Hemichordate Genomes and Deuterostome Origins
OPEN ARTICLE doi:10.1038/nature16150 Hemichordate genomes and deuterostome origins Oleg Simakov1,2*, Takeshi Kawashima3†*, Ferdinand Marlétaz4, Jerry Jenkins5, Ryo Koyanagi6, Therese Mitros7, Kanako Hisata3, Jessen Bredeson7, Eiichi Shoguchi3, Fuki Gyoja3, Jia-Xing Yue8†, Yi-Chih Chen9, Robert M. Freeman Jr10†, Akane Sasaki11, Tomoe Hikosaka-Katayama12, Atsuko Sato13, Manabu Fujie6, Kenneth W. Baughman3, Judith Levine14, Paul Gonzalez14, Christopher Cameron15, Jens H. Fritzenwanker14, Ariel M. Pani16, Hiroki Goto6, Miyuki Kanda6, Nana Arakaki6, Shinichi Yamasaki6, Jiaxin Qu17, Andrew Cree17, Yan Ding17, Huyen H. Dinh17, Shannon Dugan17, Michael Holder17, Shalini N. Jhangiani17, Christie L. Kovar17, Sandra L. Lee17, Lora R. Lewis17, Donna Morton17, Lynne V. Nazareth17, Geoffrey Okwuonu17, Jireh Santibanez17, Rui Chen17, Stephen Richards17, Donna M. Muzny17, Andrew Gillis18, Leonid Peshkin10, Michael Wu7, Tom Humphreys19, Yi-Hsien Su9, Nicholas H. Putnam8†, Jeremy Schmutz5, Asao Fujiyama20, Jr-Kai Yu9, Kunifumi Tagawa11, Kim C. Worley17, Richard A. Gibbs17, Marc W. Kirschner10, Christopher J. Lowe14, Noriyuki Satoh3, Daniel S. Rokhsar1,7,21 & John Gerhart7 Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements.
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