Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Mitochondrial genetic markers have been extensively used to study phylogenetics and phylogeography of many birds, including Procellariiformes seabirds. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated. None DNA fragment covering the entire duplication was ever obtained. We sequenced the complete mitochondrial genome of a non-albatross Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mito-genomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19kb-long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region. Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region between the control region and 12S, of undetermined length. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region indicating a complex evolution of the mitogenome in Procellariiformes

线粒体遗传标记（mitochondrial genetic markers）已被广泛应用于诸多鸟类的系统发育学与系统生物地理学研究，其中涵盖鹱形目（Procellariiformes）海鸟。已有研究证据表明，鹱形目鸟类的线粒体基因组存在部分重复现象，信天翁类（albatrosses）的该现象尤为突出。此前尚未有研究获取到覆盖完整重复区域的DNA片段。本研究采用长读长MinION（ONT）测序技术，对非信天翁类的鹱形目鸟类奥杜宾剪水鹱（Puffinus lherminieri，Audubon’s shearwater）的完整线粒体基因组开展了测序。我们从同一实验个体中组装得到两个线粒体基因组（mitogenomes），二者间存在52个单核苷酸多态性（SNPs）差异，且长度不一：较短的线粒体基因组长度为19 kb，较长的则为21 kb，长度差异源于其基因组中包含两份完全一致的nad6基因拷贝、三份转运RNA（tRNA）基因拷贝，以及两份序列相异的控制区（control region）拷贝。与信天翁类不同，该物种的cob基因并未发生重复。我们还在控制区与12S rRNA基因之间检测到一段结构复杂的重复区域，其长度尚未明确。长读长测序结果提示该物种存在线粒体异质性（heteroplasmy），且重复区域内存在全新的基因排布模式，这表明鹱形目鸟类线粒体基因组的演化过程极为复杂。