# Comparison of Transcriptome Differences in Scales of Two Closely Related Snake Species (Lycodon rufozonatus and Lycodon rosozonatus)

## TL;DR

This study compares the transcriptomes of two closely related snake species to understand the genetic basis of their scale color differences.

## Contribution

The study identifies specific genes and expression differences linked to scale color variation in two snake species.

## Key findings

- Two genes, mreg and notch1, were significantly downregulated in Lycodon rosozonatus.
- RNA sequencing revealed 350 million and 331 million clean reads from the two snake species.
- PCA and t-SNE analyses showed notable differences in scale color variation between the species.

## Abstract

The pigmentation of animal bodies can be influenced by various factors, including temperature, light, habitat characteristics, and the visual systems and behavioral patterns of prey and predators. The development of diverse body colors in animals has been attributed to long-term selection pressures. To explore the cellular mechanisms underlying color differences between species, two closely related snake species (Lycodon rufozonatus and Lycodon rosozonatus) were selected for study. We used transcriptome RNA sequencing to analyze the differences in the scale color in different parts of these two snakes and identified two different types of genes responsible for the color change. The results demonstrated that the mutation sites of common color genes in the two species exhibited discrepancies at various sites within seven genes. Notably, two genes, mreg and notch1, were substantially downregulated in L. rosozonatus. The current study suggests that color adaptation in reptiles is influenced not only by visible changes in skin pigmentation but also by underlying biological processes.

The diversity of skin colors observed in reptiles is indicative of their adaptation to different ecological niches, with these color variations playing essential roles in survival and reproduction. The present study focused on two closely related species (Lycodon rufozonatus and Lycodon rosozonatus) within the Lycodon genus that exhibit the closest color and morphological similarities. We performed RNA sequencing on the scales of both species and obtained 350,346,591 and 331,537,523 clean reads, respectively. A comparative analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases revealed that the scales of the two species exhibited similar patterns of gene enrichment. Nevertheless, the results of the PCA and the t-SNE analysis demonstrated notable differences between the scales in the diverse color variations observed in the two species. Concurrently, we conducted a comparative analysis of the skin color-related genes and the differentially expressed genes, which revealed three genes exhibiting notable disparities: RU_DN1145_c3_g2 (mreg), RU_DN10511_c0_g1 (notch1), and Unigene11172 (notch1). In light of the aforementioned results, we hypothesize that the discrepancy in the scale color between the two species is attributable to alterations in specific gene loci and variations in expression levels. The data presented herein provide a molecular basis for future studies on the genetic and habitat adaptation functions of scale color differences in reptiles.