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

- Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration.
- 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.
- Conclusions: Our results would provide insights into the molecular mechanisms of scale degeneration in G.
- The scales in fish species refer to the dermis-derived struc- tures 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 de- rived type of scale [1].
- 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
- The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material.
- If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
- The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data..
- Full list of author information is available at the end of the article.
- With the development and popularization of the next-generation se- quencing technologies (NGS), whole transcriptome sequen- cing or RNA sequencing (RNA-seq) has been widely used for transcriptome analysis at massive scale [13].
- Comparative transcriptome analysis provides a powerful tool for dissect- ing the relationship between genotype and phenotype, in- creasing our understanding of the molecular mechanisms involved in physiological process and environmental adapta- tion [14].
- For example, comparative transcriptome analysis by RNA-seq has identified genes and pathways associated with growth [15], gonad development [16], immune re- sponse [17] and skin color differentiation [18] in fish species..
- Among them, Gymnocypris fishes mainly live in the cold and high altitude area on the QTP, which are nearly esquamate, only covered with 3–4 rows of shoulder scale, and two lines of anal scale [19, 20].
- The degenerated scale and incrassated skin are two characteris- tics of Gymnocypris fishes which related to the adaptation to the extreme environment with cold climate and high- altitude.
- Uncovering the molecular basis that controlling the scale degeneration would provide new insights into how the Gymnocypris fishes adapt to the extreme environment of the QTP.
- Gymnocypris eckloni, a representative species belonging to the genus Gymnocypris, is a native fish species in the upper reaches of the Yellow River with the elevation above 2500 m.
- The aim of this study is de novo assembly of the transcrip- tome and identification of differentially expressed unigenes that may be involved in scale degeneration in G.
- The anal scale had just reached at the early stage of development, the scale papilla had differentiated in the dermis.
- The unigenes were annotated based on the public data- bases.
- Identification of differentially expressed unigenes (DEUs) Based on the criteria of |log 2 FC.
- Based on the global expression profiles, the samples were clustered into three groups corresponding to the three fish individuals (Fig.
- However, based on the expressions of DEUs, the samples were clustered into two groups representing scaleless and scaled skins (Fig.
- For overlapped DEUs, 38, 33 and 19 unigenes were anno- tated to the three databases..
- eckloni using Illumina RNA-seq.
- based on RNA-seq data.
- The results showed that the ex- pressions of the selected DEUs were all validated by qRT-PCR (Fig.
- The positions of the first appearance of scales vary among different fish species.
- In this study, the scales on the shoulder and anal of G.
- The scales appeared first on the shoulder, which was similar to other cyprinid fishes but different.
- The first scale gener- ally appears in the anterior region of the body in cyprinid fishes [5, 28], and in the posterior region of the body in cichlid and catostomid fishes [29, 30].
- Very large number of unigenes (578,046) was obtained from the assembled transcriptome in this study, which is similar to that previously reported in the same species as well as in another congeneric species .
- More DEUs were detected between SSS and NSS (428) than between ASS and NSS (142), in- dicating that more and more genes may be involved in the process of scale development..
- These GO terms have also been reported in other studies with their functions on the development and dif- ferentiation in skin, bone and muscle [33–37].
- One of the most significant up-regulated unigenes, Osteocalcin, is a marker of mature osteoblasts in mammals, which may be an important gene for scale formation [38, 39]..
- Furthermore, the two genes were also both present and expressed in the skin of channel catfish, a scaleless fish [10].
- The scale degeneration in this fish are not caused by the loss of key genes reported previously, and may be related to the expression regulation of genes identified in this study.
- Such regulation mechanism was developed to adapt to the extreme environment of the QTP, and may be mediated by transcriptional or post- transcriptional factors, such as methylation, transcription factors (TF) and microRNAs (miRNAs)..
- A number of differentially expressed unigenes were identified between scaled and scaleless skins.
- Our results would provide insights into the molecular mechanisms of scale degeneration in G.
- DN2099_c0_g1_i Melanotransferrin.
- DN16257_c0_g1_i Tensin.
- DN10934_c0_g1_i Myozenin-2.
- DN3099_c0_g1_i Myosin-16.
- DN6176_c0_g1_i Sodium/hydrogen exchanger 7.
- DN20169_c0_g1_i Ethanolamine-phosphate phospho-lyase.
