Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
Departamento de Biología, Universidad CES, Medellín, Antioquia 050022, Colombia.
Curr Biol. 2017 Jun 5;27(11):1677-1684.e4. doi: 10.1016/j.cub.2017.04.054. Epub 2017 May 18.
Red algal plastid genomes are often considered ancestral and evolutionarily stable, and thus more closely resembling the last common ancestral plastid genome of all photosynthetic eukaryotes [1, 2]. However, sampling of red algal diversity is still quite limited (e.g., [2-5]). We aimed to remedy this problem. To this end, we sequenced six new plastid genomes from four undersampled and phylogenetically disparate red algal classes (Porphyridiophyceae, Stylonematophyceae, Compsopogonophyceae, and Rhodellophyceae) and discovered an unprecedented degree of genomic diversity among them. These genomes are rich in introns, enlarged intergenic regions, and transposable elements (in the rhodellophycean Bulboplastis apyrenoidosa), and include the largest and most intron-rich plastid genomes ever sequenced (that of the rhodellophycean Corynoplastis japonica; 1.13 Mbp). Sophisticated phylogenetic analyses accounting for compositional heterogeneity show that these four "basal" red algal classes form a larger monophyletic group, Proteorhodophytina subphylum nov., and confidently resolve the large-scale relationships in the Rhodophyta. Our analyses also suggest that secondary red plastids originated before the diversification of all mesophilic red algae. Our genomic survey has challenged the current paradigmatic view of red algal plastid genomes as "living fossils" [1, 2, 6] by revealing an astonishing degree of divergence in size, organization, and non-coding DNA content. A closer look at red algae shows that they comprise the most ancestral (e.g., [2, 7, 8]) as well as some of the most divergent plastid genomes known.
红藻质体基因组通常被认为是原始的和进化稳定的，因此更接近所有光合真核生物的最后共同祖先质体基因组[1,2]。然而，对红藻多样性的采样仍然相当有限（例如，[2-5]）。我们旨在解决这个问题。为此，我们从四个采样不足且系统发育差异较大的红藻类群（Porphyridiophyceae、Stylonematophyceae、Compsopogonophyceae 和 Rhodellophyceae）中测序了六个新的质体基因组，并在其中发现了前所未有的基因组多样性。这些基因组富含内含子、扩大的基因间区和转座元件（在 Rhodellophyceae 的 Bulboplastis apyrenoidosa 中），并包含迄今为止测序的最大和内含子最丰富的质体基因组（来自 Rhodellophyceae 的 Corynoplastis japonica；1.13 Mbp）。考虑到组成异质性的复杂系统发育分析表明，这四个“基础”红藻类群形成了一个更大的单系群，即 Proteorhodophytina 亚门新亚门，并且能够自信地解决红藻中的大规模关系。我们的分析还表明，次生红质体起源于所有嗜温红藻多样化之前。我们的基因组调查通过揭示在大小、组织和非编码 DNA 含量方面令人惊讶的分化程度，挑战了红藻质体基因组作为“活化石”[1,2,6]的当前典范观点。更仔细地观察红藻表明，它们包含最原始的（例如，[2,7,8]）以及一些已知的最具分化的质体基因组。
