Comparative and evolutionary genomics of globin genes in fish

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.