Xiphinema americanum Targeted Locus (Loci)

Nematodes within the Xiphinema americanum species complex are economically important because they vector nepoviruses which cause considerable damage to a variety of agricultural crops. The taxonomy of X. americanum is controversial, with the number of putative species being the subject of debate. Accurate phylogenetic knowledge of this group is highly desirable as it may ultimately reveal genetic differences between species which do vector nepoviruses and those which do not. For this study, X. americanum populations were collected from 12 geographically disparate locations across the U.S. from different crops and in varying association with nepoviruses. Four individuals from each population were analyzed. A portion of the nuclear 18S nuclear ribosomal DNA (rDNA) gene was sequenced for all individuals while the internal transcribed spacer region 1 (ITS1) of rDNA was cloned and 4 to 7 clones per individual were sequenced. Mitochondrial genomes for numerous individuals were sequenced in parallel using high-throughput DNA sequencing (HTS) technology. Phylogenetic analysis of the 18S rDNA revealed virtually identical sequences across all populations. Analysis of ITS1 rDNA sequences revealed several well-supported clades, with some degree of congruence with geographic location and viral transmission, but also numerous presumably paralogous sequences that failed to form clades with other sequences from the same population. Analysis of mitochondrial DNA (mtDNA) indicated the presence of three distinct monophyletic clades of X. americanum species complex nematodes. Two clades contained nematodes found in association with nepovirus and the third contained divergent mtDNA sequences from three nematode populations where nepovirus was absent. The inherent heterogeneity in ITS1 rDNA sequence data and lack of informative sites in 18S rDNA analysis suggests that mtDNA may be more useful in sorting out the taxonomic confusion of the X. americanum species complex, and might serve as an effective practical tool in distinguishing virus-vectoring from non-vectoring nematode populations.

Xiphinema americanum物种复杂体内的线虫由于作为内泊病毒的载体，对多种农作物造成严重经济损失而具有重要经济意义。X. americanum的分类学存在争议，其中假定的物种数量成为争论的焦点。准确掌握该群体的系统发育知识极为迫切，因为这最终可能揭示出携带内泊病毒的物种与不携带的物种之间的遗传差异。在本研究中，从美国12个地理分布广泛的地点收集了不同作物和与内泊病毒不同关联度的X. americanum种群。对每个种群中的4个个体进行了分析。对所有个体进行了核18S核糖体DNA（rDNA）基因的部分测序，并对rDNA的内部转录间隔区1（ITS1）进行了克隆，每个个体测序4到7个克隆。利用高通量DNA测序（HTS）技术对众多个体的线粒体基因组进行了并行测序。18S rDNA的系统发育分析显示，所有种群中序列几乎完全相同。ITS1 rDNA序列分析揭示了几个得到良好支持的类群，在一定程度上与地理位置和病毒传播相一致，但也存在许多可能为平行同源物的序列，这些序列未能与同一种群中的其他序列形成类群。线粒体DNA（mtDNA）的分析表明，X. americanum物种复杂体内的线虫存在三个独特的单系类群。其中两个类群含有与内泊病毒相关联的线虫，第三个类群含有来自三个无内泊病毒线虫种群且差异较大的mtDNA序列。ITS1 rDNA序列数据中的固有异质性和18S rDNA分析中信息位点不足表明，mtDNA可能在整理X. americanum物种复杂体的分类学混乱中更有用，并可能作为区分病毒载体线虫种群和非病毒载体线虫种群的实用有效工具。