Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.
Genome Biol Evol. 2019 Apr 1;11(4):1045-1053. doi: 10.1093/gbe/evz056.
Chlorarachniophyte and cryptophyte algae are unique among plastid-containing species in that they have a nucleomorph genome: a compact, highly reduced nuclear genome from a photosynthetic eukaryotic endosymbiont. Despite their independent origins, the nucleomorph genomes of these two lineages have similar genomic architectures, but little is known about the evolutionary pressures impacting nucleomorph DNA, particularly how their rates of evolution compare to those of the neighboring genetic compartments (the mitochondrion, plastid, and nucleus). Here, we use synonymous substitution rates to estimate relative mutation rates in the four genomes of nucleomorph-bearing algae. We show that the relative mutation rates of the host versus endosymbiont nuclear genomes are similar in both chlorarachniophytes and cryptophytes, despite the fact that nucleomorph gene sequences are notoriously highly divergent. There is some evidence, however, for slightly elevated mutation rates in the nucleomorph DNA of chlorarachniophytes-a feature not observed in that of cryptophytes. For both lineages, relative mutation rates in the plastid appear to be lower than those in the nucleus and nucleomorph (and, in one case, the mitochondrion), which is consistent with studies of other plastid-bearing protists. Given the divergent nature of nucleomorph genes, our finding of relatively low evolutionary rates in these genomes suggests that for both lineages a burst of evolutionary change and/or decreased selection pressures likely occurred early in the integration of the secondary endosymbiont.
绿藻和隐藻是含有质体的物种中独特的一类，因为它们具有核质体基因组：一个来自光合真核内共生体的紧凑、高度简化的核基因组。尽管它们的起源不同，但这两个谱系的核质体基因组具有相似的基因组结构，但对于影响核质体 DNA 的进化压力知之甚少，特别是它们的进化速度与相邻遗传区室（线粒体、质体和细胞核）的进化速度相比如何。在这里，我们使用同义取代率来估计携带核质体的藻类的四个基因组的相对突变率。我们表明，在绿藻和隐藻中，宿主与内共生核基因组的相对突变率相似，尽管核质体基因序列众所周知高度分化。然而，有一些证据表明，绿藻核质体 DNA 的突变率略有升高，而在隐藻中则没有观察到这一特征。对于这两个谱系，质体的相对突变率似乎低于核和核质体（在一种情况下，还低于线粒体），这与其他含有质体的原生生物的研究一致。鉴于核质体基因的分化性质，我们发现这些基因组的进化速度相对较低，这表明对于这两个谱系，在二次内共生体的整合早期，可能发生了进化变化的爆发和/或选择压力的降低。
