The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest

Journal name:
Nature
Year published:
DOI:
doi:10.1038/nature22033
Received
Accepted
Published online

The crown-of-thorns starfish (COTS, the Acanthaster planci species group) is a highly fecund predator of reef-building corals throughout the Indo-Pacific region1. COTS population outbreaks cause substantial loss of coral cover, diminishing the integrity and resilience of reef ecosystems2, 3, 4, 5, 6. Here we sequenced genomes of COTS from the Great Barrier Reef, Australia and Okinawa, Japan to identify gene products that underlie species-specific communication and could potentially be used in biocontrol strategies. We focused on water-borne chemical plumes released from aggregating COTS, which make the normally sedentary starfish become highly active. Peptide sequences detected in these plumes by mass spectrometry are encoded in the COTS genome and expressed in external tissues. The exoproteome released by aggregating COTS consists largely of signalling factors and hydrolytic enzymes, and includes an expanded and rapidly evolving set of starfish-specific ependymin-related proteins. These secreted proteins may be detected by members of a large family of olfactory-receptor-like G-protein-coupled receptors that are expressed externally, sometimes in a sex-specific manner. This study provides insights into COTS-specific communication that may guide the generation of peptide mimetics for use on reefs with COTS outbreaks.

At a glance

Figures

  1. The crown-of-thorns starfish.
    Figure 1: The crown-of-thorns starfish.

    a, Adult COTS predating on coral. White coral skeleton (foreground), unconsumed coral (background). Photo by the Australian Institute of Marine Science. b, A COTS (foreground) and its predator, the giant triton. Photo by Oceanwide Images. c, Global distribution of COTS8 and the collection sites of the two individuals sequenced. Blue, yellow, pink and green, Pacific Ocean, north Indian Ocean, south Indian Ocean and Red Sea clades, respectively. d, Phylogeny of Deuterostomia showing placement of Acanthaster. A partially condensed maximum likelihood topology is shown. Scale bar, 0.1 substitutions per site. Bootstrap support values below 100 are shown. e, Historical effective population sizes inferred from OKI and GBR genomes using multiple sequential Markovian coalescent analysis9, assuming a generation time of 3 years and a substitution mutation rate of 1.0 × 10−8 per generation.

  2. Exoproteome of aggregating and alarmed COTS.
    Figure 2: Exoproteome of aggregating and alarmed COTS.

    a, Top, Y-maze experimental design showing arm dividers and starter zones (yellow). Middle, cumulative response of COTS over the first 45 min to seawater conditioned with six aggregating COTS (right, n = 22) and ambient seawater (left, control; n = 32). Red, the area COTS spent the most time; blue, the least time; black, no presence. Y mazes, green outline; starter zones are demarcated with yellow lines (see Supplementary Video 1). Bottom, response of COTS in a Y maze to water conditioned with aggregating COTS and ambient seawater. Movement of COTS out of the starter box (P < 0.05; tested with the Freeman–Halton extension of the Fisher’s exact test) and the cumulative duration of movement (P < 0.05) over 45 min. Mean ± s.e.m. b, Detection of 108 secreted proteins in triplicate water samples taken around aggregating and giant triton-alarmed COTS, first three and last three lanes, respectively. EPDRs detected exclusively from aggregating COTS are marked with red ovals; EPDRs secreted from both aggregating and alarmed COTS, but more prevalent from alarmed COTS, are marked with green ovals. c, Tissue expression of genes encoding the 108 secreted proteins, divided into general protein classes.

  3. Ependymin-related gene expansion and expression.
    Figure 3: Ependymin-related gene expansion and expression.

    a, Tissue expression of the COTS EPDR genes. b, Phylogeny of EPDR proteins. COTS genes are labelled and are marked with red lines; other asteroids, two shades of orange and yellow lines; sea urchins, dark green; hemichordates, light green; molluscs, pink; annelids, purple; cnidarians, black; and vertebrates, blue. The three clades to which COTS sequences belong are indicated by the outer circle. The asterisk denotes the fish-specific true ependymin clade. c, One of the COTS EPDR gene clusters on scaffold 218, with exons (grey bars and arrowheads), intergenic regions and introns (thin black lines) and direction of transcription (arrowhead at end of coding sequence) shown. Scale bar, 10 kb. In all panels, EPDRs secreted by COTS into the seawater are highlighted by red or green ovals as in Fig. 2b.

