Multiple alignment data for diatom plastomes and mitogenomes

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 120 plastome and 70 mitogenome publicly available sequences, this paper aims to elucidate the evolutionary dynamics of diatoms across diverse lineages. In comparing genomic events between plastomes and mitogenomes, gene losses and pseudogenes were more frequently observed in plastomes, while they were less commonly found in mitogenomes. Overall, gene losses were 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 greater structural rearrangements compared to mitogenomes with the exception of the genera Coscinodiscus and one group of species within Thalassiosira.

硅藻在全球氧、二氧化碳与硅循环中扮演关键角色，可通过光合作用显著贡献光合产物，同时亦是水生生态系统的核心组成组分。近年来基因组测序技术的进步阐明了硅藻的演化动力学特征，揭示出其受共生关系与水平基因转移事件影响、演化复杂度较高的基因组。本研究通过分析120条公开可用的质体基因组（plastome）与70条线粒体基因组（mitogenome）序列，旨在阐明不同演化支系中硅藻的演化动力学规律。在对比两类基因组的演化事件时，研究发现质体基因组中基因丢失与假基因化现象更为频发，而线粒体基因组中此类事件则较为少见。整体而言，星链藻（Astrosyne radiata）、波纹弯杆藻（Toxarium undulatum）以及原杆藻属未定种（Proboscia sp.）的质体基因组中存在大量基因丢失现象。频繁发生丢失与假基因化的基因为acpP、ilv、serC、tsf、tyrC、ycf42及bas1。在线粒体基因组中，mttB、secY与tatA基因在多个硅藻分类群中反复发生丢失事件。核苷酸替换速率分析结果显示，总体而言线粒体基因组的演化速率较质体基因组更快。这一结果与共线性（synteny）分析的观测结果相悖：质体基因组的结构重排程度显著高于线粒体基因组，仅小环藻属（Coscinodiscus）以及海链藻属（Thalassiosira）内的一个物种类群除外。