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, 266200, China.
BMC Genomics. 2022 Apr 27;23(1):327. doi: 10.1186/s12864-022-08532-6.
The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation on Thalassionema biodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of seven Thalassionema strains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties. The sizes of these Thalassionema cpDNAs, which showed typical quadripartite structures, varied from 124,127 bp to 140,121 bp. Comparative analysis revealed that Thalassionema cpDNAs possess conserved gene content inter-species and intra-species, along with several gene losses and transfers. Besides, their cpDNAs also have expanded inverted repeat regions (IRs) and preserve large intergenic spacers compared to other diatom cpDNAs. In addition, substantial genome rearrangements were discovered not only among different Thalassionema species but also among strains of a same species T. frauenfeldii, suggesting much higher diversity than previous reports. In addition to confirming the phylogenetic position of Thalassionema species, this study also estimated their emergence time at approximately 38 Mya. The availability of the Thalassionema species cpDNAs not only helps understand the Thalassionema species, but also facilitates phylogenetic analysis of diatoms.
世界性的塔马氏藻物种通常是浮游硅藻植物区系和除极地以外所有地区的底栖硅藻组合的主要组成部分，对初级生产力做出了重要的生态贡献。历史研究主要集中在基于形态特征的海洋环境指示功能上，基本上忽略了它们的基因组信息，这阻碍了对塔马氏藻生物多样性的深入调查。在这个项目中，我们构建了代表三个不同物种的七个塔马氏藻菌株的完整叶绿体基因组（cpDNA），这也是包括 35 个已报道的物种和变种的塔马氏藻目内的任何物种的第一个 cpDNA。这些塔马氏藻 cpDNA 的大小从 124127bp 到 140121bp 不等，表现出典型的四分体结构。比较分析表明，塔马氏藻 cpDNA 在种间和种内具有保守的基因含量，同时也存在一些基因的丢失和转移。此外，与其他硅藻 cpDNA 相比，它们的 cpDNA 还具有扩展的反向重复区（IR）和保留的大片段基因间区。除了在不同的塔马氏藻物种之间，还在同一个物种塔马氏藻 frauenfeldii 的菌株之间发现了大量的基因组重排，这表明其多样性比以前的报道要高得多。除了确认塔马氏藻物种的系统发育位置外，本研究还估计了它们大约在 3800 万年前的出现时间。塔马氏藻物种 cpDNA 的可用性不仅有助于了解塔马氏藻物种，还为硅藻的系统发育分析提供了便利。