  4. Olfactory-receptor-like GPCR genes.
    Figure 4: Olfactory-receptor-like GPCR genes.

    a, Organization and orientation of single exon genes in clade c (see panel b) on scaffolds 38, 56, 44 and 148. Genes, grey arrowheads pointing in direction of transcription; black lines, intergenic regions. Scale bar, 20 kb. b, Phylogeny of ambulacrarian rhodopsin GPCRs, and Branchiostoma and Actinopterygii olfactory receptors (OR). The 6 sea urchin GPCRs (surreal) and 11 COTS OR-like gene clades are highlighted in blue and red, respectively. c, Expression of olfactory-receptor-like and rhodopsin GPCRs (R) in COTS tissues, grouped based on clades defined in b.

  5. Deuterostome phylogeny showing placement of Acanthaster within asteroids.
    Extended Data Fig. 1: Deuterostome phylogeny showing placement of Acanthaster within asteroids.

    A concatenated supermatrix of 427 genes (95,585 amino acids, 45.16% missing data) recovering a fully resolved tree. With exception of support for hemichordate monophyly (bootstrap support value = 98%), we found maximal support for all phylum- and class-level taxa. Species sampled, annotations and characteristics of each gene analysed are presented in Supplementary Note 4. Bootstrap support values below 100 are shown. Scale bar: 0.1 substitutions per site.

  6. Acanthaster planci heterozygosity.
    Extended Data Fig. 2: Acanthaster planci heterozygosity.

    a, Single-nucleotide polymorphism (SNP) analysis showing the number of SNPs identified within and between OKI and GBR genomes. Percentage heterozygosity within these genomes and the level of nucleotide variance between genomes are shown. See Supplementary Note 2 for further details. b, k-mer (17-mer) plot. The GBR (green) and OKI (red) genomes were estimated to be 441 and 421 Mb, respectively.

  7. Pfam enrichment in the genomes of selected metazoans displayed as relative abundance heat maps.
    Extended Data Fig. 3: Pfam enrichment in the genomes of selected metazoans displayed as relative abundance heat maps.

    a, Comparison of metazoans. b, Comparison of deuterostomes. c, Comparison of ambulacrarians. See Supplementary Note 5 for further details of methods and analyses.

  8. Comparison of Hox clusters.
    Extended Data Fig. 4: Comparison of Hox clusters.

    a, Genome browser views of the Hox cluster on GBR scaffold 27 and OKI scaffold 15. Stylised Hox clusters are shown below each scaffold with the corresponding gene model for each Hox gene identified on the scaffold. b, Table of OKI and GBR Hox gene models. Prefix corresponds to scaffold. c, Micro-synteny of Hox cluster-containing OKI scaffold 15 and GBR scaffolds 27, 51 and 25. d, Mapping of OKI and GBR scaffolds containing the Hox cluster to each other. e, Molecular phylogenetic analysis of select bilaterian Hox genes by the maximum-likelihood method. Bootstrap support values over 50% are shown. Scale bar: 0.2 substitutions per site. Species abbreviations: Bfl, Branchiostoma floridae; Dme, Drosophila melanogaster; oki.scaffold.genemodel, A. planci OKI; Pfl, Ptychodera flava; Sko, Saccoglossus kowalevskii; and Spu, Stronglocentrotus purpuratus.

  9. Response of crown-of-thorns starfish to seawater conditioned with its predator the giant triton, Charonia tritonis.
    Extended Data Fig. 5: Response of crown-of-thorns starfish to seawater conditioned with its predator the giant triton, Charonia tritonis.

    a, Top, diagram showing Y-maze experimental design showing arm dividers and starter zones (yellow). Middle, heat maps showing the cumulative response of COTS over 45 min to water conditioned with a giant triton (left) and ambient seawater (right) (n = 18). Red, area in which COTS spent most of the time with descending time to blue; black, no presence. Green outline represents the Y-maze and arm divider that prevents recirculation of water into the opposite arm; starter zones are demarcated by yellow lines. b, The duration of movement (highly active threshold set at >60%; t = −2.936, P = 0.006, 2-tailed t-test). c, The meander (change in direction of movement) of active animals over 45 min (t = 4.437, P = 0.000, 2-tailed t-test). Control, ambient seawater only; giant triton, ambient seawater conditioned with giant triton exudate. Mean ± s.e.m. See Supplementary Video 3 and Supplementary Note 7 for further details.

  10. Protein classes in the crown-of-thorns starfish secretome.
    Extended Data Fig. 6: Protein classes in the crown-of-thorns starfish secretome.

    a, Overall distribution of characterized secretome. b, Distribution of structural, signalling and unclassified proteins. c, Distribution of enzyme types.

