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New Genomes Serve as Source of Information on Turtle Evolution, Adaptation

NEW YORK (GenomeWeb News) – In a study appearing online yesterday in Nature Genetics, members of the Joint International Turtle Genomes Consortium served up genomics-based details on everything from turtles' evolutionary relationships to the development of their distinct body plan.

Researchers based at BGI, RIKEN, the Wellcome Trust Sanger Institute, and elsewhere sequenced draft versions of the Chinese soft-shell turtle and green sea turtle genomes. They also gathered gene expression data on the animals by sequencing RNA transcripts from turtle embryos and adult turtle tissues.

Together with unpublished sequences from crocodile and alligator genomes provided by other researchers, the new turtle sequences served as fodder for a phylogenetic analysis that "makes clear the evolutionary history of turtles in diverging from other species and settles the disputes about the phylogenetic position of reptiles," BGI-Shenzhen's Zhuo Wang, co-first author on the study, said in a statement.

The study looked at turtle-specific adaptations, too, from general embryonic features to the underpinnings of turtle shell formation. From a broader perspective, those involved in the study noted that the work also provides a peek at the sorts of variability that can be achieved using shared genetic building blocks within the vertebrate lineage.

"[O]ur study both highlights the evolution of the turtle body plan and offers a model to explain, at the genomic level, how the vertebrate developmental program can change to produce major evolutionary novelties in morphological phenotypes," Wang and co-authors wrote.

The new turtle study comes on the heels of the first published turtle genome — that of the western painted turtle — which was described in Genome Biology last month by a group led by researchers at the University of Washington and the University of California at Los Angeles. Phylogenetic analyses in that study pointed to genetic ties between turtles and the archosaur lineage that contains birds and crocodilians.

The turtle-archosaur relationship was confirmed and described in more detail in the current study, which hinged on sequences from multiple turtle and crocodilian representatives.

The researchers did whole-genome shotgun sequencing on DNA from Chinese soft-shell turtle, Pelodiscus sinensis, and green sea turtle, Chelonia mydas, using Illumina's HiSeq 2000 instrument. The resulting sequence covered the 2.21 billion base Chinese soft-shell turtle and the 2.24 billion base green sea turtle genomes to average depths of nearly 106-fold and 82-fold, respectively.

The team's phylogenetic analysis — which folded in genome sequence data for the American alligator and the saltwater crocodile generated by the International Crocodilian Genomes Working Group — verified that turtles are more closely related to the bird-crocodilian lineage than they are to lineages such as that housing lizards and snakes.

Based on the current sequence data and fossil information, the researchers estimated that the turtle and archosaur (bird-crocodilian) arms of the vertebrate tree diverged from one another between some 248 million to almost 268 million years ago.

The team delved into some of the genetic and genomic patterns that have turned up in the turtle lineage since that split, too.

Compared to the archosaurs and other vertebrates, for instance, researchers found that both the soft-shell turtle and the green sea turtle genomes housed expansion to gene families comprising olfactory reception pathways.

While the prior turtle genome sequencing analysis revealed slow rates of genetic change in the turtle genome as a whole, the new study highlighted several genes that were notable for having undergone faster-than-usual genetic changes — among them, members of signaling pathways thought to mediate of the turtle's morphological traits.

On the other hand, investigators found an apparent dip in representation by genes involved in tasting, piquing hunger, and or governing energy homeostasis in the turtles' genomes, perhaps explaining some features of the dawdling turtle metabolism.

With the help of gene expression data generated from turtle embryos, meanwhile, the team explored features of vertebrate development, looking in particular at the shared and distinct expression profiles at play during embryogenesis — as well as the timing with which they're used — in turtles and chickens.

For instance, although researchers found 20 Wnt genes in the two newly sequenced turtle genomes, their RNA sequence information indicated that just one of these — Wnt5a — seems to be expressed in the carapacial ridge, a structure related to turtle rib and shell development.

That, in turn, suggests that at least some aspects of this body feature stem from evolutionary tweaks to a set of sequences used for limb development in other animals, study authors explained. "Wnt5 expression was found in the growth zone of the dorsal shell," they wrote, "supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty."