Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration

Xiu Feng,Zhongzhi Guan,Kemao Li,Ren Zhu,Yifeng Chen,Yintao Jia

doi:10.1186/s12864-020-07247-w

Abstract

BackgroundThe scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration.ResultsThe transcriptomes of shoulder scaled skins (SSS), anal scaled skins (ASS) and scaleless skins (NSS) were sequenced and analyzed in G. eckloni at the age of 1 year. Histological examination showed that shoulder scale had completed its differentiation and anal scale just initiated the differentiation. A total of 578,046 unigenes were obtained from the transcriptomes, with 407,799 unigenes annotated in public databases. A total of 428 and 142 differentially expressed unigenes (DEUs) were identified between SSS and NSS, and between ASS and NSS, respectively, with 45 DEUs that were overlapped. Annotation analysis indicated that these DEUs were mainly enriched in Gene Ontology (GO) terms and KEGG pathways associated with bone and muscle formation, such as myofibril, contractile fiber, cytoskeletal protein binding, muscle structure development, cardiac muscle contraction, hypertrophic cardiomyopathy (HCM) and calcium signaling pathway.ConclusionsOur results would provide insights into the molecular mechanisms of scale degeneration in G. eckloni and other congeneric fishes. In addition, the transcriptome data provides candidate genes and markers for future studies.

Highlights

The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes
Histological examination showed that the shoulder scale had completed its differentiation, and its posterior region had protruded into the epidermis which formed a fold
The anal scale had just reached at the early stage of development, the scale papilla had differentiated in the dermis

Summary

Introduction

The scale degeneration is thought to be related to the adaptation to the extreme environment with cold climate and high-altitude in schizothoracine fishes. Gymnocypris eckloni, a schizothoracine fish living in plateau waters with the elevation above 2500 m, is nearly esquamate and only covered with shoulder scales and anal scales, making it a good model species to study the molecular mechanism of scale degeneration. The scales in fish species refer to the dermis-derived structures located within the skin, and are classified into placoid, ganoid and elasmoid (cycloid and ctenoid) [1,2,3]. Comparative transcriptome analysis provides a powerful tool for dissecting the relationship between genotype and phenotype, increasing our understanding of the molecular mechanisms involved in physiological process and environmental adaptation [14]. Comparative transcriptome analysis by RNA-seq has identified genes and pathways associated with growth [15], gonad development [16], immune response [17] and skin color differentiation [18] in fish species

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