%0 Journal Article %J Nature %D 2015 %T Hemichordate genomes and deuterostome origins. %A Simakov, Oleg %A Kawashima, Takeshi %A Marlétaz, Ferdinand %A Jenkins, Jerry %A Koyanagi, Ryo %A Mitros, Therese %A Hisata, Kanako %A Bredeson, Jessen %A Shoguchi, Eiichi %A Gyoja, Fuki %A Yue, Jia-Xing %A Chen, Yi-Chih %A Freeman, Robert M %A Sasaki, Akane %A Hikosaka-Katayama, Tomoe %A Sato, Atsuko %A Fujie, Manabu %A Baughman, Kenneth W %A Levine, Judith %A Gonzalez, Paul %A Cameron, Christopher %A Fritzenwanker, Jens H %A Pani, Ariel M %A Goto, Hiroki %A Kanda, Miyuki %A Arakaki, Nana %A Yamasaki, Shinichi %A Qu, Jiaxin %A Cree, Andrew %A Ding, Yan %A Dinh, Huyen H %A Dugan, Shannon %A Holder, Michael %A Jhangiani, Shalini N %A Kovar, Christie L %A Lee, Sandra L %A Lewis, Lora R %A Morton, Donna %A Nazareth, Lynne V %A Okwuonu, Geoffrey %A Santibanez, Jireh %A Chen, Rui %A Richards, Stephen %A Muzny, Donna M %A Gillis, Andrew %A Peshkin, Leonid %A Wu, Michael %A Humphreys, Tom %A Su, Yi-Hsien %A Putnam, Nicholas H %A Schmutz, Jeremy %A Fujiyama, Asao %A Yu, Jr-Kai %A Tagawa, Kunifumi %A Worley, Kim C %A Gibbs, Richard A %A Kirschner, Marc W %A Lowe, Christopher J %A Satoh, Noriyuki %A Rokhsar, Daniel S %A Gerhart, John %K Animals %K Chordata, Nonvertebrate %K Conserved Sequence %K Echinodermata %K Evolution, Molecular %K Genome %K Multigene Family %K Phylogeny %K Signal Transduction %K Synteny %K Transforming Growth Factor beta %X

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. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

%B Nature %V 527 %P 459-65 %8 2015 Nov 26 %G eng %N 7579 %1 https://www.ncbi.nlm.nih.gov/pubmed/26580012?dopt=Abstract %R 10.1038/nature16150 %0 Journal Article %J Curr Biol %D 2012 %T Identical genomic organization of two hemichordate hox clusters. %A Freeman, Robert %A Ikuta, Tetsuro %A Wu, Michael %A Koyanagi, Ryo %A Kawashima, Takeshi %A Tagawa, Kunifumi %A Humphreys, Tom %A Fang, Guang-Chen %A Fujiyama, Asao %A Saiga, Hidetoshi %A Lowe, Christopher %A Worley, Kim %A Jenkins, Jerry %A Schmutz, Jeremy %A Kirschner, Marc %A Rokhsar, Daniel %A Satoh, Nori %A Gerhart, John %K Animals %K Biological Evolution %K Chordata, Nonvertebrate %K Genes, Homeobox %K Genome %K Molecular Sequence Data %K Multigene Family %K Phylogeny %K Transcription, Genetic %X

Genomic comparisons of chordates, hemichordates, and echinoderms can inform hypotheses for the evolution of these strikingly different phyla from the last common deuterostome ancestor. Because hox genes play pivotal developmental roles in bilaterian animals, we analyzed the Hox complexes of two hemichordate genomes. We find that Saccoglossus kowalevskii and Ptychodera flava both possess 12-gene clusters, with mir10 between hox4 and hox5, in 550 kb and 452 kb intervals, respectively. Genes hox1-hox9/10 of the clusters are in the same genomic order and transcriptional orientation as their orthologs in chordates, with hox1 at the 3' end of the cluster. At the 5' end, each cluster contains three posterior genes specific to Ambulacraria (the hemichordate-echinoderm clade), two forming an inverted terminal pair. In contrast, the echinoderm Strongylocentrotus purpuratus contains a 588 kb cluster of 11 orthologs of the hemichordate genes, ordered differently, plausibly reflecting rearrangements of an ancestral hemichordate-like ambulacrarian cluster. Hox clusters of vertebrates and the basal chordate amphioxus have similar organization to the hemichordate cluster, but with different posterior genes. These results provide genomic evidence for a well-ordered complex in the deuterostome ancestor for the hox1-hox9/10 region, with the number and kind of posterior genes still to be elucidated.

%B Curr Biol %V 22 %P 2053-8 %8 2012 Nov 06 %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/23063438?dopt=Abstract %R 10.1016/j.cub.2012.08.052