title: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.
abstract: The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ∼267.9-248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhuo
authors.initials: Z
authors.lastname: Wang
authors.affiliation: RIKEN Center for Developmental Biology, Kobe, Japan.
authors.forename: Juan
authors.initials: J
authors.lastname: Pascual-Anaya
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Amonida
authors.initials: A
authors.lastname: Zadissa
authors.affiliation: BGI-Japan, Kobe, Japan.
authors.forename: Wenqi
authors.initials: W
authors.lastname: Li
authors.affiliation: Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
authors.forename: Yoshihito
authors.initials: Y
authors.lastname: Niimura
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Huang
authors.affiliation: BGI-Japan, Kobe, Japan.
authors.forename: Chunyi
authors.initials: C
authors.lastname: Li
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: White
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Xiong
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Dongming
authors.initials: D
authors.lastname: Fang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yao
authors.initials: Y
authors.lastname: Ming
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: RIKEN Center for Developmental Biology, Kobe, Japan.
authors.forename: Shigehiro
authors.initials: S
authors.lastname: Kuraku
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Miguel
authors.initials: M
authors.lastname: Pignatelli
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Javier
authors.initials: J
authors.lastname: Herrero
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Kathryn
authors.initials: K
authors.lastname: Beal
authors.affiliation: National Institute for Basic Biology (NIBB) Core Research Facilities, NIBB, Okazaki, Japan.
authors.forename: Masafumi
authors.initials: M
authors.lastname: Nozawa
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Juan
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Japan, Kobe, Japan.
authors.forename: Hongyan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Yu
authors.affiliation: National Institute for Basic Biology (NIBB) Core Research Facilities, NIBB, Okazaki, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Shigenobu
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Junyi
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Japan, Kobe, Japan.
authors.forename: Jiannan
authors.initials: J
authors.lastname: Liu
authors.affiliation: European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Flicek
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Steve
authors.initials: S
authors.lastname: Searle
authors.affiliation: BGI-Shenzhen, Shenzhen, China.|Department of Biology, University of Copenhagen, Copenhagen, Denmark.|King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: RIKEN Center for Developmental Biology, Kobe, Japan.
authors.forename: Shigeru
authors.initials: S
authors.lastname: Kuratani
authors.affiliation: BGI-Japan, Kobe, Japan.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Bronwen
authors.initials: B
authors.lastname: Aken
authors.affiliation: BGI-Shenzhen, Shenzhen, China.|China National GeneBank, BGI-Shenzhen, Shenzhen, China.|Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: RIKEN Center for Developmental Biology, Kobe, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Irie
mesh_terms: D060105:Animal Shells / Q000378:metabolism; D000818:Animals; D019521:Body Patterning / Q000235:genetics; D002642:Chick Embryo; D002645:Chickens / Q000235:genetics; D047108:Embryonic Development / Q000235:genetics; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D018035:Receptors, Odorant / Q000235:genetics; D030162:Reptilian Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D014426:Turtles / Q000196:embryology / Q000235:genetics*; D051153:Wnt Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D018035:Receptors, Odorant; D030162:Reptilian Proteins; D051153:Wnt Proteins