Cohen Raphael, Chalifa-Caspi Vered, Williams Timothy D, Auslander Meirav, George Stephen G, Chipman James K, Tom Moshe
National Institute for Biotechnology in Negev, Ben Gurion University of Negev, Beer-Sheva 84105, Israel.
Mar Biotechnol (NY). 2007 Jul-Aug;9(4):491-9. doi: 10.1007/s10126-007-9010-8. Epub 2007 May 20.
Using an available cross-species cDNA microarray is advantageous for examining multigene expression patterns in non-model organisms, saving the need for construction of species-specific arrays. The aim of the present study was to estimate relative efficiency of cross-species hybridizations across bony fishes, using bioinformatics tools. The methodology may serve also as a model for similar evaluations in other taxa. The theoretical evaluation was done by substituting comparative whole-transcriptome sequence similarity information into the thermodynamic hybridization equation. Complementary DNA sequence assemblages of nine fish species belonging to common families or suborders and distributed across the bony fish taxonomic branch were selected for transcriptome-wise comparisons. Actual cross-species hybridizations among fish of different taxonomic distances were used to validate and eventually to calibrate the theoretically computed relative efficiencies.
使用现有的跨物种cDNA微阵列有利于检测非模式生物中的多基因表达模式，无需构建物种特异性阵列。本研究的目的是利用生物信息学工具评估硬骨鱼跨物种杂交的相对效率。该方法也可作为其他分类群类似评估的模型。理论评估是通过将比较全转录组序列相似性信息代入热力学杂交方程来完成的。选择了属于常见科或亚目且分布在硬骨鱼分类分支中的9种鱼类的互补DNA序列组装体进行转录组水平的比较。利用不同分类距离的鱼类之间的实际跨物种杂交来验证并最终校准理论计算的相对效率。
