DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation
文献类型：期刊论文
| 作者 | Li, Shuzhen; Shen, Wenli ; Lian, Shengyang; Wu, Yueni; Qu, Yuanyuan; Deng, Ye
|
| 刊名 | JOURNAL OF HAZARDOUS MATERIALS
 |
| 出版日期 | 2022-08-15 |
| 卷号 | 436期号:0页码:129230 |
| ISSN号 | 0304-3894 |
| 关键词 | HORIZONTAL TRANSFER HYDROCARBONS PAHS GENES DEGRADATION NAPHTHALENE DIVERSITY SEDIMENTS BACTERIA SOIL QUANTIFICATION |
| 英文摘要 | Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD alpha subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD alpha subunit. Here amino acid sequences of the ARHD alpha subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD alpha subunit, and gives guidance on the design and application of primers in the future. |
| 源URL | [https://ir.rcees.ac.cn/handle/311016/47775]  |
| 专题 | 生态环境研究中心_中国科学院环境生物技术重点实验室 |
| 通讯作者 | Deng, Ye |
| 作者单位 | 1.Chinese Acad Sci, Inst Urban Environm, Fujian Key Lab Watershed Ecol, Key Lab Urban Environm & Hlth,Aquat EcoHlth Grp, Xiamen 361021, Peoples R China 2.Dalian Univ Technol, Sch Environm Sci & Technol, Dalian POCT Lab, Dalian 116024, Peoples R Chin 3.Dalian Univ Technol, Sch Environm Sci & Technol, Key Lab Ind Ecol & Environm Engn, Minist Educ, Dalian 116024, Peoples R China 4.Shandong Univ, Inst Marine Sci & Technol, Qingdao 266237, Peoples R China 5.Chinese Acad Sci, Res Ctr Ecoenvironm Sci, CAS Key Lab Environm Biotechnol, Beijing 100085, Peoples R China |
| 推荐引用方式 GB/T 7714 | Li, Shuzhen,Shen, Wenli,Lian, Shengyang,et al. DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation[J]. JOURNAL OF HAZARDOUS MATERIALS,2022,436(0):129230. |
| APA | Li, Shuzhen,Shen, Wenli,Lian, Shengyang,Wu, Yueni,Qu, Yuanyuan,&Deng, Ye.(2022).DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation.JOURNAL OF HAZARDOUS MATERIALS,436(0),129230. |
| MLA | Li, Shuzhen,et al."DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation".JOURNAL OF HAZARDOUS MATERIALS 436.0(2022):129230. |
入库方式： OAI收割
来源：生态环境研究中心
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。