- DN13779_c0_g1_i Voltage-dependent calcium channel subunit alpha-2/delta-2.
- DN25484_c0_g1_i Integrin alpha-7.
- DN2286_c0_g1_i LIM domain-binding protein 3.
- DN2232_c0_g1_i Elongation factor 2.
- DN45284_c0_g1_i Growth/differentiation factor 8.
- DN5543_c0_g1_i Fibrinogen-like protein 1.
- DN19919_c0_g1_i Sclerostin.
- DN15430_c0_g1_i Homeobox protein Dlx5a.
- DN2890_c0_g1_i Pannexin-3.
- DN4077_c0_g1_i DNA-binding protein SATB2.
- DN8724_c0_g1_i Hormonally up-regulated neu tumor-associated kinase homolog A.
- DN5111_c0_g1_i Collagen alpha-1(V) chain.
- DN13869_c0_g1_i Mucin-5 AC.
- DN10512_c0_g1_i Transient receptor potential cation channel, subfamily M.
- DN8192_c0_g1_i Galectin-4.
- DN142241_c0_g1_i Osteocalcin.
- DN12086_c0_g1_i Sodium/calcium exchanger 1.
- DN8352_c0_g1_i CUB and zona pellucida-like domain-containing protein 1.
- DN34990_c0_g1_i UPF0575 protein C19orf67 homolog.
- RNA extraction, library construction and sequencing Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
- Owing to the absence of a reference genome of G.
- Analysis of differentially expressed unigenes.
- Clean reads of each RNA-seq library were aligned to the assembled reference transcriptome to obtain unique mapped reads by using bowtie2 software [49].
- 6 Validation of the RNA-seq expression profile by real-time reverse transcription quantitative PCR.
- The relative expression levels were nor- malized to the quantification of β-actin using the 2.
- Summary of the sequencing data per sample in this study..
- RNA-seq: RNA sequencing;.
- 2019QZKK0304), the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No.
- 31601844), and the Knowledge Innovation Program of the Chinese Academy of Sciences (Grant No.
- These funding bodies had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript..
- All raw transcriptome data reported in this article have been deposited in the Genome Sequence Archive (GSA.
- Note on development of scale patterns in the northern pike, Esox lucius L.
- Evidence for participation of the epidermis in the deposition of superficial layer of scales in zebrafish (Danio rerio): a SEM and TEM study.
- Adaptive evolution of the Eda gene and scales loss in.
- schizothoracine fishes in response to uplift of the Tibetan plateau.
- RNA-Seq technology and its application in fish transcriptomics.
- RNA-Seq: a revolutionary tool for transcriptomics.
- Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the southern bluefin tuna (Thunnus maccoyii).
- Origin and evolution of schizothoracine fishes in relation to the upheaval of the Xizang Plateau.
- In: The team of the comprehensive scientific expedition to the Qinghai-Xizang Plateau, Chinese Academy of Sciences, editor.
- Studies on the period, amplitude and type of the uplift of the Qinghai-Xizang Plateau.
- Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences.
- Phylogeographic studies of schizothoracine fishes on the Central Qinghai-Tibet plateau reveal the highest known glacial microrefugia.
- Strong evidence for changing fish reproductive phenology under climate warming on the Tibetan plateau.
- Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan plateau using single-molecule long-read sequencing and RNA-seq.
- The scale formation process and its relation to the growth of five species of fish.
- Structure and development of the ctenial spines on the scales of a teleost fish, the cichlid Cichlasoma nigrofasciatum.
- Early development and pattern of scale formation in the spotted sucker, Minytrema melanops (Catostomidae).
- comparative study of the karyotypes of 8 species of schizothoracine fishes.
- hydroxyprolyl-glycine, ameliorate skin barrier dysfunction and alter gene expression profiles in the skin.
- Gene expression profiling of trout regenerating muscle reveals common transcriptional signatures with hyperplastic growth zones of the post-embryonic myotome.
- Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection..
- dedifferentiation of osteoblasts in the zebrafish fin.
- Integrated analysis of mRNA and miRNA expression profiles in Ptychobarbus dipogon and Schizothorax oconnori, insight into genetic mechanisms of high altitude adaptation in the schizothoracine fishes

Xem thử không khả dụng, vui lòng xem tại trang nguồn
hoặc xem Tóm tắt