Wang, Hui and Liu, Kuiyan and He, Ziyan and Chen, Yang and Leaw, Chui Pin and Chen, Nansheng (2025) Rich molecular diversity of ribosomal RNA genes in Pseudo-nitzschia species (Bacillariophyceae) revealed through single-strain high throughput sequencing. Algal Research:Biomass, Biofuels and Bioproducts, 85. p. 103869. ISSN 2211-9264, DOI https://doi.org/10.1016/j.algal.2024.103869.
Full text not available from this repository.Abstract
Ribosomal RNA genes (rDNAs) are widely used as molecular markers in phytoplankton identification and diversity analysis, showing significant efficacy in metabarcoding studies. Recent analysis of amplicon sequencing results of the 18S rDNA V4 domain in multiple strains of the toxigenic Pseudo-nitzschia multistriata revealed that, in addition to the presence of a dominant copy of 18S rDNA V4 in each strain, there also exists a large number of low-abundance 18S rDNA V4 sequence variants, indicating the existence of high levels of intragenomic variations (IGVs). Many of these low-abundance variants identified in P. multistriata also show high similarity to that of other Pseudo-nitzschia species. In this study, we analyzed the molecular diversity of 18S rDNA V4 sequences of additional 56 clonal strains of nine Pseudo-nitzschia species collected along the coast of China and the South China Sea using high-throughput amplicon sequencing. The results showed that each strain harbors high levels of IGVs as expected. Although a common dominant sequence variant is often shared by all strains of the same species, these variants are usually also found at low frequencies in other species, suggesting that IGVs in these diatoms, like most protists, are linked to the biological processes of genome evolution. Understanding the nature of IGVs is not only critical for ascertaining the species evolution, but also for precise interpretation of the molecular diversity revealed in metabarcoding studies.
| Item Type: | Article |
|---|---|
| Funders: | Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao) (LSKJ202203700), National Key Research and Development (R&D) Program of China (2022YFC3105200), National Natural Science Foundation of China (NSFC) (42176162), Taishan Scholar Project Special Fund, Chinese Academy of Sciences (XDB42000000), Chinese Academy of Sciences Pioneer Hundred Talents Program |
| Uncontrolled Keywords: | Intragenomic variations; Metabarcoding; Molecular diversity; Homogenization; Pseudo-nitzschia; SSU rDNA |
| Subjects: | Q Science > QH Natural history Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics |
| Divisions: | Deputy Vice Chancellor (Research & Innovation) Office > Institute of Ocean and Earth Sciences |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 12 Mar 2025 02:29 |
| Last Modified: | 12 Mar 2025 02:29 |
| URI: | http://eprints.um.edu.my/id/eprint/47782 |
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