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    Grafting or pruning in the animal tree: Lateral gene transfer and gene loss?

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    Author
    Dunning, Hotopp, J.C.
    Date
    2018
    Journal
    BMC Genomics
    Publisher
    BioMed Central Ltd.
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://dx.doi.org/10.1186/s12864-018-4832-5
    Abstract
    Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate. Results: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes. Conclusions: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes. © 2018 The Author(s)..
    Sponsors
    We would like to thank John Werren at the University of Rochester for helpful discussions, James Munro at the Institute for Genome Science for his help with running PROTTEST, and John Mattick for his help adding taxonomy information to the phylogenetic trees from RAxML at the Institute for Genome Science.
    Keyword
    ACY3
    ASPA
    Bacteria
    Chordate
    Evolution
    Gene loss
    Horizontal gene transfer
    Lateral gene transfer
    Rate variation
    Vertebrate
    Identifier to cite or link to this item
    https://www.scopus.com/inward/record.uri?eid=2-s2.0-85048705965&doi=10.1186%2fs12864-018-4832-5&partnerID=40&md5=130360bd477221f75ad79a3d63a2e415; http://hdl.handle.net/10713/8754
    ae974a485f413a2113503eed53cd6c53
    10.1186/s12864-018-4832-5
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