Insights into the adaptive evolution of chromosome and essential traits through chromosome-level genome assembly of Gekko japonicus

Abstract

Gekko japonicus possesses flexible climbing and detoxification abilities under insectivorous habits. Still, the evolutionary mechanisms behind these traits remain unclarified. This study presents a chromosome-level G. japonicus genome, revealing that its evolutionary breakpoint regions were enriched with specific repetitive elements and defense response genes. Gene families unique to G. japonicus and positively selected genes are mainly enriched in immune, sensory, and nervous pathways. Expansion of bitter taste receptor type 2 primarily in insectivorous species could be associated with toxin clearance. Detox cytochrome P450 in G. japonicus has undergone more birth and death processes than biosynthesis-type P450 genes. Proline, cysteine, glycine, and serine in corneous beta proteins of G. japonicus might influence flexibility and setae adhesiveness. Certain thermosensitive transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus might enhance adaptation to climate change. This genome assembly offers insights into the adaptive evolution of gekkotans.

Keywords: Evolutionary biology; Phylogenetics; Zoology.

Graphical abstract

Figure 1

Circos plot of the Gekko japonicus genome The outermost circle indicates the 19 chromosome information, with a tick unit of 10 Mb. Linkages between or within chromosomes show the synteny of paralogous genes. The circles labeled with a, b, and c correspond to GC content, gene density, and repeat coverage, respectively, with darker colors representing higher corresponding features.

Figure 2

Synteny analysis of G. japonicus and two other sauropsids "Gj", "Ac", and "Gg" are abbreviations of G. japonicus, A. carolinensis, and G. gallus, respectively. The numbers following them to the right correspond to the respective chromosome numbers. The circle indicates chromosome information with a tick unit of 10 Mb. (A) Circos plot based on the results of synteny analysis between G. japonicus and A. carolinensis. The chromosomes of G. japonicus are marked in non-black and those of A. carolinensis in black, and the lines represent the synteny between the corresponding chromosomes. (B) Circos plot based on the results of the synteny analysis between G. japonicus and G. gallus. The chromosomes of G. japonicus are marked in non-black, and those of G. gallus are marked in black. The lines represent the synteny between the corresponding chromosomes.

Figure 3

Phylogenetic and gene family analysis of 18 sauropsids and outgroups "G. japonicus" and "G. japonicusResearch" correspond to the previous version and the genome assembly of this study, respectively. (A) Phylogenetic tree for 18 sauropsids and outgroups. The bootstrap value for all branches was 100. The numbers on each node and parentheses represent the estimated divergence time (million years ago, MYA) and the 95% confidence interval. Pie charts represent the proportion of gene family expansions and contractions, with purple corresponding to expansions, orange to contractions, and colored numbers corresponding to each of them. The genes of each species are divided into five categories, the colors of which correspond to those in the legend on the right and are shown in the bar chart. At the same time, the white numbers inside represent the number of genes in the corresponding category, and "n" represents the total number. (B) Venn diagram of the shared and unique gene families among the six sauropsids. Text and numbers represent the corresponding species and the number of gene families, respectively.

Figure 4

Phylogenetic and selection pressure analysis of the T2R gene in sauropsids (A) Phylogenetic tree of T2R genes in seven sauropsids. The scale bar for the branch length of the tree and the corresponding color of the species are labeled in the legend, and the number to the right of the species name represents the number of T2Rs. The bootstrap values not equal to 100 are labeled by numbers at each node. Branches marked with "P" represent branches tested as under positive selection using the aBSREL model. (B) Venn diagram of standard and unique positively selected sites in the T2R gene of seven sauropsids identified by four methods. Text and numbers represent the corresponding method and the number of positively selected sites. (C) Bar graph of the number of positively selected sites in different regions of the T2R gene in seven sauropsids. The X axis corresponds to the different areas of the T2R gene, and the Y axis represents the number of positively selected sites in the corresponding regions.

Figure 5

Location and selection pressure analysis of the T2R gene in G. japonicus (A) All 51 T2R genes were clustered on chromosome 6 of G. japonicus. Red triangles represent T2R genes, gray triangles represent other genes, and the obtuse angle direction to the right means the forward strand, and to the left means the reverse strand. (B) The subtree of the T2R gene in G. japonicus. The branch length scale bar is marked in the upper right corner, and branches marked with "P" represent branches detected as under positive selection using the aBSREL model. (C) Venn diagram of standard and unique positively selected sites in G. japonicus T2R genes identified by four methods. Text and numbers represent the corresponding method and the number of positively selected sites. (D) Bar chart of the number of positively selected sites in different regions of the G. japonicus T2R genes. The X axis corresponds to the different regions of the T2R genes, and the Y axis represents the number of positively selected sites in the corresponding regions.

Figure 6

MIPhy analysis and phylogeny of the P450 of sauropsids The numbers correspond to clan, gene family, and specific gene name from the outside to the inside of the circle. The width of each black circle arc fits the size of the MIphy score. The color of the endpoints in the tree corresponds to the species, as shown in the legend in the upper left corner, and the numbers in the legend indicate the size of the number of genes in the corresponding species.

Figure 7

Phylogenetic tree of CBP gene families in 20 species The red background indicates geckos, the orange background indicates lizards, the yellow background indicates snakes, the green background indicates turtles and crocodiles, and the blue background shows crocodiles. The CBP sequences of G. japonicus are shown in red font.

Figure 8

Phylogenetic tree of the TRP gene family and the ω values of each gene (A) Phylogenetic tree of TRP genes in 16 sauropsids, two mammals, and one amphibian. The outer circle is divided by different TRP subfamilies and their submembers, with the same subfamilies labeled with the same color and the submembers labeled with text. Different colored branches correspond to different species, as shown in the legend on the right. (B) Bar graph of ω values of different TRP genes. The X axis represents the ω value and the Y axis represents the corresponding gene. ω values identified with M0 and YN00 are labeled with different colors, as shown in the legend on the right.