Rich molecular diversity of ribosomal RNA genes in Pseudo-nitzschia species (Bacillariophyceae) revealed through single-strain high throughput sequencing
Document Type
Article
Publication Date
1-1-2025
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.
Keywords
Intragenomic variations, Metabarcoding, Molecular diversity, Homogenization, Pseudo-nitzschia, SSU rDNA
Divisions
ocean
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
Publication Title
Algal Research:Biomass, Biofuels and Bioproducts
Volume
85
Publisher
Elsevier
Publisher Location
RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS