reference genome assembly

Assembling and annotating a high-quality reference genome for the Jamaican turquoise anole, Anolis grahami.

Anolis grahami. Photo from wikipedia.

Highly complete and contiguous genome assemblies are necessary to answer many evolutionary questions. While Anolis lizards have been the focus of decades of ecological and evolutionary research, only a few of the 400+ species have high-quality genome assemblies available.

One of the many anoles lacking a genome assembly is Anolis grahami, a widespread species native to Jamaica and introduced to Bermuda. There are currently two recognized subspecies, Anolis grahami grahami and Anolis grahami aquarum (see photos below). A. g. grahami is a beautiful rainbow color and found throughout most of the island, while A. g. aquarum is restricted to certain areas east of the Blue Mountains and is a striking lime green color. A. grahami is also one of the few anole species that vocalize. To learn more about A. grahami and other Jamaican anoles, check out my blog post. This trunk-crown anole has long been the focus of ecological and evolutionary research. Previous research has shown that haplotypes from geographic populations of A. grahami are highly divergent suggesting that this species may be a complex of species (Jackman et al. 2002)1. Blake (1986)2 also showed that there are multiple fission events in this species, as well as extensive chromosomal variation that did not coincide with subspecies borders. With this highly complete and contiguous reference genome, we can begin to dive into some of these interesting observations.

Left: A. g. grahami. Right: A. g. aquarum.

To provide modern genomic resources for the study of this species, we sequenced, assembled, and annotated a high-quality reference genome. We present a highly contiguous (N50 = 137 Mb) and complete (only 11.4% vertebrate BUSCO genes missing) genome. Using this genome, we infer the phylogenomic relationships among squamates, report sex chromosome evolution of A. grahami, and evaluate chromosome synteny of A. grahami with other anole species.


  1. Jackman TD, Irschick DJ, de Quieroz K, Losos JB, Larson A. 2002. Molecular Phylogenetic Perspective on Evolution of Lizards of the Anolis grahami Series. J Exp Zool. 294: 1-16. 

  2. Black JA. 1986. Complex chromosomal variation in natural populations of the Jamaican lizard Anolis grahami. Genetica. 69: 3-17.