Draft genome of six Cuban Anolis lizards and insights into genetic changes during their diversification

Abstract

Background: Detecting genomic variants and their accumulation processes during species diversification and adaptive radiation is important for understanding the molecular and genetic basis of evolution. Anolis lizards in the West Indies are good models for studying evolutionary mechanisms because of the repeated evolution of their morphology and the ecology. We performed de novo genome assembly of six Cuban Anolis lizards with different ecomorphs and thermal habitats (Anolis isolepis, Anolis allisoni, Anolis porcatus, Anolis allogus, Anolis homolechis, and Anolis sagrei). We carried out a comparative analysis of these genome assemblies to investigate the genetic changes that occurred during their diversification.

Results: We reconstructed novel draft genomes with relatively long scaffolds and high gene completeness, with the scaffold N50 ranging from 5.56 to 39.79 Mb and vertebrate Benchmarking Universal Single-Copy Orthologs completeness ranging from 77.5% to 86.9%. Comparing the repeat element compositions and landscapes revealed differences in the accumulation process between Cuban trunk-crown and trunk-ground species and separate expansions of several families of LINE in each Cuban trunk-ground species. Duplicated gene analysis suggested that the proportional differences in duplicated gene numbers among Cuban Anolis lizards may be associated with differences in their habitat ranges. Additionally, Pairwise Sequentially Markovian Coalescent analysis suggested that the effective population sizes of each species may have been affected by Cuba's geohistory.

Conclusions: We provide draft genomes of six Cuban Anolis lizards and detected species and lineage-specific transposon accumulation and gene copy number changes that may be involved in adaptive evolution. The change processes in the past effective population size was also estimated, and the factors involved were inferred. These results provide new insights into the genetic basis of Anolis lizard diversification and are expected to serve as a stepping stone for the further elucidation of their diversification mechanisms.

Keywords: Anole; Comparative genomics; Effective population size; Gene duplication; Repeat elements.

Fig. 1

Phylogenetic relationships between the Anolis lizards included in this study and descriptive statistics of their genome assemblies

Fig. 2

The distribution of GC content in 5-kb windows of genome assemblies for Anolis lizards. The green lines and points indicate the distributions of A. isolepis, A. allisoni, and A. porcatus from the Cuban trunk-crown lineage, and their relative, A. carolinensis; yellow lines and points indicate the distribution for A. allogus, A. homolechis, and A. sagrei from the Cuban trunk-ground lineage; navy blue, light blue, and gray lines and points indicate the distributions of A. frenatus, A. auratus, and A. apletophallus, respectively

Fig. 3

Repeat content and landscape of Anolis genomes. A Phylogenetic relationships between Anolis lizards included in the repeat element analysis and the sequence percentages of each transposable element (TE) class. B Repeat landscape for each TE class of Anolis lizards included in the repeat element analysis. The arrow points to a steep peak for LTR observed only in A. carolinensis

Fig. 4

Phylogenetic relationships, the expansion or contraction in the number of genes in each branch, and the proportion of duplicated genes for the six Cuban Anolis lizards. The numbers above each branch of the phylogenetic tree represent the increase or decrease in the number of genes estimated in orthogroups, which includes genes from all species used in the analysis

Fig. 5

Past effective population sizes of the six Cuban Anolis lizards. Top: the Earth’s surface temperature [36]; six lower panels: the estimated past effective population sizes of six Cuban Anolis lizards estimated using the Pairwise Sequentially Markovian Coalescent (PSMC) model. The generation time was set as one year for all six species. The mutation rates for A. isolepis, A. allisoni, A. porcatus, A. allogus, A. homolechis, and A. sagrei were set as 1.4 × 10⁻⁹, 1.5 × 10⁻⁹, 1.8 × 10⁻⁹, 1.6 × 10⁻⁹, 2.0 × 10⁻⁹, and 2.1 × 10⁻⁹, respectively