背景:棘头是专性体内寄生虫的进化枝,其线粒体基因组(有丝分裂基因组)和进化仍然相对知之甚少。以前的研究报告说,atp8缺乏从棘头有丝分裂基因组,并且tRNA基因通常具有非标准结构。Heterosentispseudobagri(Arhthrmacanthidae)是一种棘头鱼内寄生虫,目前尚无分子数据,和生物学信息在英语中不可用。此外,目前尚无有丝分裂基因组可用于食齿科。
方法:我们对其有丝分裂基因组和转录组进行了测序,并对几乎所有可用的棘头有丝分裂基因组进行了比较有丝分裂基因组分析。
结果:有丝分裂基因组具有在数据集中的相同链上和独特基因顺序上编码的所有基因。在12个蛋白质编码基因中,几个基因高度分歧,难以注释。此外,几个tRNA基因不能自动识别,所以我们必须通过与直系同源物的详细比较来手动识别它们。就像棘头动物一样,一些tRNA缺乏TWC臂或DHU臂,但是在一些情况下,我们仅在包含反密码子的保守的狭窄中央区段的基础上注释了tRNA基因,而侧翼5'和3'末端与直系同源物没有任何相似之处,并且它们不能折叠成tRNA二级结构。我们证实,这些不是通过从转录组数据组装有丝分裂基因组来测序人工制品。尽管在以前的研究中没有观察到这种现象,我们的比较分析显示,在多个棘头菌谱系中存在高度不同的tRNA。
结论:这些发现表明,多个tRNA基因是无功能的,或者(某些)棘头菌中的(某些)tRNA基因可能会经历广泛的转录后tRNA加工,从而将其恢复为更常规的结构。有必要对尚未表示的谱系中的有丝分裂基因组进行测序,并进一步探索Acanthocephala中tRNA进化的异常模式。
BACKGROUND: Acanthocephala is a clade of obligate endoparasites whose mitochondrial genomes (mitogenomes) and evolution remain relatively poorly understood. Previous studies reported that atp8 is lacking from acanthocephalan mitogenomes, and that tRNA genes often have nonstandard structures. Heterosentis pseudobagri (Arhythmacanthidae) is an acanthocephalan fish endoparasite for which no molecular data are currently available, and biological information is unavailable in the English language. Furthermore, there are currently no mitogenomes available for Arhythmacanthidae.
METHODS: We sequenced its mitogenome and transcriptome, and conducted comparative mitogenomic analyses with almost all available acanthocephalan mitogenomes.
RESULTS: The mitogenome had all genes encoded on the same strand and unique gene order in the dataset. Among the 12 protein-coding genes, several genes were highly divergent and annotated with difficulty. Moreover, several tRNA genes could not be identified automatically, so we had to identify them manually via a detailed comparison with orthologues. As common in acanthocephalans, some tRNAs lacked either the TWC arm or the DHU arm, but in several cases, we annotated tRNA genes only on the basis of the conserved narrow central segment comprising the
anticodon, while the flanking 5\' and 3\' ends did not exhibit any resemblance to orthologues and they could not be folded into a tRNA secondary structure. We corroborated that these are not sequencing artefacts by assembling the mitogenome from transcriptomic data. Although this phenomenon was not observed in previous studies, our comparative analyses revealed the existence of highly divergent tRNAs in multiple acanthocephalan lineages.
CONCLUSIONS: These findings indicate either that multiple tRNA genes are non-functional or that (some) tRNA genes in (some) acanthocephalans might undergo extensive posttranscriptional tRNA processing which restores them to more conventional structures. It is necessary to sequence mitogenomes from yet unrepresented lineages and further explore the unusual patterns of tRNA evolution in Acanthocephala.