鉴定基因水平转移方法.docVIP

Box 2 | Detection of horizontal gene transfer Horizontal gene transfer (HGT) can be detected using several methods, each with important advantages and caveats23,?24,?25,?26,?35,?123. Phylogenetic methods Phylogenetic trees of proteins or DNA sequences can show incongruent relationships among taxa, which might be the result of HGT. However, lineage-specific gene losses,?CONVERGENCE?and unequal mutation rates in different taxa can cause similar effects. Because protein sequences change more slowly than their DNA coding regions, ancient HGT can be best detected by using protein trees, whereas nucleotide trees are better for studying closely related species. Overall, phylogenetic analysis is the most robust indicator of ancient HGT. Nucleotide composition analysis Shifts in nucleotide composition between neighbouring sequences, such as an increase in the frequencies of GC bases over AT bases, could indicate that a gene or non-coding region from another species has been inserted into the genome. However, it is important to realize that intra-genome regional biases in nucleotide composition can introduce a false signal. The signal will be degraded as DNA sequences?AMELIORATE?over time, making ancient HGT difficult to detect. Unusual species distributions of genes The presence, in a particular species, of one or more genes that are also found in distant relatives but not in closely related species indicates the occurrence of HGT. If the genes are physically close (for example, if they are in the same operon), HGT might have facilitated the incorporation of a new biochemical pathway. However, this approach does not work for universally occurring genes. Furthermore, the gene order on the chromosome is often poorly conserved even among closely related species. The alternative hypothesis of extensive gene loss in the intervening lineages must also be considered. Homology Significant homology of a gene to that of a distantly related species, as determined using the database sea