College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China.
Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany.
PLoS One. 2021 Jun 1;16(6):e0250968. doi: 10.1371/journal.pone.0250968. eCollection 2021.
Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.
在过去的十年中，绿潮已成为中国黄海的一个重要生态问题，而 U. compressa 作为一种全球性的绿藻物种，被鉴定为绿潮的组成部分。本研究对 U. compressa 的完整叶绿体基因组进行了测序和注释，并重点评估了基因组长度、同源性、基因顺序和方向、内含子大小、选择强度和替换率。我们将叶绿体基因组与线粒体基因组进行了比较。基于 Ulva 叶绿体基因组中的单个和对齐基因与线粒体基因的比较，生成的系统发育树进行了分析，以检测进化趋势。U. compressa 和 U. mutabilis 叶绿体基因组具有相似的基因队列，单个基因具有高度的同源性。叶绿体基因组在整个系统发育树中聚集在一起，并共享几个正向/回文/串联重复，与 U. prolifera 和 U. linza 相似。然而，U. fasciata 和 U. ohnoi 则更加分化，特别是在互补/回文重复方面。此外，对叶绿体基因组和线粒体基因组中对齐基因的系统发育分析证实了核外基因组的进化趋势。从系统发育分析中，我们确定了 petA 叶绿体基因是与 tufA 标记相似的潜在遗传标记。互补/正向/回文间隔重复在叶绿体基因组中比在线粒体基因组中更为丰富。有趣的是，一些串联重复在一些 Ulva 亚种中更为显著，并且在线粒体中比在叶绿体中更为明显。最后，在 U. compressa 的线粒体基因组和同种菌株 U. mutabilis 中发现了串联重复[GAAATATATAATAATA×3，缩写为 TRg)]，但在黄海的其他藻类物种中未发现。由于 U. compressa 具有高度的形态可塑性，因此本研究的发现对于该地区绿潮发生时对该物种进行快速非测序检测具有重要意义。
