Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera
Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera
复制标题
DOI：
10.1093/gbe/evaa042
复制
发表时间：
2020-02
影响因子：
3.3
通讯作者：
E. Shoguchi;Y. Yoshioka;Chuya Shinzato;Asuka Arimoto;D. Bhattacharya;N. Satoh
中科院分区：
文献类型：
--
作者：
E. Shoguchi;Y. Yoshioka;Chuya Shinzato;Asuka Arimoto;D. Bhattacharya;N. Satoh
摘要 为了制定成功的珊瑚礁保护策略，研究宿主珊瑚和共生藻类的生物学至关重要。在琉球群岛，包括分布在太平洋上约 500 公里的许多岛屿，使用全基因组鸟枪法 (WGS) 序列分析对珊瑚鹿角珊瑚的四个主要种群进行了研究（Shinzato C、Mungpakdee S、Arakaki N、Satoh N. 2015。全基因组单核苷酸多态性 (SNP) 分析解释了琉球群岛的珊瑚多样性和恢复情况群岛。科学报告 5：18211。）。相比之下，与这些指状甲藻种群相关的共生甲藻的多样性尚不清楚。因此，尚不清楚珊瑚全生物的这两个核心组成部分是否具有共同的进化历史。通过研究共生藻类线粒体和质体的细胞器基因组，可以解决共生藻类的这个问题。在这里，我们分析了约 150 个成年 A. digitalifera 的 WGS 数据，并通过将读数映射到可用的参考基因组序列，我们提取了代表共生科 15 个细胞器基因的 2,250 个序列。对这些线粒体和质体基因集的分子系统发育分析表明，来自八重山群岛南部的A. digitalifera拥有与北部冲绳岛和庆良间岛不同的共生体种群，表明共生体种群的分布与四个宿主种群的分布部分匹配。有趣的是，我们发现许多 SNP 对应于 14 个共生科细胞器基因中已知的 RNA 编辑位点，其中线粒体基因比质体基因表现出更强的对应性。这些结果表明，共生甲藻的两个细胞器基因组中的 RNA 编辑和 SNP 之间可能存在相关性。
Abstract In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.