Atopkin Dmitry M, Semenchenko Alexander A, Solodovnik Daria A, Ivashko Yana I, Vinnikov Kirill A
Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the RAS, Vladivostok, Russia.
Department of Cell Biology and Genetics, Far Eastern Federal University, Vladivostok, Russia.
Parasitol Res. 2021 Jun;120(6):2037-2046. doi: 10.1007/s00436-021-07159-y. Epub 2021 Apr 24.
The first data on a whole mitochondrial genome of Haploporidae, Parasaccocoelium mugili (Digenea: Haploporata: Haploporidae) was generated using the next-generation sequencing (NGS) approach. We sequenced the complete mitochondrial DNA (mtDNA) and ribosomal operon of Parasaccocoelium mugili, intestine parasite of mullet fish. The mtDNA of P. mugili contained 14,021 bp, including 12 protein-coding genes, two ribosomal genes, 22 tRNA genes, and non-coding region. The ribosomal operon of P. mugili was 8308 bp in length, including 18S rRNA gene (1981 bp), ITS1 rDNA (955 bp), 5.8S rRNA gene (157 bp), ITS2 rDNA (268 bp), 28S rRNA gene (4180 bp), and ETS (767 bp). We used the mtDNA protein-coding regions to make phylogenetic reconstructions of Haploporidae. Additionally, we performed the sequence cluster analysis based on codon usage bias of most of currently available mitochondrial genome data for trematodes. The observed gene arrangement in mtDNA sequence of P. mugili is identical to those of Plagiorchis maculosus (Rudolphi, 1802). Results of maximum likelihood (ML) phylogenetic analysis showed that P. mugili was closely related to Paragonimus species from the suborder Xiphidiata. The results of sequence cluster analysis based on codon usage bias showed that P. mugili has the highest similarity with Plagiorchis maculosus (Xiphidiata). Our results do not contradict to proposing a new suborder for Haploporoidea-Haploporata. On the basis of obtained results, the relationship between mitochondrial protein-coding gene rearrangements and synonymous nucleotide substitutions in mitochondrial genomes has been suggested.
利用下一代测序（NGS）方法首次获得了单殖科的缪氏副囊腔吸虫（复殖目：单殖总科：单殖科）完整线粒体基因组的数据。我们对鲻鱼肠道寄生虫缪氏副囊腔吸虫的完整线粒体DNA（mtDNA）和核糖体操纵子进行了测序。缪氏副囊腔吸虫的mtDNA包含14,021 bp，包括12个蛋白质编码基因、两个核糖体基因、22个tRNA基因和非编码区。缪氏副囊腔吸虫的核糖体操纵子长度为8308 bp，包括18S rRNA基因（1981 bp）、ITS1 rDNA（955 bp）、5.8S rRNA基因（157 bp）、ITS2 rDNA（268 bp）、28S rRNA基因（4180 bp）和ETS（767 bp）。我们利用mtDNA蛋白质编码区对单殖科进行了系统发育重建。此外，我们基于目前大多数可用的吸虫线粒体基因组数据的密码子使用偏好进行了序列聚类分析。在缪氏副囊腔吸虫mtDNA序列中观察到的基因排列与黄斑斜睾吸虫（Rudolphi，1802）的相同。最大似然（ML）系统发育分析结果表明，缪氏副囊腔吸虫与剑水亚目的并殖吸虫物种密切相关。基于密码子使用偏好的序列聚类分析结果表明，缪氏副囊腔吸虫与黄斑斜睾吸虫（剑水亚目）的相似度最高。我们的结果与为单殖总科-单殖科提出一个新亚目并不矛盾。基于所得结果，提出了线粒体基因组中蛋白质编码基因重排与同义核苷酸替换之间的关系。
