Yamamoto Takumi, Tachihara Katsunori, Toda Mamoru
Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan Graduate School of Engineering and Science, University of the Ryukyus Nishihara, Okinawa Japan.
Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan Laboratory of Fisheries Biology and Coral Reef Studies, Faculty of Science, University of the Ryukyus Nishihara, Okinawa Japan.
Biodivers Data J. 2024 Aug 15;12:e126744. doi: 10.3897/BDJ.12.e126744. eCollection 2024.
Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.
当采样标记中不同物种间存在足够的序列变异时，基于DNA条形码技术就能实现准确的物种鉴定。一般来说，随着序列变短，区分物种的能力会下降；然而，较短区域在通过聚合酶链反应进行扩增时具有优势。在任何一种情况下，在进行条形码分析之前研究物种间的序列变异，以了解其可靠性和局限性都很重要。在本研究中，我们探究了线粒体12S核糖体RNA（12S）基因的短但高变部分（约180 bp的MiFish区域）与同一基因的较长区域（约750 bp）相比，用于鉴定多样化雀鲷科鱼类中各个物种的准确性如何。我们准备了三个数据集，分别包含150个物种的301条MiFish区域序列、相同的301条较长12S区域序列以及183个物种的476条MiFish区域序列。邻接法（NJ）分析和遗传距离分析揭示了这些DNA区域中几对无法区分的物种。尽管MiFish区域中这类物种对的数量更多，但即使在MiFish区域，83.6%（183个物种中的153个）的物种也拥有各自独特的序列（而较长12S区域中这一比例为96.0%[150个物种中的144个]）。部分无法区分的物种对可能是由线粒体DNA渐渗和分类学上未解决的问题导致的。我们的分析阐明了使用DNA条形码技术对雀鲷科进行物种鉴定的有效性和局限性，并且我们在此提供的序列有助于扩展雀鲷科线粒体12S序列的参考数据。
