Limits...
Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes.

Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G - Genome Biol. (2015)

Bottom Line: We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates.We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes.We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

View Article: PubMed Central - PubMed

ABSTRACT

Background: A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well-known in single-celled organisms such as bacteria, but its existence in higher organisms, including animals, is less well established, and is controversial in humans.

Results: We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates. Genome-wide comparative and phylogenetic analyses show that HGT in animals typically gives rise to tens or hundreds of active 'foreign' genes, largely concerned with metabolism. Our analyses suggest that while fruit flies and nematodes have continued to acquire foreign genes throughout their evolution, humans and other primates have gained relatively few since their common ancestor. We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes.

Conclusions: We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

Show MeSH

Related in: MedlinePlus

Mean origin of class C foreign genes for each taxon. Numbers show percentage contribution within each taxon (row). The same analyses for Class B or A genes show very similar patterns. The colour scheme is as in Figure 3: origin from archaea is light blue, from bacteria is dark blue, from protists is grey, from plants is green and from fungi is pink.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4358723&req=5

Fig4: Mean origin of class C foreign genes for each taxon. Numbers show percentage contribution within each taxon (row). The same analyses for Class B or A genes show very similar patterns. The colour scheme is as in Figure 3: origin from archaea is light blue, from bacteria is dark blue, from protists is grey, from plants is green and from fungi is pink.

Mentions: When calculating h, the likely taxon of origin of a foreign gene was taken to be the taxon of the best-matching protein. Bacteria and protists are the most common donors in all groups (Figure 4), which might reflect the relative abundance of the respective donor species in the environments of the recipient organisms. The phylogenetic validation of the foreign genes occasionally indicated a different origin than the original calculation (based on alignments and h index), but both methods agreed on average 92% of the time; performing the analysis shown in Figure 4 using phylogenetically predicted origins instead shows the same pattern of donors (data not shown). The identity of the actual donor species is much harder to determine, as the identified ‘donor’ is almost certainly just the most closely related species currently sequenced. This is especially the case for older HGT events where the same foreign gene appears in more than one species, that is, where horizontal transfer predates the divergence of species. However, we did find a number of recent transfers (present in only a single studied species) that were identified as originating specifically from Wolbachia, with one example each in D. ananassae, C. briggsae and C. japonica (GF19976, CBG07424 and Cjp-ubc-6, respectively).Figure 4


Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes.

Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G - Genome Biol. (2015)

Mean origin of class C foreign genes for each taxon. Numbers show percentage contribution within each taxon (row). The same analyses for Class B or A genes show very similar patterns. The colour scheme is as in Figure 3: origin from archaea is light blue, from bacteria is dark blue, from protists is grey, from plants is green and from fungi is pink.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4358723&req=5

Fig4: Mean origin of class C foreign genes for each taxon. Numbers show percentage contribution within each taxon (row). The same analyses for Class B or A genes show very similar patterns. The colour scheme is as in Figure 3: origin from archaea is light blue, from bacteria is dark blue, from protists is grey, from plants is green and from fungi is pink.
Mentions: When calculating h, the likely taxon of origin of a foreign gene was taken to be the taxon of the best-matching protein. Bacteria and protists are the most common donors in all groups (Figure 4), which might reflect the relative abundance of the respective donor species in the environments of the recipient organisms. The phylogenetic validation of the foreign genes occasionally indicated a different origin than the original calculation (based on alignments and h index), but both methods agreed on average 92% of the time; performing the analysis shown in Figure 4 using phylogenetically predicted origins instead shows the same pattern of donors (data not shown). The identity of the actual donor species is much harder to determine, as the identified ‘donor’ is almost certainly just the most closely related species currently sequenced. This is especially the case for older HGT events where the same foreign gene appears in more than one species, that is, where horizontal transfer predates the divergence of species. However, we did find a number of recent transfers (present in only a single studied species) that were identified as originating specifically from Wolbachia, with one example each in D. ananassae, C. briggsae and C. japonica (GF19976, CBG07424 and Cjp-ubc-6, respectively).Figure 4

Bottom Line: We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates.We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes.We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

View Article: PubMed Central - PubMed

ABSTRACT

Background: A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well-known in single-celled organisms such as bacteria, but its existence in higher organisms, including animals, is less well established, and is controversial in humans.

Results: We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates. Genome-wide comparative and phylogenetic analyses show that HGT in animals typically gives rise to tens or hundreds of active 'foreign' genes, largely concerned with metabolism. Our analyses suggest that while fruit flies and nematodes have continued to acquire foreign genes throughout their evolution, humans and other primates have gained relatively few since their common ancestor. We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes.

Conclusions: We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

Show MeSH
Related in: MedlinePlus