Bai Xiaodong, Adams Byron J, Ciche Todd A, Clifton Sandra, Gaugler Randy, Hogenhout Saskia A, Spieth John, Sternberg Paul W, Wilson Richard K, Grewal Parwinder S
Department of Entomology, The Ohio State University, OARDC, Wooster, Ohio, USA.
BMC Genomics. 2009 Apr 30;10:205. doi: 10.1186/1471-2164-10-205.
The entomopathogenic nematode Heterorhabditis bacteriophora and its symbiotic bacterium, Photorhabdus luminescens, are important biological control agents of insect pests. This nematode-bacterium-insect association represents an emerging tripartite model for research on mutualistic and parasitic symbioses. Elucidation of mechanisms underlying these biological processes may serve as a foundation for improving the biological control potential of the nematode-bacterium complex. This large-scale expressed sequence tag (EST) analysis effort enables gene discovery and development of microsatellite markers. These ESTs will also aid in the annotation of the upcoming complete genome sequence of H. bacteriophora.
A total of 31,485 high quality ESTs were generated from cDNA libraries of the adult H. bacteriophora TTO1 strain. Cluster analysis revealed the presence of 3,051 contigs and 7,835 singletons, representing 10,886 distinct EST sequences. About 72% of the distinct EST sequences had significant matches (E value < 1e-5) to proteins in GenBank's non-redundant (nr) and Wormpep190 databases. We have identified 12 ESTs corresponding to 8 genes potentially involved in RNA interference, 22 ESTs corresponding to 14 genes potentially involved in dauer-related processes, and 51 ESTs corresponding to 27 genes potentially involved in defense and stress responses. Comparison to ESTs and proteins of free-living nematodes led to the identification of 554 parasitic nematode-specific ESTs in H. bacteriophora, among which are those encoding F-box-like/WD-repeat protein theromacin, Bax inhibitor-1-like protein, and PAZ domain containing protein. Gene Ontology terms were assigned to 6,685 of the 10,886 ESTs. A total of 168 microsatellite loci were identified with primers designable for 141 loci.
A total of 10,886 distinct EST sequences were identified from adult H. bacteriophora cDNA libraries. BLAST searches revealed ESTs potentially involved in parasitism, RNA interference, defense responses, stress responses, and dauer-related processes. The putative microsatellite markers identified in H. bacteriophora ESTs will enable genetic mapping and population genetic studies. These genomic resources provide the material base necessary for genome annotation, microarray development, and in-depth gene functional analysis.
昆虫病原线虫嗜菌异小杆线虫及其共生细菌发光光杆状菌是重要的害虫生物防治剂。这种线虫-细菌-昆虫的关联代表了一种新兴的三方模型，用于研究互利共生和寄生共生。阐明这些生物过程的潜在机制可为提高线虫-细菌复合体的生物防治潜力奠定基础。这项大规模的表达序列标签（EST）分析工作有助于基因发现和微卫星标记的开发。这些ESTs也将有助于注释即将完成的嗜菌异小杆线虫全基因组序列。
从嗜菌异小杆线虫TTO1菌株成虫的cDNA文库中总共产生了31485个高质量的ESTs。聚类分析显示存在3051个重叠群和7835个单拷贝序列，代表10886个不同的EST序列。约72%的不同EST序列与GenBank的非冗余（nr）和Wormpep190数据库中的蛋白质有显著匹配（E值<1e-5）。我们鉴定出12个ESTs，对应8个可能参与RNA干扰的基因；22个ESTs，对应14个可能参与滞育相关过程的基因；51个ESTs，对应27个可能参与防御和应激反应的基因。与自由生活线虫的ESTs和蛋白质进行比较，在嗜菌异小杆线虫中鉴定出554个寄生线虫特异性ESTs，其中包括编码F-box样/WD重复蛋白theromacin、Bax抑制剂-1样蛋白和含PAZ结构域蛋白的ESTs。基因本体论术语被分配到10886个ESTs中的6685个。总共鉴定出168个微卫星位点，其中141个位点可设计引物。
从嗜菌异小杆线虫成虫cDNA文库中总共鉴定出10886个不同的EST序列。BLAST搜索揭示了可能参与寄生、RNA干扰、防御反应、应激反应和滞育相关过程的ESTs。在嗜菌异小杆线虫ESTs中鉴定出的假定微卫星标记将有助于遗传图谱绘制和群体遗传学研究。这些基因组资源为基因组注释、微阵列开发和深入的基因功能分析提供了必要的物质基础。
