Controlling the hungry starfish

Controlling the hungry starfish

The Crown-of-Thorns Starfish (COTS) Acanthaster planci plays an important role in maintaining a healthy coral reef population in it’s native habitat in the Indo-Pacific region by digesting fast-growing corals. Probably because of increased water temperatures, increased nutrients running off from land to water and increased fishing of the starfish’s natural predators, populations and distribution have increased significantly. The great barrier reef and other important biodiversity hot spots are being threatened by these outbreaks (along with other threats) as the COTS are eating they way through the reef. The outbreaks of starfish are more dangerous to the reefs than bleaching events and disease infections combined!

Counter-control measures by humans currently focus on injections of sodium bisulphate by divers - or maybe by robots in the future. Even though a trained diver might be able to kill over 100 COTS per hours, this work is difficult and will not reach all underwater areas.

Now the genome of Acanthaster planci was sequenced and analysed by researchers at the University of Queensland's Centre for Marine Science in Brisbane (Professor Bernard Degnan from the School of Biological Sciences as the corresponding author). It was published in Nature (Michael R. Hall et al.: The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest) and might lead to new methods of population control in this and other species.

JBrowser showing gene and transcriptome models of the starfish

Two individuals from Japan and Australia respectively were sequenced by multiple MiSeq and HiSeq runs. Paired-end reads were assembled using the GS De novo Assembler version 2.3 (Newbler, Roche; usually only used for 454 sequencing data) and mate-pair sequencing data were scaffolded with SSPACE 3.0 (used to extend the assembled regions). With a coverage of 66x the genome sizes of the Australian and Japanese COTS were estimated at 441 Mb and 421 Mb respectively. The genomes are however highly homologous and believed to belong to the same species. A genome browser displaying the reference and transcriptome sequences was set up using JBrowse (a flexible HTML5-JavaScript-based web interface) at marine genomics.oist.jp. From the assembled genomes the researchers identified 24 500 protein-coding using an array of methods (PASATransDecoder, AugustusCEGMA mappings, SNAP, GeneMark-ES) combining the predictions with EVM.

The team also analysed the proteins released by COTS using mass spectrometry, looked at the potentially active domains and compared their genes. The hope was to isolate candidate proteins that are secreted and act as a chemical aggregation signal. When many individuals can be gathered together using these signals artificially, they would be easier to control and capture. In particular G-protein coupled receptor proteins (GPCRs) were analysed as potential receptors of the signal in the cell membrane.

As a result it was possible to identify "species-specific secreted factors associated with aggregating starfish, which can lead to the development of peptide mimetics for biocontrol measures. The high similarity of the two genomes indicates that genome-based mitigation strategies developed for one locale can be applied throughout the species’ range. These genomic data will also be useful in ecological and population studies into the causes of COTS outbreaks, contributing to regional-scale management of this coral reef pest." (Nature article)
 
The next phase of the project will see these results be put into action by recreating the signals as well as look for species-specific factors for other invasive starfish.

Sources: 
NatureGenomeWeb, Wikipedia, image: M. Wright, Wikipedia