Comparative transcriptome analysis of trout skin pigment cells

Abstract

Background Enormous variability in skin colour and patterning is a characteristic of teleost fish, including Salmonidae fishes, which present themselves as a suitable model for studying mechanisms of pigment patterning. In order to screen for candidate genes potentially involved in the specific skin pigment pattern in marble trout (labyrinthine skin pattern) and brown trout (spotted skin pattern), we conducted comparative transcriptome analysis between differently pigmented dermis sections of the adult skin of the two species. Results Differentially expressed genes (DEGs) possibly associated with skin pigment pattern were identified. The expression profile of 27 DEGs was further tested with quantitative real-time PCR on a larger number of samples. Expression of a subset of ten of these genes was analysed in hybrid (marble x brown) trout individuals and compared with the complexity of their skin pigment pattern. A correlation between the phenotype and the expression profile assessed for hybrid individuals was detected for four ( gja5 , clcn2 , cdkn1a and tjp1 ) of the ten candidate genes tested. The potential role of these genes in skin pigment pattern maintenance is discussed. Conclusions Our results indicate that the maintenance of different pigment patterns in trout is dependent upon specific communication—involving gap junctions, tight junctions and ion channels—between chromatophores present in differentially pigmented skin regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5714-1) contains supplementary material, which is available to authorized users.

Spotting genome-wide pigmentation variation in a brown trout admixture context

“…This information allowed for the detection of CPLs associated to candidate genes formerly identified in former pigmentation studies. These CPLs complement gene expression studies by Sivka et al (2013) and Djurdjevič et al (2019) and improve knowledge on the genomic basis of pigmentation in the brown trout. While pigmentation patterns are important to evaluate the impact of hatchery individuals into wild trout populations (Mezzera et al, 1997; Aparicio et al, 2005), we showed that it is premature to rely on phenotypic colour patterns as a proxy of genome-wide admixture to promote management decisions.…”

“…The RAD-locus detected by both RDA and single-trait GWAS for black spotting is located ∼21kb downstream of GJD2 (Gap-junction protein Δ2 gene; located on LG9 of S. trutta ; Table S4). This gene was found differentially expressed in trout skin (marble vs fario/Atlantic morph) by Djurdjevič et al (2019).…”

“…O’Connor, Metcalfe, & Taylor, 2000; Wedekind, Jacob, Evanno, Nusslé, & Müller, 2008; Marie-Orléach et al, 2014; Watt, Swanson, Miller, Chen, & May, 2017, Parolini, Iacobuzio, Bassano, Penatti, & Saino, 2018; Auld, Noakes, & Banks, 2019). However, if the physiological basis of colour changes are known (Leclercq, Taylor, & Migaud, 2010), the genomic basis of their pigmentation patterns remains largely unexplored, with only limited insights coming from quantitative trait loci (QTL) (Boulding et al, 2008) or few gene expression studies (Sivka, Snoj, Palandačic, & Sušnik Bajec, 2013; Djurdjevič, Furmanek, Miyazawa, & Sušnik Bajec, 2019). Furthermore, as pigmentation patterns may reflect admixture in salmonids (e.g.…”

Comprehensive RNA-seq Analysis to Evaluate the Pigmentation-Related Genes Involved in Albinism of Cichlid Fish, Aulonocara baenschi

“…In the color pattern variability of skin pigment of the trout, the expression of MITF decreased to a greater extent in the light region than in the black spot, which is a similar pattern MITFA showed in the A. baenschi. However, MITFB showed a different expression pattern in the same species (Djurdjevič et al, 2019). MITF found in the chicken did not show any significant differential expression patterns between the white type and the black type (Zhang J. et al, 2015).…”

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses

“…In order to further analyze the DEGs of two distinct color morphs of C. argus, we screened the number of DEGs using the AT1-3 as a control group. In previous studies, a large number of DEGs were found in black and light skin of freshwater sticklebacks (Greenwood et al, 2012); and a total of 244 DEGs (177 up-and 67 down-regulated) were found in normal and albino Triplophysa rosa (Xiao, 2017); and over 3000 DEGs were obtained in three phenotypic Pristella maxillaris (Bian, 2019), and 18,087, 61,751, and 87,737 DEGs between marble and brown trout were grouped by using GO analysis (Djurdjevič et al, 2019). In this study, a total of 1024 DEGs were found, including 559 up-and 465 down-regulated.…”