NEW YORK (GenomeWeb News) – Researchers from the US, Sweden, and UK reported in the early, online edition of Nature today that they have sequenced the draft genome of the North American green anole lizard, Anolis carolinensis.
"People have been sequencing animals from different parts of the vertebrate tree, but lizards had not been previously sampled," senior author Kerstin Lindblad-Toh, a comparative genomics researcher at Uppsala University and scientific director of the Broad Institute's vertebrate genome biology program, said in a statement. "This was an important branch to look at."
The genome is not only providing information about the biology of the green anole lizard itself, but also offering clues about the evolution of closely related lizard species and animals in the broader amniote lineage, which includes other reptiles and mammals. By comparing the new lizard genome to those of birds and mammals, for example, the team found evidence of especially rapid evolution of genes and proteins contributing to amniote egg development.
The lizard, snake, and tuatara-containing lepidosaur clade separated from the other main reptile clade, the archosaurs (crocodilians and birds), an estimated 280 million years ago, the study authors noted. Within the broader amniote lineage, an even older split between reptiles and mammals is thought to have occurred around 320 million years ago.
While numerous bird and mammal genomes have already been sequenced and reported, A. carolinensis is the first non-avian reptile to have its genome sequenced and published. The species is native to the US, researchers explained, and often used as a model organism in reptile studies. With the lizard genome sequence in hand, they added, it's now possible to do genomic comparisons across the amniote lineage.
"The genome of the lizard A. carolinensis … fills an important gap in the coverage of amniotes, splitting the long brain between mammals and birds and allowing more robust evolutionary analysis of amniote genomes," they wrote.
The researchers tackled the 1.78 billion base genome of a female green anole lizard from South Carolina using whole-genome shotgun Sanger sequencing of plasmid and fosmid libraries.
Data from bacterial artificial chromosome clones generated for a male lizard, also from South Carolina, was used to help anchor and assemble the genome sequence, which are housed on six large chromosome pairs and a dozen microchromosomes.
The group's analyses of the lizard genome pointed to an estimated 17,472 protein-coding genes and more than 2,900 RNA genes. The new genome also contains a slew of tandem repeats and transposable elements, the researchers reported, with mobile elements such as LINE and SINE elements making up an estimated 30 percent of the genome sequence.
Comparisons between the lizard genome and the genome of its closest sequenced relative, the chicken, indicate that the green anole genome has undergone relatively few rearrangements, still containing hundreds of syntenic blocks with the chicken genome.
The team also saw synteny between lizard and chicken microchromosomes. But while the chicken version of these microchromosomes typically contain fewer repeats and an abundance of guanine and cytosine nucleotides compared to the rest of the chicken genome, lizard microchromosomes were not especially low in repeats or rich in GC sequences.
Moreover, while GC content often varies across different parts of mammalian and bird genomes, the researchers found that GC representation was fairly uniform from one part of the green anole lizard genome to the next.
The sex chromosome patterns found in the lizard seem to be distinct from that seen in birds, which have ZW sex chromosomes. Instead, data from the male and female lizards tested indicates that the animal has evolved an XY chromosome system more similar to that found in most mammals.
The team's comparisons between the lizard genome and sequences from eight other vertebrate species uncovered many orthologs for green anole genes in other vertebrates. But they also identified some genes that are present in the reptile lineage but missing in mammals. Among them: 11 opsin genes involved in color vision, along with several genes involved in egg laying.
By using a combination of genetic data and mass spectrometry experiments looking at the protein content of anole lizard eggs, the team found evidence that egg proteins have evolved especially rapidly in the amniote lineage, leading to numerous egg-related gene and protein differences between the green anole lizard and the chicken.
In an effort to learn more about anole lizard evolutionary history, local adaptations, and convergent evolution, the researchers also used the A. carolinensis genome to help put together a refined phylogeny for 93 of the estimated 400 or so anole species found around the world.
"Anoles are rich in ecology and morphology and have just the right amount of diversity to make them interesting yet tractable to study," Harvard University evolutionary biologist Jonathan Losos, a co-author on the study, said in a statement. "But a big stumbling block in studying them has been that they have not been great organisms for classical genetic study."
"The genome is going to revolutionize our ability to study that aspect of their evolutionary diversification," Losos added.
Despite the information already gleaned from the new genome, though, those involved in the study emphasized that many more genome sequences are needed to determine how representative A. carolinensis genetics are of other lizard species — and to fill in gaps in the reptile lineage as a whole.
"[T]he tree of sequenced reptilian genomes is still extremely sparse, and the sequencing of additional non-avian reptiles would be necessary to fully understand how typical A. carolinensis and the sequenced bird genomes are of the entire reptile clade," they wrote.