Genomic Architecture of Reef Fish in the Red Sea and Arabian Sea


Our collaborative sampling program in the Red Sea and Arabian Sea, funded by KAUST and the National Geographic Society have allowed us to develop genomic approaches to address questions of connectivity and adaptability in a number of non-model reef fish. We are particularly interested in characterizing historical and contemporary barriers to larval dispersal in this geologically complex region. This project has direct applications to the fields of biogeography, phylogeography, population genetics, meta-population dynamics, and regulating the international exchange of marine resources.



Double-digest RAD tags


Beginning in May 2013, we developed reduced-representation genome sequencing experiments (i.e., RAD tags) on Illumina sequencers in collaboration with the KAUST Bioscience Core Lab (BCL). The aim was to identify Single Nucleotide Polymorphisms (SNPs) within and across our study species. The double-digest RAD (or ddRAD) method we used at KAUST is based on Peterson et al. 2012, which includes a double restriction enzyme digest, a custom combinatorial indexing method for multiplexing samples, and the availability of software tools to facilitate downstream genotyping across hundreds of individuals (see Figure 2 from Peterson et al. 2012).


For a detailed description of the bench protocol, click here.


For a detailed description of the bioinformatics pipeline package for processing ddRAD data, click here.



We have thus far generated SNP datasets using the ddRAD method for the following species of biogeographic importance in the Red Sea and Arabian Sea:

genomics project fish1.jpg
Amphiprion bicinctus

genomics project fish2.jpg
Amphiprion omanensis


genomics project fish3.jpg
Chaetodon austriacus

genomics project fish4.jpg
Chaetodon fasciatus
genomics project fish5.jpg
Chaetodon larvatus
genomics project fish6.jpg
Chaetodon melapterus

Chaetodon mesoleucos
genomics project fish8.jpg
Chaetodon paucifasciatus
genomics project fish9.jpg
Chaetodon pictus
genomics project fish10.jpg
Chaetodon semilarvatus
genomics project fish11.jpg
Chaetodon trifascialis
genomics project fish12.jpg
Ctenochaetus striatus





Whole Genome Sequencing


We selected one of the most iconic Red Sea endemic butterflyfish species, Chaetodon austriacus, for whole genome sequencing. This species is distributed almost exclusively in the northern and central Red Sea region. Chaetodon austriacus has three closely related sister taxa found together in the Coralochaetodon subgenus, Chaetodon trifasciatus, Chaetodon lunulatus, and Chaetodon melapterus, which live exclusively in the Indian Ocean, Pacific Ocean, and Arabian Sea, respectively. Our study at KAUST represents the first draft genome of a Red Sea endemic reef fish and one of the first draft genomes available for any reef fish. The genome of C. austriacus will provide a scaffold for analyzing apparent patterns in our SNP datasets, especially loci that appear to be under some form of selection. This genome will also provide a means to identify genes that may control unique adaptations to the Red Sea environment.

genomics project fish13.jpg

Raw sequences will be available from NCBI soon​.

Primary accessions

(All photos by Tane Sinclair-Taylor unless otherwise indicated on the photo.)


Joseph DiBattista, KAUST
Pablo Saenz-Agudelo, Austral University of Chile
Marek Piatek, KAUST
Manuel Aranda, KAUST
Xin Wang, KAUST
​Michelle Gaither, Durham University
Luiz Rocha, California Academy of Sciences
John Howard Choat, James Cook University
Brian Bowen, Hawai'i Institute of Marine Biology