Decoding and Analysis of the Crown-of-Thorns Starfish Acanthaster planci Genome

Okinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyEchinoderms are at the base of the deuterostome clade, yet have radial body plans, a watervascular system, and exoskeletons. In order to investigate how genomes control development, I studied the “Crown-of-Thorns Starfish” (COTS) or Acanthaster planci genome. I made four discoveries from sequencing two COTS specimens, one from the Great Barrier Reef, Australia (‘GBR’) and the other from Okinawa, Japan (‘OKI’). Separate 384 megabase (Mb) assemblies containing ~24,500 genes were generated. First, I discovered that both genomes displayed unexpectedly low heterozygosity; reciprocal BLAST alignment of scaffolds longer than 10 kilobases (Kb) revealed 98.8% nucleotide identity, consistent with a single pacific COTS clade undergoing a recent population expansion. Second, although the unique Hox gene order in sea urchins was hypothesized to be related to pentaradial body plans, I discovered that COTS Hox and ParaHox clusters resemble hemichordate and chordate clusters. The COTS Hox cluster shares with sea urchins the transposition of even-skipped (Evx), as well as posterior Hox reorganization. I thus proposed an evolutionary scenario for how shuffling of the Hox cluster in urchins may have arisen. Third, recent studies show that hemichordates possess a deuterostome-specific cluster of transcription factors associated with development of pharyngeal gill slits. Although extant echinoderms do not have pharyngeal gill slits, I found the cluster in the COTS genome, supporting an ancient origin for pharyngeal gill slits as a deuterostome-defining morphological feature. Fourth, using systems biology notation, I mapped COTS candidate genes for 1-methlyadenine (1-MA)-mediated oocyte maturation. This thesis confirms that the high quality of the COTS genome is biologically significant, and amendable to future studies. Although COTS are famous for decimating coral reefs, this thesis shows that COTS can also be used for genomic and evolutionary developmental research.doctoral thesi