Negrisolo Enrico, Bargelloni Luca, Patarnello Tomaso, Ozouf-Costaz Catherine, Pisano Eva, di Prisco Guido, Verde Cinzia
Department of Public Health, Comparative Pathology, and Veterinary Hygiene, University of Padova, Legnaro, Italy.
Methods Enzymol. 2008;436:511-38. doi: 10.1016/S0076-6879(08)36029-7.
Sequencing genomes of model organisms is a great challenge for biological sciences. In the past decade, scientists have developed a large number of methods to align and compare sequenced genomes. The analysis of a given sequence provides much information on the genome structure but to a lesser extent on the function. Comparative genomics are a useful tool for functional and evolutionary annotation of genomes. In principle, comparison of genomic sequences may allow for identification of the evolutionary selection (negative or positive) that the functional sequences have been subjected to over time. Positively selected genome regions are the most important ones for evolution, because most changes are adaptive and often induce biological differences in organisms. The draft genomes of five fish species have recently become available. We herewith review and discuss some new insights into comparative genomics in fish globin genes. Special attention will be given to a complementary methodological approach to comparative genomics, fluorescence in situ hybridization (FISH). Internet resources for analyzing sequence alignments and annotations and new bioinformatic tools to address critical problems are thoroughly discussed.
对模式生物的基因组进行测序是生命科学面临的一项巨大挑战。在过去十年中，科学家们开发了大量方法来比对和比较已测序的基因组。对给定序列的分析可提供有关基因组结构的大量信息，但在功能方面提供的信息较少。比较基因组学是对基因组进行功能和进化注释的有用工具。原则上，基因组序列的比较可以识别功能序列随时间所经历的进化选择（负向或正向）。正向选择的基因组区域对进化最为重要，因为大多数变化是适应性的，并且常常在生物体中引发生物学差异。最近已有五种鱼类的基因组草图可供使用。我们在此回顾并讨论鱼类珠蛋白基因比较基因组学的一些新见解。将特别关注比较基因组学的一种补充性方法——荧光原位杂交（FISH）。还将全面讨论用于分析序列比对和注释的互联网资源以及解决关键问题的新生物信息学工具。
