Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.
Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.
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RNA-Seq 转录定量揭示了草莓红色和黄色果实中差异表达的基因
DOI：
10.1371/journal.pone.0144356
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Zhang Z
中科院分区：
文献类型：
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作者：
Zhang Y;Li W;Dou Y;Zhang J;Jiang G;Miao L;Han G;Liu Y;Li H;Zhang Z
野草莓（Fragaria vesca，2n = 2x = 14）是一种多年生草本植物，基因组序列较小（240 Mb）。它通常被用作草莓属和蔷薇科的遗传模式植物。草莓果实的果皮颜色是决定其商品价值和观赏价值的重要性状之一。花青素是草莓中最突出的色素，它们为果实带来红色、粉红色、白色和黄色色调。在这项研究中，我们进行了从头组装的林地草莓果实转录组，并比较了黄色（黄色奇迹，YW）和红色（Ruegen，RG）果实的基因表达谱。从头组装得到75，426个unigenes，其中21.3%的长度超过1，000 bp。在高质量的独特序列中，45，387（60.2%）与现有基因模型至少有一个显著匹配。在YW和RG中共有595个基因差异表达，占总unigenes的0.79%。其中，224个基因在YW果实中表达上调，371个基因表达下调。特别是，一些类黄酮生物合成途径的基因，包括C4 H，CHS，CHI，F3 H，DFR和ANS，以及一些转录因子（TF），包括MYB（推定的MYB 86和MYB 39），WDR和MADS，在YW果实中下调，同时减少花青素积累的黄色色素表型，而推定的转录抑制因子MYB 1 R在YW果实中上调。通过定量RT-PCR证实了编码类黄酮生物合成酶和TF的基因的表达水平的改变。我们的研究提供了重要的见解的分子机制，黄色素表型在F。维斯卡
Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca.