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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.

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Related in: MedlinePlus

Phylogenetic relationships of the main taxonomic groups studied. The blue numbers indicate the ortholog groups mapping to each branch (HGT events). Events may have occurred anywhere along the branch, not just where the number is indicated. Events found at the base of the tree have occurred anywhere between the origin of the phylum and the base of the tree. Trees are not drawn to scale with each other.
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Fig1: Phylogenetic relationships of the main taxonomic groups studied. The blue numbers indicate the ortholog groups mapping to each branch (HGT events). Events may have occurred anywhere along the branch, not just where the number is indicated. Events found at the base of the tree have occurred anywhere between the origin of the phylum and the base of the tree. Trees are not drawn to scale with each other.

Mentions: To determine the scale of HGT across well-characterised taxonomic groups, we examined 12 Drosophila species, four Caenorhabditis species and 10 primates (Figure 1) for which high quality genomes and transcriptomes are available. For each transcribed gene, we calculated the HGT index, h (the difference between the bitscores of the best non-metazoan and the best metazoan matches), which gives a relative quantitative measure of how well a given gene aligns to non-metazoan versus metazoan sequences, with positive numbers indicating a better alignment to non-metazoan sequences [12]. For example, the C. elegans gene gut-obstructed 1 (gob-1), which encodes a trehalose-6-phosphate phosphatase, has a best non-metazoan match with a bitscore of 135 and a best metazoan match with a bitscore of 39.3 resulting in an HGT index of 95.7. As we were interested in more than just very recent HGT, we excluded members of the test species’ phylum from the metazoan matches. This allowed us to identify HGT over evolutionary periods encompassing hundreds of millions of years, as opposed to only identifying HGT that occurred since the test species’ divergence from its most closely related species (likely up to tens of millions of years). Hereafter, when we refer to matches to metazoan sequences, we mean these subsets.Figure 1


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)

Phylogenetic relationships of the main taxonomic groups studied. The blue numbers indicate the ortholog groups mapping to each branch (HGT events). Events may have occurred anywhere along the branch, not just where the number is indicated. Events found at the base of the tree have occurred anywhere between the origin of the phylum and the base of the tree. Trees are not drawn to scale with each other.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Phylogenetic relationships of the main taxonomic groups studied. The blue numbers indicate the ortholog groups mapping to each branch (HGT events). Events may have occurred anywhere along the branch, not just where the number is indicated. Events found at the base of the tree have occurred anywhere between the origin of the phylum and the base of the tree. Trees are not drawn to scale with each other.
Mentions: To determine the scale of HGT across well-characterised taxonomic groups, we examined 12 Drosophila species, four Caenorhabditis species and 10 primates (Figure 1) for which high quality genomes and transcriptomes are available. For each transcribed gene, we calculated the HGT index, h (the difference between the bitscores of the best non-metazoan and the best metazoan matches), which gives a relative quantitative measure of how well a given gene aligns to non-metazoan versus metazoan sequences, with positive numbers indicating a better alignment to non-metazoan sequences [12]. For example, the C. elegans gene gut-obstructed 1 (gob-1), which encodes a trehalose-6-phosphate phosphatase, has a best non-metazoan match with a bitscore of 135 and a best metazoan match with a bitscore of 39.3 resulting in an HGT index of 95.7. As we were interested in more than just very recent HGT, we excluded members of the test species’ phylum from the metazoan matches. This allowed us to identify HGT over evolutionary periods encompassing hundreds of millions of years, as opposed to only identifying HGT that occurred since the test species’ divergence from its most closely related species (likely up to tens of millions of years). Hereafter, when we refer to matches to metazoan sequences, we mean these subsets.Figure 1

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