Comparative evaluation of 18S rDNA V4 and 28S rDNA D1-2 regions for resolving Alexandrium species diversity to improve its use for metabarcoding
文献类型：期刊论文
| 作者 | Ding, Xiangxiang1,2,3,4; Huang, Xianliang1,2,3,4; Chen, Nansheng1,2,3 |
| 刊名 | HARMFUL ALGAE
 |
| 出版日期 | 2026-03-01 |
| 卷号 | 153页码:15 |
| 关键词 | Metabarcoding analysis Molecular marker Intra-genomic variations Resolution Reference database |
| ISSN号 | 1568-9883 |
| DOI | 10.1016/j.hal.2026.103073 |
| 通讯作者 | Chen, Nansheng(chenn@qdio.ac.cn) |
| 英文摘要 | Many Alexandrium species can develop harmful algal blooms (HABs) associated with paralytic shellfish poisoning (PSP), making their accurate identification critical. Morphological similarity among Alexandrium species limits their identification, whereas molecular marker-based methods are effective, resulting in the accumulation of vast molecular data. However, the existence of these massive molecular sequences makes it confusing to select reference sequences for taxonomical and diversity studies. To address this, we mined and curated molecular marker sequences of 18S rDNA V4 and 28S rDNA D1-2 for Alexandrium species from NCBI NT database. We built the first reference 28S rDNA D1-2 database for 27 Alexandrium species, and for the 18S rDNA V4 region, our results expanded PR2 database by adding sequences for two additional Alexandrium species and proposed to eliminate two contaminated sequences. Furthermore, we characterized intra-genomic variations (IGVs) for both 18S rDNA V4 and 28S rDNA D1-2, and experimentally confirmed the existence of 18S rDNA V4 IGVs in Alexandrium species. Both single-cell sequencing and database analysis results showed that an Alexandrium cell typically harbors IGVs with the co-existence of usually one dominant and multiple non-dominant sequences, with non-dominant sequences potentially matching another species' dominant sequence. Therefore, only dominant sequences of each Alexandrium species were proposed to be included in reference databases for clarity. We also confirmed that 28S rDNA D1-2 has higher resolution for identifying Alexandrium species. Through clarifying the characteristics of these molecular markers and providing curated datasets, this work enhances metabarcoding accuracy for early detection of toxic Alexandrium populations. |
| WOS关键词 | LSU RDNA ; DINOPHYCEAE ; MORPHOLOGY ; TAMARENSE ; PHYLOGENY ; SEQUENCE ; COMMUNITY ; RESOLUTION ; TOXICITY ; WATERS |
| 资助项目 | Independent Deployment Project of the Institute of Oceanology, Chinese Academy of Sciences ; Natural Science Foundation of China[42176162] ; Taishan Scholar Project Special Fund |
| WOS研究方向 | Marine & Freshwater Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:001687354500001 |
| 出版者 | ELSEVIER |
| 源URL | [http://ir.qdio.ac.cn/handle/337002/204739]  |
| 专题 | 海洋研究所_海洋生态与环境科学重点实验室 |
| 通讯作者 | Chen, Nansheng |
| 作者单位 | 1.Chinese Acad Sci, Ctr Ocean Mega Sci, Qingdao 266071, Peoples R China 2.Qingdao Marine Sci & Technol Ctr, Lab Marine Ecol & Environm Sci, Qingdao 266200, Peoples R China 3.Chinese Acad Sci, Inst Oceanol, Lab Marine Ecol & Environm Sci, Qingdao 266071, Peoples R China 4.Univ Chinese Acad Sci, Coll Marine Sci, Beijing 100039, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ding, Xiangxiang,Huang, Xianliang,Chen, Nansheng. Comparative evaluation of 18S rDNA V4 and 28S rDNA D1-2 regions for resolving Alexandrium species diversity to improve its use for metabarcoding[J]. HARMFUL ALGAE,2026,153:15. |
| APA | Ding, Xiangxiang,Huang, Xianliang,&Chen, Nansheng.(2026).Comparative evaluation of 18S rDNA V4 and 28S rDNA D1-2 regions for resolving Alexandrium species diversity to improve its use for metabarcoding.HARMFUL ALGAE,153,15. |
| MLA | Ding, Xiangxiang,et al."Comparative evaluation of 18S rDNA V4 and 28S rDNA D1-2 regions for resolving Alexandrium species diversity to improve its use for metabarcoding".HARMFUL ALGAE 153(2026):15. |
入库方式： OAI收割
来源：海洋研究所
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