Huston Daniel C, Khudhir Manda, Hodda Mike
Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT 2601, Australia.
J Nematol. 2022 Jul 29;54(1):20220024. doi: 10.2478/jofnem-2022-0024. eCollection 2022 Feb.
Difficulties inherent in the morphological identification of cyst nematodes of the genus Schmidt, 1871, an important lineage of plant parasites, has led to broad adoption of molecular methods for diagnosing and differentiating species. The pool of publicly available sequence data has grown significantly over the past few decades, and over half of all known species of have been characterized using one or more molecular markers commonly employed in DNA barcoding (18S, internal transcribed spacer [ITS], 28S, ). But how reliable are these data and how useful are these four markers for differentiating species? We downloaded all 18S, ITS, 28S, and gene sequences available on the National Center for Biotechnology Information (NCBI) database, GenBank, for all species of for which data were available. Using a combination of sequence comparison and tree-based phylogenetic methods, we evaluated this dataset for erroneous or otherwise problematic sequences and examined the utility of each molecular marker for the delineation of species. Although we find the rate of obviously erroneous sequences to be low, all four molecular markers failed to differentiate between at least one species pair. Our results suggest that while a combination of multiple markers is best for species identification, the marker shows the most utility for species differentiation and should be favored over 18S, ITS, and 28S, where resources are limited. Presently, less than half the valid species of have a sequence of available, and only a third have more than one sequence of this marker.
施密特属（1871年）囊肿线虫是植物寄生虫的一个重要谱系，其形态鉴定存在固有困难，这导致分子方法被广泛用于诊断和区分物种。在过去几十年中，公开可用的序列数据池显著增长，所有已知物种中有超过一半已使用DNA条形码中常用的一种或多种分子标记（18S、内转录间隔区[ITS]、28S等）进行了特征描述。但这些数据的可靠性如何，以及这四种标记在区分物种方面有多有用呢？我们从美国国立生物技术信息中心（NCBI）数据库GenBank中下载了所有有数据的施密特属物种的18S、ITS、28S和[具体基因]基因序列。我们结合序列比较和基于树的系统发育方法，评估了该数据集是否存在错误或其他有问题的序列，并检验了每个分子标记在物种划分中的效用。虽然我们发现明显错误序列的比例较低，但所有这四种分子标记都至少无法区分一对物种。我们的结果表明，虽然多个标记组合最适合物种鉴定，但在资源有限的情况下，[具体基因]标记在物种区分方面显示出最大效用，应优先于18S、ITS和28S。目前，施密特属有效物种中不到一半有[具体基因]序列可用，只有三分之一有该标记的多个序列。
