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Nature 2015 Nov 26;5277579:459-65. doi: 10.1038/nature16150.
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Hemichordate genomes and deuterostome origins.

Simakov O , Kawashima T , Marlétaz F , Jenkins J , Koyanagi R , Mitros T , Hisata K , Bredeson J , Shoguchi E , Gyoja F , Yue JX , Chen YC , Freeman RM , Sasaki A , Hikosaka-Katayama T , Sato A , Fujie M , Baughman KW , Levine J , Gonzalez P , Cameron C , Fritzenwanker JH , Pani AM , Goto H , Kanda M , Arakaki N , Yamasaki S , Qu J , Cree A , Ding Y , Dinh HH , Dugan S , Holder M , Jhangiani SN , Kovar CL , Lee SL , Lewis LR , Morton D , Nazareth LV , Okwuonu G , Santibanez J , Chen R , Richards S , Muzny DM , Gillis A , Peshkin L , Wu M , Humphreys T , Su YH , Putnam NH , Schmutz J , Fujiyama A , Yu JK , Tagawa K , Worley KC , Gibbs RA , Kirschner MW , Lowe CJ , Satoh N , Rokhsar DS , Gerhart J .

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.

PubMed ID: 26580012
PMC ID: PMC4729200
Article link: Nature
Grant support: [+]

Species referenced: Echinodermata
Genes referenced: ago1b arxl bmp2 clock cmahp dvr1 foxa1 gscl isl1 lbx1 lefty1 LOC100887844 LOC100889503 LOC100889527 LOC100891068 LOC100892350 LOC105443840 LOC115925415 LOC579992 LOC582802 LOC588607 LOC590297 LOC591618 LOC752022 msx1 msxl nkx2-1 nodall otp pax2l rx1 sema5bl six1 six4 six6 slc25a21 univin

Article Images: [+] show captions
References [+] :
Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997, Pubmed