Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.
Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.
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DOI：
10.1371/journal.pone.0108200
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Xu P
中科院分区：
文献类型：
--
作者：
Jiang Y;Zhang S;Xu J;Feng J;Mahboob S;Al-Ghanim KA;Sun X;Xu P
鲤鱼是一种重要的水产养殖品种，在世界范围内分布广泛。在漫长的鲤鱼驯化历史中，已经建立了许多不同肤色的鲤鱼品系。皮肤颜色被用作视觉标准来确定鲤鱼的市场价值。然而，鲤鱼肤色的遗传基础尚未得到广泛的研究。在这项研究中，我们进行了Illumina测序两个常见的鲤鱼品系：红色兴国红鲤和棕黑色黄河鲤鱼。共生成435，348，868个读段，产生198，781个组装的重叠群，用作参考序列。皮肤转录组文件的比较显示，在两个普通鲤鱼品系中有2，012个显著差异表达的单一基因，其中兴国红鲤中上调的基因为874个，黄河鲤中上调的基因为1，138个。随机选取20个差异表达基因，采用定量RT-PCR方法验证其表达模式。差异表达基因的基因通路分析表明，黑色素的生物合成，沿着Wnt和MAPK信号通路，很可能影响皮肤色素沉着过程。参与皮肤色素沉着过程的几个关键基因，包括TYRP 1，SILV，ASIP和xCT，在两株之间的表达模式存在显著差异。本研究对兴国红鲤和黄河鲤皮肤进行了比较转录组分析，并对鲤鱼皮肤色素形成过程中的关键基因进行了检测。我们建议，共同鲤鱼皮肤色素沉着取决于至少三个途径。了解鱼的肤色遗传规律，将有助于将来从分子水平上选择具有较高市场价值的鱼的肤色。
The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied. In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains. In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.5
作者：
Hellström AR;Watt B;Fard SS;Tenza D;Mannström P;Narfström K;Ekesten B;Ito S;Wakamatsu K;Larsson J;Ulfendahl M;Kullander K;Raposo G;Kerje S;Hallböök F;Marks MS;Andersson L
通讯作者：
Andersson L
影响因子：
3.4
作者：
Alonso S;Izagirre N;Smith-Zubiaga I;Gardeazabal J;Díaz-Ramón JL;Díaz-Pérez JL;Zelenika D;Boyano MD;Smit N;de la Rúa C
通讯作者：
de la Rúa C
影响因子：
1.6
作者：
Karlsson, Anna-Carin;Kerje, Susanne;Jensen, Per
通讯作者：
Jensen, Per
影响因子：
2.7
作者：
Fujimura, Naoko;Taketo, Makoto M.;Kozmik, Zbynek
通讯作者：
Kozmik, Zbynek