title: Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia).
abstract: BACKGROUND
  Gene duplication followed by adaptive selection is a well-accepted process leading to toxin diversification in venoms. However, emergent genomic, transcriptomic and proteomic evidence now challenges this role to be at best equivocal to other processess . Cnidaria are arguably the most ancient phylum of the extant metazoa that are venomous and such provide a definitive ancestral anchor to examine the evolution of this trait.
  
  
  METHODS
  Here we compare predicted toxins from the translated genome of the coral Acropora digitifera to putative toxins revealed by proteomic analysis of soluble proteins discharged from nematocysts, to determine the extent to which gene duplications contribute to venom innovation in this reef-building coral species. A new bioinformatics tool called HHCompare was developed to detect potential gene duplications in the genomic data, which is made freely available ( https://github.com/rgacesa/HHCompare ).
  
  
  RESULTS
  A total of 55 potential toxin encoding genes could be predicted from the A. digitifera genome, of which 36 (65 %) had likely arisen by gene duplication as evinced using the HHCompare tool and verified using two standard phylogeny methods. Surprisingly, only 22 % (12/55) of the potential toxin repertoire could be detected following rigorous proteomic analysis, for which only half (6/12) of the toxin proteome could be accounted for as peptides encoded by the gene duplicates. Biological activities of these toxins are dominatedby putative phospholipases and toxic peptidases.
  
  
  CONCLUSIONS
  Gene expansions in A. digitifera venom are the most extensive yet described in any venomous animal, and gene duplication plays a significant role leading to toxin diversification in this coral species. Since such low numbers of toxins were detected in the proteome, it is unlikely that the venom is evolving rapidly by prey-driven positive natural selection. Rather we contend that the venom has a defensive role deterring predation or harm from interspecific competition and overgrowth by fouling organisms. Factors influencing translation of toxin encoding genes perhaps warrants more profound experimental consideration.
authors.affiliation: Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, SE1 9NH, UK.
authors.forename: Ranko
authors.initials: R
authors.lastname: Gacesa
authors.affiliation: Proteomics Facility, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London, SE5 8AF, UK.
authors.forename: Ray
authors.initials: R
authors.lastname: Chung
authors.affiliation: Coral Reefs Ecosystems Laboratory, School of Biological Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Dunn
authors.affiliation: Mass Spectrometry Laboratory, UCL School of Pharmacy, 29/39 Brunswick Square, London, WC1N 1AX, UK.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Weston
authors.affiliation: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil.
authors.forename: Adrian
authors.initials: A
authors.lastname: Jaimes-Becerra
authors.affiliation: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil.|Centro de Biologia Marinha, Universidade de São Paulo, Rodovia Manoel Hypólito do Rego, km. 131,5, 11600-000, São Sebastião, Brazil.
authors.forename: Antonio C
authors.initials: AC
authors.lastname: Marques
authors.affiliation: Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua Matao, Trav. 14, 101, 05508-090, São Paulo, SP, Brazil.
authors.forename: André C
authors.initials: AC
authors.lastname: Morandini
authors.affiliation: Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
authors.forename: Daslav
authors.initials: D
authors.lastname: Hranueli
authors.affiliation: Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia.
authors.forename: Antonio
authors.initials: A
authors.lastname: Starcevic
authors.affiliation: Proteomics Facility, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, London, SE5 8AF, UK.
authors.forename: Malcolm
authors.initials: M
authors.lastname: Ward
authors.affiliation: Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, SE1 9NH, UK. paul.long@kcl.ac.uk.|Department of Chemistry, King's College London, Strand, London, WC2R 2LS, UK. paul.long@kcl.ac.uk.|Brazil Institute, King's College London, Strand, London, WC2R 2LS, UK. paul.long@kcl.ac.uk.|Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000, São Paulo, SP, Brazil. paul.long@kcl.ac.uk.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Long
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D037421:Anthozoa / Q000235:genetics* / Q000472:pathogenicity; D003064:Cnidarian Venoms / Q000235:genetics / Q000633:toxicity; D019143:Evolution, Molecular; D020440:Gene Duplication; D016678:Genome; D058894:Nematocyst / Q000378:metabolism; D010802:Phylogeny; D020543:Proteome / Q000235:genetics* / Q000633:toxicity; D012641:Selection, Genetic
chemical_list: D003064:Cnidarian Venoms; D020543:Proteome