Data_Sheet_2_Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics.PDF

To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of Actinocyclus subtilis to 135.8 kb of Stephanopyxis turris. Plastomes in Paraliales and Stephanopyxales tended to be larger than those in Rhizosoleniales and Coscinodiacales, which were due to the expansion of the inverted repeats (IRs) and to the marked increase of the large single copy (LSC). Phylogenomic analysis indicated that Paralia and Stephanopyxis clustered tightly to form the Paraliales-Stephanopyxales complex, which was sister to the Rhizosoleniales-Coscinodiscales complex. The divergence time between Paraliales and Stephanopyxales was estimated at 85 MYA in the middle Upper Cretaceous, indicating that Paraliales and Stephanopyxales appeared later than Coscinodiacales and Rhizosoleniales according to their phylogenetic relationships. Frequent losses of housekeeping protein-coding genes (PCGs) were observed in these coscinodiscophycean plastomes, indicating that diatom plastomes showed an ongoing reduction in gene content during evolution. Two acpP genes (acpP1 and acpP2) detected in diatom plastomes were found to be originated from an early gene duplication event occurred in the common progenitor after diatom emergence, rather than multiple independent gene duplications occurring in different lineages of diatoms. The IRs in Stephanopyxis turris and Rhizosolenia fallax-imbricata exhibited a similar trend of large expansion to the small single copy (SSC) and slightly small contraction from the LSC, which eventually led to the conspicuous increase in IR size. Gene order was highly conserved in Coscinodiacales, while multiple rearrangements were observed in Rhizosoleniales and between Paraliales and Stephanopyxales. Our results greatly expanded the phylogenetic breadth in Coscinodiscophyceae and gained novel insights into the evolution of plastomes in diatoms.

为解析中心硅藻纲（Coscinodiscophyceae）物种的演化历程，本研究构建并分析了6种中心硅藻纲硅藻的质体基因组（plastome）序列，使该类群已解析的质体基因组序列数量提升一倍。中心硅藻纲的质体基因组大小差异显著，跨度从细弱辐环藻（Actinocyclus subtilis）的119.1 kb至扭曲旋链藻（Stephanopyxis turris）的135.8 kb。平行藻目（Paraliales）与旋链藻目（Stephanopyxales）的质体基因组普遍大于根管藻目（Rhizosoleniales）和中心硅藻目（Coscinodiscales，原文疑似笔误），这一现象源于反向重复序列（inverted repeats, IRs）的扩张以及大单拷贝区（large single copy, LSC）的显著扩增。系统发育基因组学分析显示，平行藻属（Paralia）与旋链藻属（Stephanopyxis）聚为一支，形成平行藻目-旋链藻目支系，该支系与根管藻目-中心硅藻目支系互为姊妹群。经估算，平行藻目与旋链藻目的分化时间发生在晚白垩世中期，约85百万年前（MYA）；结合系统发育关系可知，平行藻目与旋链藻目的起源时间晚于中心硅藻目和根管藻目。在这些中心硅藻纲质体基因组中，频繁出现持家蛋白编码基因（protein-coding genes, PCGs）的丢失现象，表明硅藻质体基因组在演化过程中持续发生基因含量的缩减。在硅藻质体基因组中检测到的2个acpP基因（acpP1与acpP2），起源于硅藻起源后共同祖先发生的一次早期基因复制事件，而非不同硅藻谱系独立发生的多次基因复制事件。扭曲旋链藻（Stephanopyxis turris）和柔弱根管藻（Rhizosolenia fallax-imbricata）的反向重复序列（IRs）呈现出相似的扩张趋势：向小单拷贝区（small single copy, SSC）大幅扩张，同时从大单拷贝区（LSC）发生小幅收缩，最终导致IR区段长度显著增加。中心硅藻目的基因共线性高度保守，而根管藻目以及平行藻目与旋链藻目之间则存在大量基因重排现象。本研究结果极大拓宽了中心硅藻纲的系统发育覆盖范围，为硅藻质体基因组的演化研究提供了全新的认知。