CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
Int J Environ Res Public Health. 2022 Aug 14;19(16):10024. doi: 10.3390/ijerph191610024.
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including , , spp., , , two strains of , , , and sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera , , and . Additionally, comparative analysis suggested that the positioning of species in the genus should be transferred to the genus . Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
甲藻门是一类物种丰富、生态意义重大的甲藻。尽管它们作为初级生产者和有害藻华（HAB）发展的关键因素在海洋生态系统中具有重要意义，但由于其形态特征有限、形态可塑性以及常见分子标记分辨率低，对甲藻门物种的分类研究受到了阻碍。因此，迫切需要分辨率更高的分子标记。细胞器基因组可以利用高通量 DNA 测序技术的最新发展和生物信息学工具的进步来构建，它们被提议作为超级条形码，因为它们具有更高的分辨率，可以区分不同的物种和种内基因组变异。在这项研究中，我们通过构建 11 株甲藻门类的叶绿体基因组（cpDNAs），包括、、、、、、、和 sp.，测试了全长叶绿体基因组（cpDNAs）作为区分硅藻物种的超级条形码的价值。对 cpDNAs 的比较分析表明，cpDNAs 不仅足以区分不同的物种，而且还能够识别不同物种之间 cpDNAs 的高水平基因组重排，特别是对于属、、和的物种。此外，比较分析表明，属中的物种位置应转移到属中。叶绿体基因组进化分析表明，甲藻门物种最早出现在白垩纪，大约 6500 万年前大灭绝后物种多样性增加。这项研究强调了 cpDNAs 在研究甲藻门物种多样性和进化中的价值，并且随着更多代表其他属的 cpDNAs 的构建，将更深入地了解甲藻门物种的多样性和进化关系。
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