  11. Extended phylogeny of the EPDR proteins.
    Extended Data Fig. 7: Extended phylogeny of the EPDR proteins.

    a, Phylogenetic tree of EPDRs incorporating those identified from ambulacrarian transcriptomes. COTS genes are indicated in red, those from non-COTS taxa within the order Valvatida in orange, from non-valvatid taxa within the class Asteroidea in yellow, and from non-asteroid taxa within the phylum Echinodermata in green. Branches with maximum-likelihood bootstrap values >70 and Bayesian posterior probability values >0.9 are indicated by a solid line; those with lower values are indicated by a dashed line. The scale bar indicates the number of substitutions per site. Major EPDR clades are indicated by numbers on the outer circle. Sequences used in the alignment can be found in Supplementary Note 8. b, Sequence logos constructed from the conserved region of sequences from each of the seven clades identified in a. The height of the amino acid residues indicates the level of conservation, residues highlighted in blue are highly conserved across all clades. Clade 1 is the most highly conserved EPDR clade (ultraconserved motifs are boxed). Clades 3–7 show much lower sequence conservation overall, and possess an extra pair of cysteine residues (highlighted in red).

  12. GPCR abundance, structure and expression in crown-of-thorns starfish.
    Extended Data Fig. 8: GPCR abundance, structure and expression in crown-of-thorns starfish.

    a, Abundance of GPCR genes in ambulacrarians and amphioxus, showing the distribution of the five GPCR classes in each species. See Supplementary Note 9 for further details on genes and analyses. b, Tissue expression of each non-rhodopsin class GPCRs in COTS tissues. c, Additional examples of GPCR gene clusters in COTS, with genes in clades b, and f–h shown in Fig. 4b. All genes have one exon and are depicted as grey arrowheads that point in the direction of transcription. GBR scaffold numbers are shown above the line; scale bar, 20 kb.

Tables

  1. Summary of GBR and OKI COTS genomes and transcriptomes
    Extended Data Table 1: Summary of GBR and OKI COTS genomes and transcriptomes
  2. The GPCR gene familiy in ambulacrarians and amphioxus
    Extended Data Table 2: The GPCR gene familiy in ambulacrarians and amphioxus

Videos

  1. Response of crown-of-thorns starfish over 45 minutes to factors released by aggregating starfish.
    Video 1: Response of crown-of-thorns starfish over 45 minutes to factors released by aggregating starfish.
    Time-lapse videos of 45 min Y-maze behavioural assays showing in the first instance two crown-of-thorns starfish subjected to flowing ambient seawater (control) and then two different COTS subjected to flowing seawater conditioned with factors released by aggregating COTS. Two example Y-mazes are shown (1, 2), with right (R) and left (L) arms. 270x real time speed.
  2. Response of crown-of-thorns starfish over 8 hours to factors released by aggregating starfish.
    Video 2: Response of crown-of-thorns starfish over 8 hours to factors released by aggregating starfish.
    Time-lapse videos of 8 h Y-maze behavioural assays showing in the first instance two crown-of-thorns starfish subjected to flowing ambient seawater (control) and then two different COTS subjected to flowing seawater conditioned with factors released by aggregating COTS. Two example Y-mazes are shown (1, 2), with right (R) and left (L) arms. 480x real time speed.
  3. Response of crown-of-thorns starfish over 45 minutes to factors released by their predator, the giant triton.
    Video 3: Response of crown-of-thorns starfish over 45 minutes to factors released by their predator, the giant triton.
    Time-lapse videos of 45 min Y-maze behavioural assays showing two crown-of-thorns starfish, one subjected to flowing ambient seawater (control) and the other subjected to flowing seawater conditioned with factors released by their predator, the giant triton. Two Y-mazes are shown (1, 2), with right (R) and left (L) arms. 270x real time speed.

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Author information

  1. Present addresses: Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, Alabama 35487, USA (K.M.K.); CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico (S.L.F.-V.).

    • Kevin M. Kocot &
    • Selene L. Fernandez-Valverde
  2. These authors contributed equally to this work.

