title: Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs.
abstract: Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: N J
authors.initials: NJ
authors.lastname: Kenny
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: K W
authors.initials: KW
authors.lastname: Chan
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: W
authors.initials: W
authors.lastname: Nong
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: Z
authors.initials: Z
authors.lastname: Qu
authors.affiliation: Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain.
authors.forename: I
authors.initials: I
authors.lastname: Maeso
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: H Y
authors.initials: HY
authors.lastname: Yip
authors.affiliation: School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: T F
authors.initials: TF
authors.lastname: Chan
authors.affiliation: School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: H S
authors.initials: HS
authors.lastname: Kwan
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: P W H
authors.initials: PW
authors.lastname: Holland
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: K H
authors.initials: KH
authors.lastname: Chu
authors.affiliation: Simon F.S. Li Marine Science Laboratory, School of Life Sciences, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
authors.forename: J H L
authors.initials: JH
authors.lastname: Hui
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D020440:Gene Duplication; D005801:Genes, Homeobox; D016678:Genome; D006737:Horseshoe Crabs / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA