Evolution of dna transposons in eukaryotes

The availability of genomic sequences from all kingdoms of life and sophisticated searching algorithms has revolutionized our ability to detect distantly related transposons purely on the basis of sequence similarity, thus improving our understanding of their macroevolutionary trends. This chapter focuses on DNA transposons in eukaryotic genomes and particularly the four available genomes from plants and animals. Phylogenetic analysis of such a megafamily is fraught with difficulties because only this shared D,D35E domain can be employed, and even then the alignment of many of the amino acids in-between is uncertain without structural information, which is only available for several integrases and the Tn5 transposase. An interesting feature of this superfamily is that the transposase genes of members of the pogo family have occasionally been recruited to perform host functions. The genomic sequences from Arabidopsis and Oryza have also revealed many sequences encoding related proteins. Bacterial transposons experience a very different host environment from those in eukaryotes, and even among eukaryotes, there is huge variation in these dynamics due to vagaries of the transposonhost interaction. The chapter focuses what recent eukaryotic genomic sequences tell us about the history of DNA transposons. Many other DNA transposons exist at relatively low copy numbers, for example, in filamentous fungi, and have multiple lineages in particular hosts, for example, the Mutator-like elements of plants; however, these situations require extensive analysis of large sequence sets within species and consideration of the evolution of the transposon family across species.