Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities
文献类型：期刊论文
| 作者 | Zhan, Aibin ; Bailey, Sarah A. ; Heath, Daniel D. ; Macisaac, Hugh J. |
| 刊名 | MOLECULAR ECOLOGY RESOURCES
 |
| 出版日期 | 2014 |
| 卷号 | 14期号:5页码:1049-1059 |
| 关键词 | 454 pyrosequencing aquatic community cytochrome c oxidase subunit I (COI) efficiency test mitochondrial 16S ribosomal RNA (mt16S) small subunit ribosomal DNA (18S) |
| ISSN号 | 1755-098X |
| 中文摘要 | Metabarcode surveys of DNA extracted from environmental samples are increasingly popular for biodiversity assessment in natural communities. Such surveys rely heavily on robust genetic markers. Therefore, analysis of PCR efficiency and subsequent biodiversity estimation for different types of genetic markers and their corresponding primers is important. Here, we test the PCR efficiency and biodiversity recovery potential of three commonly used genetic markers - nuclear small subunit ribosomal DNA (18S), mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (mt16S) - using 454 pyrosequencing of a zooplankton community collected from Hamilton Harbour, Ontario. We found that biodiversity detection power and PCR efficiency varied widely among these markers. All tested primers for COI failed to provide high-quality PCR products for pyrosequencing, but newly designed primers for 18S and 16S passed all tests. Furthermore, multiple analyses based on large-scale pyrosequencing (i.e. 1/2 PicoTiter plate for each marker) showed that primers for 18S recover more (38 orders) groups than 16S (10 orders) across all taxa, and four vs. two orders and nine vs. six families for Crustacea. Our results showed that 18S, using newly designed primers, is an efficient and powerful tool for profiling biodiversity in largely unexplored communities, especially when amplification difficulties exist for mitochondrial markers such as COI. Universal primers for higher resolution markers such as COI are still needed to address the possible low resolution of 18S for species-level identification. |
| WOS记录号 | WOS:000340425100015 |
| 公开日期 | 2015-03-24 |
| 源URL | [http://ir.rcees.ac.cn/handle/311016/9419]  |
| 专题 | 生态环境研究中心_环境化学与生态毒理学国家重点实验室 |
| 推荐引用方式 GB/T 7714 | Zhan, Aibin,Bailey, Sarah A.,Heath, Daniel D.,et al. Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities[J]. MOLECULAR ECOLOGY RESOURCES,2014,14(5):1049-1059. |
| APA | Zhan, Aibin,Bailey, Sarah A.,Heath, Daniel D.,&Macisaac, Hugh J..(2014).Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities.MOLECULAR ECOLOGY RESOURCES,14(5),1049-1059. |
| MLA | Zhan, Aibin,et al."Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities".MOLECULAR ECOLOGY RESOURCES 14.5(2014):1049-1059. |
入库方式： OAI收割
来源：生态环境研究中心
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