    • Michael R. Hall,
    • Kevin M. Kocot &
    • Kenneth W. Baughman

Affiliations

  1. Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville, Queensland 4810, Australia

    • Michael R. Hall,
    • Cherie A. Motti &
    • Utpal Bose
  2. Centre for Marine Science, School of Biological Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia

    • Kevin M. Kocot,
    • Selene L. Fernandez-Valverde,
    • Marie E. A. Gauthier,
    • William L. Hatleberg,
    • Arunkumar Krishnan,
    • Carmel McDougall,
    • Xueyan Xiang,
    • Min Zhao,
    • Sandie M. Degnan &
    • Bernard M. Degnan
  3. Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan

    • Kenneth W. Baughman,
    • Eiichi Shoguchi,
    • Chuya Shinzato,
    • Kanako Hisata &
    • Noriyuki Satoh
  4. Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia

    • Tianfang Wang,
    • Min Zhao,
    • Utpal Bose &
    • Scott F. Cummins
  5. DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan

    • Manabu Fujie &
    • Miyuki Kanda

Contributions

M.R.H. and B.M.D. conceived and designed the project. N.S. and B.M.D. coordinated genome and transcriptome sequencing undertaken by K.W.B., E.S., S.L.F.-V., M.E.A.G., K.M.K., C.M., C.S., K.H., M.F. and M.K. S.M.D. and B.M.D. coordinated genome and transcriptome analyses undertaken by K.M.K., C.M., W.L.H., A.K., X.X. and M.Z. S.F.C. coordinated proteome analyses undertaken by T.W., M.Z. and U.B. M.R.H., S.F.C and C.A.M. undertook the behavioural studies. B.M.D., S.M.D., M.R.H., K.M.K. and K.W.B. wrote the manuscript with contributions from other all authors.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

Reviewer Information Nature thanks M. Matz, M. Medina, C. Vogel and K. Worley for their contribution to the peer review of this work.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: Deuterostome phylogeny showing placement of Acanthaster within asteroids. (511 KB)

    A concatenated supermatrix of 427 genes (95,585 amino acids, 45.16% missing data) recovering a fully resolved tree. With exception of support for hemichordate monophyly (bootstrap support value = 98%), we found maximal support for all phylum- and class-level taxa. Species sampled, annotations and characteristics of each gene analysed are presented in Supplementary Note 4. Bootstrap support values below 100 are shown. Scale bar: 0.1 substitutions per site.

  2. Extended Data Figure 2: Acanthaster planci heterozygosity. (104 KB)

    a, Single-nucleotide polymorphism (SNP) analysis showing the number of SNPs identified within and between OKI and GBR genomes. Percentage heterozygosity within these genomes and the level of nucleotide variance between genomes are shown. See Supplementary Note 2 for further details. b, k-mer (17-mer) plot. The GBR (green) and OKI (red) genomes were estimated to be 441 and 421 Mb, respectively.

  3. Extended Data Figure 3: Pfam enrichment in the genomes of selected metazoans displayed as relative abundance heat maps. (438 KB)

    a, Comparison of metazoans. b, Comparison of deuterostomes. c, Comparison of ambulacrarians. See Supplementary Note 5 for further details of methods and analyses.

  4. Extended Data Figure 4: Comparison of Hox clusters. (883 KB)

    a, Genome browser views of the Hox cluster on GBR scaffold 27 and OKI scaffold 15. Stylised Hox clusters are shown below each scaffold with the corresponding gene model for each Hox gene identified on the scaffold. b, Table of OKI and GBR Hox gene models. Prefix corresponds to scaffold. c, Micro-synteny of Hox cluster-containing OKI scaffold 15 and GBR scaffolds 27, 51 and 25. d, Mapping of OKI and GBR scaffolds containing the Hox cluster to each other. e, Molecular phylogenetic analysis of select bilaterian Hox genes by the maximum-likelihood method. Bootstrap support values over 50% are shown. Scale bar: 0.2 substitutions per site. Species abbreviations: Bfl, Branchiostoma floridae; Dme, Drosophila melanogaster; oki.scaffold.genemodel, A. planci OKI; Pfl, Ptychodera flava; Sko, Saccoglossus kowalevskii; and Spu, Stronglocentrotus purpuratus.

