<P> Gene transfer between plants and fungi has been posited for a number of cases, including rice (Oryza sativa). </P> <P> Genetic engineering is essentially horizontal gene transfer, albeit with synthetic expression cassettes . The Sleeping Beauty transposon system (SB) was developed as a synthetic gene transfer agent that was based on the known abilities of Tc1 / mariner transposons to invade genomes of extremely diverse species . The SB system has been used to introduce genetic sequences into a wide variety of animal genomes . (See also Gene therapy .) </P> <P> Horizontal gene transfer is a potential confounding factor in inferring phylogenetic trees based on the sequence of one gene . For example, given two distantly related bacteria that have exchanged a gene a phylogenetic tree including those species will show them to be closely related because that gene is the same even though most other genes are dissimilar . For this reason it is often ideal to use other information to infer robust phylogenies such as the presence or absence of genes or, more commonly, to include as wide a range of genes for phylogenetic analysis as possible . </P> <P> For example, the most common gene to be used for constructing phylogenetic relationships in prokaryotes is the 16S ribosomal RNA gene since its sequences tend to be conserved among members with close phylogenetic distances, but variable enough that differences can be measured . However, in recent years it has also been argued that 16s rRNA genes can also be horizontally transferred . Although this may be infrequent, the validity of 16s rRNA - constructed phylogenetic trees must be reevaluated . </P>

What are the three ways that bacteria horizontally share genes