Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molec
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RESEARCH ARTICLE
Open Access
Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration Xiu Feng1 , Yintao Jia1, Ren Zhu1, Kemao Li2, Zhongzhi Guan2 and Yifeng Chen1*
Abstract Background: 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. Results: The 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. Conclusions: Our 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. Keywords: Gymnocypris eckloni, Transcriptome, Skin, Scale degeneration
Background 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) [1–3]. Most scales in teleosts belong to the elasmoid type, which is a highly derived type of scale [1]. Many studies have described the scale formation process at the tissue and cellular level [1, 4–7], but little is known at the molecular level. Only several candidate * Correspondence: [email protected] 1 Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China Full list of author information is available at the end of the article
genes are supposed to contribute the fish scale formation. In zebrafish (Danio rerio), whole-mount in situ hybridization revealed that sonic hedgehog (shh) may be involved in the control of scale morphogenesis and differentiation [1]. In medaka (Oryzias latipes), a mutation at the rs-3 locus encoding ectodysplasin-A receptor (EDAR) leads to almost complete loss of scales, indicating that EDAR is required for scale development [8, 9]. Based on phylogenetic analyse
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