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Gecko Genome Gives Glimpse of Genetic Basis of Adaptive Traits

NEW YORK (GenomeWeb) – A Nantong University-led team of researchers has sequenced the gecko genome, getting a glimpse into its abilities to scale smooth surfaces, adapt to nocturnal living, and shed and regrow its tail.

Xiaosong Gu and his colleagues sequenced the genome of Gekko japonicus, also known as Sclegel's Japanese Gecko, and compared the genome they assembled and annotated to those of other reptiles, as they reported today in Nature Communications. They traced the gecko's evolution of adaptive traits to changes in certain key genes, linking, for instance, an expansion of β-keratin genes to the gecko's clinging ability.

"[The gecko genome] provides valuable insights into the adaptive evolution of geckos as well as the genomic basis of their characteristic traits," the researchers wrote in their paper.

Gu and his colleagues sequenced and assembled the genome of an adult male G. japonicus, generating a 2.55-gigabase genome, some 50 percent larger than the genome of the green anole, Anolis carolinensis. Repeat elements — mostly transposable elements — made up nearly half of the G. japonicus genome, they noted.

The researchers further predicted that the G. japonicus genome contains nearly 22,500 coding regions, most of which could be functionally annotated, and 1,300 non-coding RNAs. From this, they reported that G. japonicus has some 11,500 orthologous gene pairs with An. carolinensis and nearly 13,000 orthologous gene families when compared to An. carolinensis, Alligator sinensis (Chinese alligator), and Chelonia mydas (green sea turtle). Of those, 1,240 were specific to G. japonicus, which led the researchers to speculate that these could be the key to species-specific adaptations.

Geckos have evolved a number of lineage-specific morphologic features, including the adhesive setae on their feet that enable them to cling to smooth surfaces. The emergence of this ability coincides with a duplication and diversion of β-keratin genes, Gu and his colleagues said, noting that the G. japonicus, An. carolinensis, and Al. sinensis genomes contain 71, 23, and two β-keratin genes, respectively.

About half of the 71 G. japonicus β-keratin genes house an S-core box, and most setae-linked β-keratin genes clustered on a single scaffold of its genome assembly, suggesting regional duplication events. An. carolinensis, meanwhile, has 16 setae β-keratin genes and Al. sinensis has none.

A phylogenetic analysis based on these genes indicated that setae β-keratins underwent two expansions: one between 105 million and 96 million years ago and the other between 87 million and 80 million years ago. This expansion period largely jibes with fossil evidence, the researchers noted.

The gecko has also adapted to nocturnal living, with changes to its vision and smell. Most geckos, the researchers noted, have retinas composed of single and double cones, and one theory argues that the cones in nocturnal geckos are derived from those of a diurnal ancestor. Within the G. japonicus genome, the researchers uncovered nine opsin genes, as compared to 20 in the diurnal An. carolinensis genome.

The G. japonicus genome, though, doesn't harbor a complete set of opsin paralogs as the An. carolinensis genome does. Instead, it has three functional genes — SWS1, LWS, and RH2 — that are typically found in cones. When the researchers looked for the additional opsin genes, RH1 and SWS2, they found them as non-functional pseudogenes.

In addition, they noted that RH1 was more diverged between G. japonicus and An. carolinensis than SWS2 was, indicating that RH1 was lost prior to SWS2. This finding, the researchers added, is in line with the theory that the ancestors of modern geckos were diurnal and lacked rod opsins.

The researchers then investigated what functional opsin could be behind the gecko's nocturnal vision. Its RH2 gene, they found, has an amino acid change that could lead it to have a rod pigment-specific biochemical characteristic, allowing the cone to receive more light.

At the same time, geckos developed a sharper sense of smell, which enable them to better survive in a low-light environment. As Gu and his colleagues reported, the G. japonicus genome harbors a significant expansion of olfactory genes, and exhibited greater diversity of α-, β- and γ-OR genes than any other reptile. The 251 OR genes in G. japonicus is some three times greater than those in An. carolinensis.

Another adaptive trait in gecko is its ability to detach its tail and then regrow a new one. Gu and his colleagues sifted through the G. japonicus genome as well as five other reptiles for regions exhibiting positive selection for tail regeneration. G. japonicus, they reported, had 155 PSGs, and a Gene Ontology annotation found that many of these genes were involved in cell proliferation and prostaglandin biosynthesis.

In particular, they noted that prostacyclin synthase (PTGIS) and prostaglandin–endoperoxide synthase 1 (PTGS1) were both under positive selection in G. japonicus and in A. carolinensis. Through a transcriptome study of regenerating stump tissue, the researchers found that the expression of PTGIS and PTGS1 increased three days after tail amputation.

"Although our study cannot be considered as an in-depth analysis at the present stage, it provides a foundation for future mechanistic studies, particularly with regard to regeneration," Gu and his colleagues wrote.