Department of Environmental Health Science, University of Georgia, Athens 30602 GA, USA.
Parasit Vectors. 2013 Oct 17;6(1):300. doi: 10.1186/1756-3305-6-300.
Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium.
We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium.
We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse.
About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance.
由埃及血吸虫引起的泌尿生殖系统血吸虫病广泛分布于非洲，并越来越多地成为控制的目标。基因组序列和群体遗传参数可以深入了解种群或物种水平药物抗性的潜力。微卫星 DNA 基因座是血吸虫研究人员广泛使用的遗传标记，但可供埃及血吸虫使用的引物却很少。
我们从感染单一埃及血吸虫尾蚴的蜗牛中收集了 1,058,114 个随机 DNA 片段，并对其进行了测序。我们将埃及血吸虫序列组装并与曼氏血吸虫和日本血吸虫基因组进行了比对，确定了这三个物种中的微卫星 DNA 基因座，并设计了引物来扩增埃及血吸虫中的基因座。为了验证我们的引物，我们用埃及血吸虫种群样本筛选了 32 对随机选择的引物对。
我们设计了超过 13,790 对引物来扩增埃及血吸虫中独特的微卫星基因座（可在 http://www.cebio.org/projetos/schistosoma-haematobium-genome 获得）。三个血吸虫基因组中微卫星的总体频率相似，但特定基序的频率和长度分布在物种间存在差异。我们确定了 15 对扩增一致且易于评分的引物。我们在来自六个地点的埃及血吸虫个体中对这 15 个基因座进行了基因分型：桑给巴尔的多样性水平最高；马拉维、毛里求斯、尼日利亚和塞内加尔的多样性几乎相同；但南非的样本多样性要低得多。
数据库中大约一半的埃及血吸虫微卫星 DNA 基因座引物应该能够产生可扩增和易于评分的多态性标记，从而提供数千个潜在的标记。埃及血吸虫、日本血吸虫和曼氏血吸虫之间的序列保守性相对较高，因此现在应该可以识别出在血吸虫物种中普遍存在的标记（即使用在物种间保守的 DNA 序列），以及其他针对物种或物种群的特异性标记（即使用在物种间存在差异的 DNA 序列）。对额外的埃及血吸虫、日本血吸虫和曼氏血吸虫物种和标本进行全基因组测序，以更好地描述这些物种内和物种间的差异，开发更多的遗传标记，并研究与药物抗性相关的基因以及保守的非编码元件，是可取的。
