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Stony Coral Resequencing Offers Clues to Japanese Reef Relationships

NEW YORK (GenomeWeb) – A population sequencing study of the stony coral species Acropora digitifera suggests it undergoes long distance migrations relatively rarely and that reefs can't necessarily rely on migration from neighboring coral to rebuild after damage.

As they reported online today in Scientific Reports, researchers from the Okinawa Institute of Science and Technology Graduate University (OIST) sequenced the genomes of more than 150 A. digitifera samples. Their focus was on a reef near Okinawa Island that were severely damaged by bleaching in 1998, along with samples from other areas of the coral reef-rich island region off of southern Japan.

The sequences yielded more than 900,000 variants used to cluster the coral into four genetic groups, including an Okinawa Island coral cluster that were genetically distinct from those found at a nearby island chain called Kerama. The results suggest coral migration contributed relatively little to the reemergence of A. digitifera around Okinawa Island since 1998, though coral there did share historical genetic ties to those from a site much farther away.

"This result shows that the coral populations of the Okinawa and Kerama Islands have not met recently," first author Chuya Shinzato, a marine genomic researcher at OIST, said in a statement. "It means that long-distant larvae migration by spawning within the Ryukyu Archipelago is less common than what was previously thought."

After more than a decade, the team explained, coral reefs surrounding Okinawa Island have started recovering from a bleaching event in 1998 that wiped out a significant proportion of coral in that area. The same bleaching event left Acropora relatively unscathed at the Kerama islands, an area roughly 19 miles away that was designated a National Park last year.

Given the islands' proximity to one another, the researchers turned to genome sequence to look not only at the relative resilience of corals in the Kerama area, but also to explore the source of new coral populations in the previously damaged Okinawa Island area.

For example, A. digitifera corals disperse sperm and eggs during carefully orchestrated, synchronized spawning events take place in precise light and water temperature conditions. But it was unclear whether this brand of so-called broadcast spawning may have contributing to coral migrations that helped Okinawa Island corals recover.

To investigate this possibility, the team used Illumina GAIIx and HiSeq 2000 instruments to sequence the genomes of 155 A. digitifera corals collected between 2011 and 2014 in Japan's Ryukyu Archipelago, a region that encompasses Okinawa Island, the Kerama island, and the Yaeyama islands.

After making improvements to an A. digitifera genome assembly described in Nature in 2011 by researchers in Japan and Australia, the researchers compared the re-sequenced stony coral sequences to this reference, identifying 905,561 SNPs in the A. digitifera collection.

Using these SNPs, the team grouped 122 of the newly sequenced corals into four distinct but related clusters: one from the northern Yaeyama region, another from southern Yaeyama, and one cluster apiece from the Kerama islands and Okinawa Island.

The genetic differentiation between corals from the Okinawa and Kerama regions argued against a recent re-population of bleached coral by A. digitifera from the Kerama islands area. Instead, the researchers proposed a model placing the Kerama island reefs at the receiving end of past coral migrations, consistent with their apparent diversity.

They also saw signs of a historical relationship between Okinawa Island corals and those living near the Yaeyama Islands, almost 250 miles away, hinting at rare long-distance migration events for A. digitifera

"We detected strong historical migration from the [Yaeyama Islands] to [Okinawa Island], and suggest that the [Yaeyama Islands] are the original source of [Okinawa Island] corals," Shinzato and co-authors explained.