Horizontal Gene Transfer in Marine Environment: A Technical Perspective on Metagenomics

Abstract

In the environment, unicellular organisms such as prokaryotes are exposed to direct invasion of viruses and its consequent transduction. In addition, some of the prokaryotic species can uptake naked DNA molecules outside or transfer their own DNA to other species through conjugative plasmids. Hence, prokaryotic genomes could be often mosaic: they may have the extrinsic genes which are not vertically transmitted from the ancestor but horizontally transferred from other organisms. Such a phenomenon, namely, “horizontal (or lateral) gene transfer,” is the main issue of this chapter. Horizontal gene transfer can rapidly cause genotypic/phenotypic changes in the recipient organisms, apparently beyond the theory of traditional population genetics based on mutation. Thus, it has been considered that horizontal gene transfer has influenced very much on the evolution of prokaryotes. In response to the accumulation of genomic data, the amount of horizontally transferred genes has been estimated at the large scale, but the significance of horizontal gene transfer in real environment has not been fully assessed. How often does horizontal gene transfer occur among taxa? How much does it affect the gene pool in environment? The challenging studies have just started. Metagenomic approaches have a great potential for this purpose, but many methodological limitations for treating the data remains unsolved. In this chapter, traditional genomics methods for estimating horizontally transferred genes are first reviewed. In the latter part, technical perspectives on prediction of horizontal gene transfer from the metagenomics data are discussed.