  5. Extended Data Figure 5: Response of crown-of-thorns starfish to seawater conditioned with its predator the giant triton, Charonia tritonis. (283 KB)

    a, Top, diagram showing Y-maze experimental design showing arm dividers and starter zones (yellow). Middle, heat maps showing the cumulative response of COTS over 45 min to water conditioned with a giant triton (left) and ambient seawater (right) (n = 18). Red, area in which COTS spent most of the time with descending time to blue; black, no presence. Green outline represents the Y-maze and arm divider that prevents recirculation of water into the opposite arm; starter zones are demarcated by yellow lines. b, The duration of movement (highly active threshold set at >60%; t = −2.936, P = 0.006, 2-tailed t-test). c, The meander (change in direction of movement) of active animals over 45 min (t = 4.437, P = 0.000, 2-tailed t-test). Control, ambient seawater only; giant triton, ambient seawater conditioned with giant triton exudate. Mean ± s.e.m. See Supplementary Video 3 and Supplementary Note 7 for further details.

  6. Extended Data Figure 6: Protein classes in the crown-of-thorns starfish secretome. (197 KB)

    a, Overall distribution of characterized secretome. b, Distribution of structural, signalling and unclassified proteins. c, Distribution of enzyme types.

  7. Extended Data Figure 7: Extended phylogeny of the EPDR proteins. (690 KB)

    a, Phylogenetic tree of EPDRs incorporating those identified from ambulacrarian transcriptomes. COTS genes are indicated in red, those from non-COTS taxa within the order Valvatida in orange, from non-valvatid taxa within the class Asteroidea in yellow, and from non-asteroid taxa within the phylum Echinodermata in green. Branches with maximum-likelihood bootstrap values >70 and Bayesian posterior probability values >0.9 are indicated by a solid line; those with lower values are indicated by a dashed line. The scale bar indicates the number of substitutions per site. Major EPDR clades are indicated by numbers on the outer circle. Sequences used in the alignment can be found in Supplementary Note 8. b, Sequence logos constructed from the conserved region of sequences from each of the seven clades identified in a. The height of the amino acid residues indicates the level of conservation, residues highlighted in blue are highly conserved across all clades. Clade 1 is the most highly conserved EPDR clade (ultraconserved motifs are boxed). Clades 3–7 show much lower sequence conservation overall, and possess an extra pair of cysteine residues (highlighted in red).

  8. Extended Data Figure 8: GPCR abundance, structure and expression in crown-of-thorns starfish. (225 KB)

    a, Abundance of GPCR genes in ambulacrarians and amphioxus, showing the distribution of the five GPCR classes in each species. See Supplementary Note 9 for further details on genes and analyses. b, Tissue expression of each non-rhodopsin class GPCRs in COTS tissues. c, Additional examples of GPCR gene clusters in COTS, with genes in clades b, and f–h shown in Fig. 4b. All genes have one exon and are depicted as grey arrowheads that point in the direction of transcription. GBR scaffold numbers are shown above the line; scale bar, 20 kb.

Extended Data Tables

  1. Extended Data Table 1: Summary of GBR and OKI COTS genomes and transcriptomes (301 KB)
  2. Extended Data Table 2: The GPCR gene familiy in ambulacrarians and amphioxus (72 KB)

Supplementary information

Video

  1. Video 1: Response of crown-of-thorns starfish over 45 minutes to factors released by aggregating starfish. (1.03 MB, Download)
    Time-lapse videos of 45 min Y-maze behavioural assays showing in the first instance two crown-of-thorns starfish subjected to flowing ambient seawater (control) and then two different COTS subjected to flowing seawater conditioned with factors released by aggregating COTS. Two example Y-mazes are shown (1, 2), with right (R) and left (L) arms. 270x real time speed.
  2. Video 2: Response of crown-of-thorns starfish over 8 hours to factors released by aggregating starfish. (3.61 MB, Download)
    Time-lapse videos of 8 h Y-maze behavioural assays showing in the first instance two crown-of-thorns starfish subjected to flowing ambient seawater (control) and then two different COTS subjected to flowing seawater conditioned with factors released by aggregating COTS. Two example Y-mazes are shown (1, 2), with right (R) and left (L) arms. 480x real time speed.
  3. Video 3: Response of crown-of-thorns starfish over 45 minutes to factors released by their predator, the giant triton. (446 KB, Download)
    Time-lapse videos of 45 min Y-maze behavioural assays showing two crown-of-thorns starfish, one subjected to flowing ambient seawater (control) and the other subjected to flowing seawater conditioned with factors released by their predator, the giant triton. Two Y-mazes are shown (1, 2), with right (R) and left (L) arms. 270x real time speed.

PDF files

  1. Supplementary Information (4.6 MB)

    This file contains Supplementary Notes, Figures and additional references.

Zip files

  1. Supplementary Tables (9.4 MB)

    This zipped file contains Supplementary Tables S1-9 and a Supplementary Table guide.

Additional data