Background: Animal mitochondrial genomes are typically circular, 14-20 kb in length, maternally inherited, contain 13 coding genes, two ribosomal genes and are homoplasmic. In contrast, plant mitogenomes display frequent gene rearrangements, often contain greatly expanded repetitive regions, encode various open reading frames of unknown function and may be heteroplasmic due to differential repeat expansions between molecules. Error correction by recombination is common in plant mitochondria and has been proposed as the driver behind the rearrangements and repeat expansions that are often observed. In contrast, most animal mitochondria never or only very seldomly recombine and their utilisation of other repair mechanisms for mitochondrial genome error correction is a potential driver of their non-coding DNA reduction. Results: Using PacBio long reads for genome assembly and structural variant detection, we identify evidence of heteroplasmy in the form of variable repeat lengths within two blocks of repetitive DNA within the expanded 46 kb mitochondrial genome of the bivalve mollusc, quagga mussel, Dreissena rostriformis. The quagga mussel also has a greatly expanded repertoire of coding genes in comparison to most animals which includes an additional nine open reading frames (ORFs) encoding predicted transmembrane peptides of unknown orthology. Conclusions: The genome size, repeat content and coding gene repertoire of the quagga mussel mitogenome closely resemble those of plants and the identification of repeat-associated heteroplasmy is consistent with the utilisation of plant-like recombination-based error correction mechanisms. Given the frequency of mitochondrial repeat expansions within the Bivalvia, recombination may be an underappreciated mechanism for mitogenomic error correction within this and other animal lineages.

中文翻译：

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双壳软体动物的植物样线粒体基因组中的异质性和重复扩增

背景：动物线粒体基因组通常是圆形的，长度为14-20 kb，是母体遗传的，包含13个编码基因，两个核糖体基因并且是同质的。相比之下，植物有丝分裂基因组显示频繁的基因重排，通常包含大大扩展的重复区域，编码功能未知的各种开放阅读框，并且由于分子之间不同的重复扩增而可能是异质的。通过重组进行的纠错在植物线粒体中很常见，并且被提议作为重排和重复扩展的驱动力，而这种重排和重复扩展通常被观察到。相反，大多数动物线粒体从不重组或很少重组，而利用其他修复机制进行线粒体基因组错误校正是其非编码DNA还原的潜在驱动力。结果：使用PacBio进行基因组组装和结构变异检测的长读物，我们鉴定了双壳软体动物，杂种贻贝，Dreissena rostriformis扩大的46 kb线粒体基因组中两个重复DNA区域内可变重复长度形式的异质性证据。与大多数动物相比，杂种贻贝还具有大大扩展的编码基因库，其中包括另外九个开放阅读框（ORF），它们编码预测的矫形未知的跨膜肽。结论：贻贝有丝分裂基因组的基因组大小，重复含量和编码基因组成与植物相似，重复相关杂种的鉴定与利用基于植物的重组错误校正机制相一致。