Chang Aimee Caye G, Amaral Mailor W W, Greenwood Megan, Ikudaisi Catherine, Li Jingchun, Hamsher Sarah E, Miller Scott, Kociolek Patrick
Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America.
Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.
PLoS One. 2025 Sep 5;20(9):e0331749. doi: 10.1371/journal.pone.0331749. eCollection 2025.
Diatoms are pivotal in global oxygen, carbon dioxide, and silica cycling, contributing significantly to photosynthesis and serving as fundamental components in aquatic ecosystems. Recent advancements in genomic sequencing have shed light on their evolutionary dynamics, revealing evolutionary complex genomes influenced by symbiotic relationships and horizontal gene transfer events. By analyzing publicly available sequences for 120 plastomes and 70 mitogenomes, this paper aims to elucidate the evolutionary dynamics of diatoms across diverse lineages. Gene losses and pseudogenes were more frequently observed in plastomes compared with mitogenomes. Overall, gene losses were particularly abundant in the plastomes of Astrosyne radiata, Toxarium undulatum, and Proboscia sp. Frequently lost and pseudogenized genes were acpP, ilv, serC, tsf, tyrC, ycf42 and bas1. In mitogenomes, mttB, secY and tatA genes were lost repeatedly across several diatom taxa. Analysis of nucleotide substitution rates indicated that, in general, mitogenomes were evolving at a more rapid rate compared to plastomes. This is contrary to what was observed in synteny analyses, where plastomes exhibited more structural rearrangements than mitogenomes, with the exception of the genus Coscinodiscus and one group of species within Thalassiosira.
硅藻在全球氧气、二氧化碳和硅循环中起着关键作用，对光合作用有重大贡献，并且是水生生态系统的基本组成部分。基因组测序的最新进展揭示了它们的进化动态，显示出受共生关系和水平基因转移事件影响的进化复杂基因组。通过分析120个质体基因组和70个线粒体基因组的公开可用序列，本文旨在阐明不同谱系硅藻的进化动态。与线粒体基因组相比，质体基因组中基因丢失和假基因的出现更为频繁。总体而言，基因丢失在辐射星杆藻、波状弯角藻和长鼻藻的质体基因组中尤为丰富。经常丢失和假基因化的基因有acpP、ilv、serC、tsf、tyrC、ycf42和bas1。在线粒体基因组中，mttB、secY和tatA基因在几个硅藻分类群中反复丢失。核苷酸替换率分析表明，一般来说，线粒体基因组的进化速度比质体基因组更快。这与共线性分析的结果相反，在共线性分析中，除了圆筛藻属和海链藻属内的一组物种外，质体基因组比线粒体基因组表现出更多的结构重排。
