Author: Renata Pirani

We recently published a chromosome-scale assembly of the slender anole (Anolis apletophallus) genome, a species that has been studied for decades at the Smithsonian Tropical Research Institute in Panama.

Here is the abstract: The slender anole, Anolis apletophallus, is a small arboreal lizard of the rainforest understory of central and eastern Panama. This species has been the subject of numerous ecological and evolutionary studies over the past 60 years as a result of attributes that make it especially amenable to field and laboratory science. Slender anoles are highly abundant, short-lived (nearly 100% annual turnover), easy to manipulate in both the lab and field, and are ubiquitous in the forests surrounding the Smithsonian Tropical Research Institute in Panama, where researchers have access to high-quality laboratory facilities. Here, we present a high-quality genome for the slender anole, which is an important new resource for studying this model species. We assembled and annotated the slender anole genome by combining three technologies; Oxford Nanopore, 10X Genomics linked-reads, and Dovetail Omni-C. We compared this genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. Our genome is the first assembled for an Anolis lizard from mainland Central or South America, the regions that host the majority of diversity in the genus. This new reference genome is one of the most complete genomes of any anole assembled to date and should facilitate deeper studies of slender anole evolution, as well as broader scale comparative genomic studies of both mainland and island species. In turn, such studies will further our understanding of the well-known adaptive radiation of Anolis lizards.

And here is a slightly longer summary of what we did (and some results): We used a hybrid genome assembly by combining three technologies: Oxford Nanopore, 10X Genomics linked-reads, and Dovetail Omni-C. We annotated our slender anole genome using the Dovetail Genomics annotation pipeline and compared our genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. We also estimated the repeat elements composition and repetitive landscape using the RepeatModeler and RepeatMasker pipelines.

After several rounds of improvement, our final genome assembly for the slender anole was ~2.4 Gbp in size with with a scaffold N50 of 154.6 Kbp and a GC content of 43.8%. The slender anole genome was thus substantially larger than both the green anole (1.89 Gbp) and brown anole (1.93 Gbp) genomes. Our annotation using the Dovetail pipeline identified a total of 46,763,836 bp coding regions and a total of 33,912 gene models. The number of gene models identified for the slender anole was higher than that of both the green anole (22,292) and brown anole (20,033).

Authors: Renata M. Pirani^1,2*†, Carlos F. Arias^2,3, Kristin Charles¹, Albert K. Chung^2,4, John David Curlis^2,5, Daniel J. Nicholson^2,6, Marta Vargas², Christian L. Cox^2,7, W. Owen McMillan², Michael L. Logan^1,2

Affiliation:

(1) Department of Biology and program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Reno, 89557, United States

(2) Smithsonian Tropical Research Institute, Panama City, Panama

(3) Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, 20013, United States

(4) Department of Ecology and Evolutionary Biology, Princeton University, Princeton, 08544-2016, United States

(5) Department of Ecology and Evolution, University of Michigan, Ann Arbor, 48109-1085, United States

(6) University of Texas, Arlington, Arlington, 76019, United States

(7) Florida International University, Miami, 33199, United States

*Corresponding author: renatampirani@gmail.com

† Present address: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 90095, USAFigure 1 Figure_2

This year at SICB, I had the great opportunity to talk about part of my work as a postdoctoral researcher in the lab of Dr. Michael Logan at the University of Nevada, Reno. In collaboration with John David Curlis (University of Michigan), Christian Cox (Florida International University), W. Owen McMillan (Smithsonian Tropical Research Institute), and Carlos Arias (STRI), we have been studying the Panamanian slender anole Anolis apletophallus, which has a dewlap polymorphism: males either have a solid orange dewlap (solid morph) or a white dewlap with an orange spot (bicolor morph). Preliminary results from John David Curlis’ PhD dissertation research suggests that, in our mainland study population, the frequencies of these morphs change in conjunction with understory light levels—the solid morph is more frequently observed in brighter areas where more light reaches the understory, whereas  the opposite is true for the bicolor dewlap, which is more frequently observed in darker areas of the forest. Thus, it seems possible that selection is maintaining this polymorphism following the predictions of the sensory drive hypothesis, which states that sexual signals should have characteristics that make them the most transmissible given the physical characteristics of the local habitat.

As part of an effort to understand how this trait is evolving in the wild, I set out to understand the genetic basis of this dewlap polymorphism. To do this, my collaborators and I first assembled the full slender anole genome which we then used as a reference for a pooled population sequencing (Pool-Seq) approach using half individuals with solid dewlaps and half individuals with bicolor dewlaps to identify the genomic region underlying this dewlap polymorphism.

Our genome assembly showed pretty good results (Scaffold N50 154,613,287). The Pool-Seq results presented a clear peak of differentiation between solid and bicolor morph groups that corresponded to a region on Scaffold 3. We have a promising candidate gene within this region that may underly the dewlap polymorphism, but will continue to explore these data further to understand the genetic basis of this charismatic trait.