drynaria[J].Guihaia,2021,41(2):266-273.[点击复制] |
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| 槲蕨属叶绿体基因组密码子偏好性分析 |
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沈宗芳1,3, 陆添权1, 张志荣2, 蔡传涛1, 田 波1*
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1. 中国科学院西双版纳热带植物园 热带植物资源可持续利用重点实验室, 昆明 650223;2. 中国科学院昆明植物研究所 中国西南野生生物种质资源库, 昆明 650201;3. 中国科学院大学, 北京101408
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| 摘要: |
| 叶绿体基因组密码子偏好性使用模式往往影响基因表达效率,为促进药用植物叶绿体基因工程的发展,提高槲蕨药用品质,该研究以川滇槲蕨、栎叶槲蕨和槲蕨三个近缘药用植物为材料,使用CodonW、 CUSP 和 SPSS等软件分析其叶绿体基因组编码基因密码子使用偏好性,筛选出三个物种的最优密码子。结果表明:川滇槲蕨、栎叶槲蕨和槲蕨叶绿体基因组的有效密码子数(ENC)范围分别为40.10～61、40.33～61和40.15～61,其密码子偏好性较弱; ndhE、rpl22、rpl14、rpl20、ccsA、rps4和rpl16编码基因的ENC值差异较大,表明近缘物种中,部分基因的密码子偏好性存在一定差异; 三个物种编码基因的ENC频数集中于-0.1～0.1 之间,说明槲蕨属基因密码子偏好性主要受到突变的影响。川滇槲蕨12个最优密码子有6个和栎叶槲蕨相同,分别是UCU、ACU、GCU、CAA、AAA和GAU; 栎叶槲蕨10个最优密码子有2个和槲蕨相同,分别是UUA和AUU,而川滇槲蕨与槲蕨无相同的最优密码子。该研究结果可为槲蕨属药用植物基因工程中外源基因的改良及其表达奠定基础。 |
| 关键词: 川滇槲蕨, 栎叶槲蕨, 槲蕨, 叶绿体基因组, 密码子偏好性 |
| DOI：10.11931/guihaia.gxzw201904013 |
| 分类号:Q943.2 |
| 文章编号:1000-3142(2021)02-0266-08 |
| 基金项目:国家战略性热带植物资源收集利用的理论与实践项目(2017XTBG-F05)[Supported by Conservation and Application of National Strategic Tropical Plant Resources: Theory and Practice(2017XTBG-F05)]。 |
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| Condon preference of chloroplast genome of Drynaria |
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SHEN Zongfang1,3, LU Tianquan1, ZHANG Zhirong2, CAI Chuantao1, TIAN Bo1*
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1. CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences,
Kunming 650223, China;2. The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy
of Sciences, Kunming 650201, China;3. University of Chinese Academy of Sciences, Beijing 101408, China
1. CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences,
Kunming 650223, China; 2. The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy
of Sciences, Kunming 650201, China; 3. University of Chinese Academy of Sciences, Beijing 101408, China
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| Abstract: |
| The codon usage patterns of the chloroplast genes were related to the expression efficiency of genes. In order to improve the development of the chloroplast genetic engineering of medicinal plant and to promote the quality of medicinal plant Drynaria roosii, the optimal codons in chloroplast genome were identified through analyzing the factors shaping of codon bias of D. delavayi, D. quercifolia and D. roosii using CodonW, CUSP and SPSS softwares. The results were as follows: The effective number of codons(ENC)of the chloroplast gene ranged from 40.10 to 61, from 40.33 to 61, and from 40.15 to 61 in D. delavayi, D. quercifolia, and D. roosii, respectively, which suggested the codon bias was weak among the three species; The ENC of gene ndhE, rpl22, rpl14, rpl20, ccsA, rps4 and rpl16 showed significant difference among species, which suggested the codon bias of some genes was various in closely species; The distribution of ENC frequency ratio of most coding gene ranged from -0.1 to 0.1, suggesting the codon usage bias was produced by gene mutation in Drynaria species. In addition, 12 codons were identified as optimal codons in D. delavayi, ten in D. quercifolia, and three in D. roosii. The codons UCU, ACU, GCU, CAA, AAA and GAU were the optimal codons in D. delavayi and D. quercifolia, the codons UUA and AUU were the optimal codons in D. quercifolia and D. roosii, while did not in D. delavayi and D.roosii. Our results will be useful for the codon preference analysis of ferns and the chloroplast genetic engineering of medicinal plant. |
| Key words: Drynaria delavayi, D. quercifolia, D. roosii, chloroplast genome, codon preference |
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