Wang Minghua, Guerrero Felix D, Pertea Geo, Nene Vishvanath M
Lorus Therapeutics Inc; 2 Meridian Road, Toronto, ON M9W 4Z7, Canada.
BMC Genomics. 2007 Oct 12;8:368. doi: 10.1186/1471-2164-8-368.
The southern cattle tick, Rhipicephalus (Boophilus) microplus, is an economically important parasite of cattle and can transmit several pathogenic microorganisms to its cattle host during the feeding process. Understanding the biology and genomics of R. microplus is critical to developing novel methods for controlling these ticks.
We present a global comparative genomic analysis of a gene index of R. microplus comprised of 13,643 unique transcripts assembled from 42,512 expressed sequence tags (ESTs), a significant fraction of the complement of R. microplus genes. The source material for these ESTs consisted of polyA RNA from various tissues, lifestages, and strains of R. microplus, including larvae exposed to heat, cold, host odor, and acaricide. Functional annotation using RPS-Blast analysis identified conserved protein domains in the conceptually translated gene index and assigned GO terms to those database transcripts which had informative BlastX hits. Blast Score Ratio and SimiTri analysis compared the conceptual transcriptome of the R. microplus database to other eukaryotic proteomes and EST databases, including those from 3 ticks. The most abundant protein domains in BmiGI were also analyzed by SimiTri methodology.
These results indicate that a large fraction of BmiGI entries have no homologs in other sequenced genomes. Analysis with the PartiGene annotation pipeline showed 64% of the members of BmiGI could not be assigned GO annotation, thus minimal information is available about a significant fraction of the tick genome. This highlights the important insights in tick biology which are likely to result from a tick genome sequencing project. Global comparative analysis identified some tick genes with unexpected phylogenetic relationships which detailed analysis attributed to gene losses in some members of the animal kingdom. Some tick genes were identified which had close orthologues to mammalian genes. Members of this group would likely be poor choices as targets for development of novel tick control technology.
南方牛蜱，微小扇头蜱（Rhipicephalus (Boophilus) microplus），是牛的一种具有重要经济意义的寄生虫，在取食过程中可将多种致病微生物传播给其牛宿主。了解微小扇头蜱的生物学和基因组学对于开发控制这些蜱的新方法至关重要。
我们对微小扇头蜱的基因索引进行了全面的比较基因组分析，该索引由从42,512个表达序列标签（EST）组装而成的13,643个独特转录本组成，这是微小扇头蜱基因互补体的很大一部分。这些EST的来源材料包括来自微小扇头蜱的各种组织、生活阶段和菌株的多聚A RNA，包括暴露于热、冷、宿主气味和杀螨剂的幼虫。使用RPS-Blast分析进行功能注释，在概念上翻译的基因索引中鉴定出保守的蛋白质结构域，并为那些具有信息丰富的BlastX命中的数据库转录本分配GO术语。Blast得分比和SimiTri分析将微小扇头蜱数据库的概念转录组与其他真核生物蛋白质组和EST数据库进行了比较，包括来自3种蜱的数据库。还通过SimiTri方法分析了BmiGI中最丰富的蛋白质结构域。
这些结果表明，BmiGI条目的很大一部分在其他已测序基因组中没有同源物。使用PartiGene注释管道进行的分析表明，BmiGI的64%成员无法分配GO注释，因此关于蜱基因组的很大一部分的信息很少。这突出了蜱基因组测序项目可能在蜱生物学方面带来的重要见解。全面的比较分析确定了一些蜱基因具有意想不到的系统发育关系，详细分析将其归因于动物界某些成员中的基因丢失。鉴定出了一些与哺乳动物基因具有密切直系同源物的蜱基因。这一组的成员作为新型蜱控制技术开发的目标可能不是理想选择。
