Ishinomaki Senshu University, 1 Shinmito Minamisakai, Ishinomaki, Miyagi, 986-8580, Japan.
National Institute for Environmental Studies, 16-2, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
Mol Biol Rep. 2023 Sep;50(9):7183-7196. doi: 10.1007/s11033-023-08647-3. Epub 2023 Jul 6.
The mitochondrial genomes (mitogenomes) of the family Serpulidae are characterized by a high nucleotide sequence divergence and a significant number of gene order rearrangements compared with other families within the phylum Annelida. However, only two of 50 genera of serpulids have mitogenomes already sequenced. In this study, we report the first sequencing and assembly of the complete mitogenome of Ficopomatus, thus providing further knowledge on mitochondrial gene sequences of Serpulidae.
A mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus was amplified by long PCR and sequenced using the Illumina MiSeq System. It comprised 15,853 bp and consisted of 12 protein-coding genes (atp8 was not found), 23 tRNA, and two rRNA genes. The AT and GC skew values were infrequent when compared to annelid mitogenomes but similar to other serpulids sequenced to date (i.e., Spirobranchus and Hydroides). The mitochondrial gene order of F. enigmaticus was highly rearranged compared to other serpulids. To amplify 16S rRNA gene sequences, we developed a 16S rRNA primer set by modifying the universal primer set 16SarL/16SbrH. We detected the 16S rRNA sequence of F. enigmaticus deposited in GenBank erroneously characterized as of serpulid origin. We reported for the first time the presence of two lineages of F. enigmaticus in Japan, which have already been identified in California, Australia, and the Mediterranean.
The first mitochondrial genome of F. enigmaticus showed a unique gene order rearrangement, corroborating the remarkable diversity in the previously reported mitogenomes of other serpulid species. The presence of the two lineages of F. enigmaticus identified for the first time in Japan represents another case of cryptic invasion. The first 16S rRNA gene sequences of F. enigmaticus obtained in the present study can be used as reference sequences in future DNA metabarcoding studies.
与环节动物门内的其他科相比，盘管科的线粒体基因组（线粒体基因组）具有很高的核苷酸序列差异和大量基因排列重排。然而，盘管科的 50 个属中只有两个属的线粒体基因组已经测序。在这项研究中，我们报告了第一个盘管科的完整线粒体基因组的测序和组装，从而提供了关于盘管科线粒体基因序列的进一步知识。
通过长 PCR 扩增和 Illumina MiSeq 系统测序，获得了入侵造礁多毛类动物 Ficopomatus enigmaticus 的线粒体基因组。它由 15853bp 组成，包括 12 个蛋白质编码基因（未发现 atp8）、23 个 tRNA 和两个 rRNA 基因。与环节动物的线粒体基因组相比，AT 和 GC 倾斜值不常见，但与迄今为止测序的其他盘管科相似（即 Spirobranchus 和 Hydroides）。与其他盘管科相比，F. enigmaticus 的线粒体基因排列高度重排。为了扩增 16S rRNA 基因序列，我们通过修改通用引物对 16SarL/16SbrH 开发了一个 16S rRNA 引物对。我们检测到在 GenBank 中错误地将 F. enigmaticus 的 16S rRNA 序列鉴定为盘管科起源。我们首次报道了日本存在两种 F. enigmaticus 谱系，这些谱系已经在加利福尼亚、澳大利亚和地中海地区被发现。
F. enigmaticus 的第一个线粒体基因组显示出独特的基因排列重排，证实了以前报道的其他盘管科物种的线粒体基因组具有显著的多样性。在日本首次发现的 F. enigmaticus 的两种谱系代表了另一个隐蔽入侵的案例。本研究获得的 F. enigmaticus 的第一个 16S rRNA 基因序列可作为未来 DNA 宏条形码研究的参考序列。
