Nature, August 31, 2011
First lizard genome sequenced
From the Broad Institute, Aug. 31, 2011
Leaping Lizards! Researchers sequence first lizard genome
By Geoff Spencer
Associate Communications Director for Extramural Research
If Little Orphan Annie had a DNA sequencing machine at Daddy Warbucks' mansion, she would probably start by sequencing the genome of a lizard to see why it leaped. And, she might be interested to discover that some elements of the lizard genome are active, mobile and, yes, still leaping.
That's what researchers have discovered from analyzing the genome of the first lizard, the North American green anole. The results are published in the August 31 advance online publication of the journal Nature. The work was led by researchers at the Broad Institute of Harvard and MIT, which is supported in part by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).
"NHGRI-supported researchers have sequenced and analyzed more than two dozen animals, from platypus to primates, to reveal the fundamental processes that have contributed to the evolution of mammalian genomes, including our own," said Adam Felsenfeld, Ph.D., program director of NHGRI's Large-Scale Genome Sequencing Program. "Comparisons between the genomes of different animals like the green anole lizard reveal conserved features, which in turn illuminate what portions of the genomes are likely to be functional."
The North American green anole lizard (Anolis carolinensis), is a native of the Southeastern United States. It is the first non-bird species of reptile to have its genome sequenced and assembled. Like mammals, lizards and birds are amniotes, which lay eggs that are protected by membranes. The green anole was selected because it may offer insights into how the genomes of humans, mammals, and their reptilian counterparts have evolved since mammals and reptiles parted ways 320 million years ago.
Researchers found that around 30 percent of the green anole genome is comprised of mobile elements, which are drivers of genome evolution. Such elements have a restless lifestyle often shuttling themselves from one chromosome to another and contributing to genomic innovations in the process. In humans, many of these so called "jumping genes" have lost their jumping ability, but they are still actively leaping in anole lizards.
"Anoles have a living library of transposable elements," said Jessica Alfödi, co-first author of the paper and a research scientist in the vertebrate genome biology group at the Broad Institute in Cambridge, Mass. "In anoles, these transposons are still hopping around, but evolution has used them for its own purposes, turning them into something functional in humans."
The researchers aligned these mobile elements to the human genome, and found that close to 100 mobile elements in the human genome are derived from these mobile elements in mammals and are conserved, meaning that they probably have some important function. Most of them reside in portions of the human genome that do not code for proteins, and could have a function in regulating genes. One of the elements that is mobile in lizards, and was in the common ancestor of humans and lizards, is now being used as an important part of a gene for formation of certain embryonic tissues in humans.
The green anole genome contains approximately 17,500 protein-coding genes. Of those genes, 4,000 are also found in human, mouse, dog, opossum, platypus, chicken, zebra finch and pufferfish.
The researchers found many genes in the anole's genome associated with color vision, which the lizards rely on to identify choice mates (males and females of some species display vividly colored flaps of skin beneath their necks called dewlaps). The analysis shows that 11 of these genes, while present in fish, frogs, and even invertebrates, have been lost during mammalian evolution.
The researchers were also able to create a parts list of proteins found in green anole eggs. They compared the green anole proteins to those found in eggs from chickens. The researchers found that egg proteins evolve more rapidly than non-egg proteins.
The team then looked at the anole genome microchromosomes - tiny chromosomes sometimes found in the genomes of reptiles (including birds), amphibians, and fish but never in mammals. The green anole genome contains 12 microchromosomes compared to the chicken genome, which has 28 pairs. The researchers suggest that the microchromosomes shared between the green anole and chicken may have arisen in a reptilian ancestor, while the remaining chicken microchromosomes may be derived from the evolution of birds.
Additionally, the team finally identified the sex chromosomes of the lizard - something that researchers had only been able to hypothesize about before. Like mammals, green anoles appear to have XX and XY chromosomes (unlike birds, in which males have two identical sex chromosomes called ZZ and females have two different ones known as ZW). The lizard's X chromosome turned out to be one of its many microchromosomes.
The researchers also observed that relatively few large chromosome rearrangements have occurred over the 280 million years since anole and chicken diverged. In contrast, the researchers found that more chromosome rearrangements have occurred during the 148 million years that separate the opossum and human genomes.
In addition to insights into human and mammalian genomes, the anole lizard's genome also offers up clues about how lizard species evolved to populate islands in the Greater Antilles. The researchers were able to make a preliminary map of how more than 90 lizard species evolved to colonize the islands.
Much like Darwin's finches, anoles adapted to fill all of the ecological niches the islands have to offer. Some lizards have short legs and can walk along narrow twigs; others are green in color with big toe pads suited for living high up in trees; others are yellow and brown and live in the grass. But unlike the finches, lizards on different islands have independently evolved diverse communities of these twig, canopy, and grass-dwelling species — almost identical lizard species have evolved in parallel on the islands of Hispaniola, Puerto Rico, Cuba and Jamaica.
To learn more about NHGRI's Large-Scale Genome Sequencing Program, please visit The NHGRI Genome Sequencing Program (GSP). A complete list of NHGRI's approved sequencing targets is available at Approved Sequencing Targets.
Last Reviewed: November 14, 2012