Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.

Yuchao Zhang,Junxiang Zhang,He Li,Weijia Li,Guihua Jiang,Lixiang Miao,Yuexue Liu,Zhihong Zhang,Yujuan Dou,Guofen Han,Changjie Xu

doi:10.1371/journal.pone.0144356

Yuchao Zhang, Junxiang Zhang + Show 9 more

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https://doi.org/10.1371/journal.pone.0144356

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Abstract

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.

Highlights

IntroductionCommonly called woodland strawberry, is emerging as an advantageous alternative system for the cultivated octoploids as well as the Rosaceae family due to its small
Fragaria vesca, commonly called woodland strawberry, is emerging as an advantageous alternative system for the cultivated octoploids as well as the Rosaceae family due to its smallPLOS ONE | DOI:10.1371/journal.pone.0144356 December 4, 2015RNA-Seq of Red and Yellow Woodland Strawberry genome size (240 Mb), diploidy (2n = 2x = 14), small herbaceous stature, ease of propagation, short reproductive cycle, and facile transformation [1]
No significant variation in the amounts of anthocyanins in Yellow Wonder (YW) fruit was observed during fruit ripening progress (Fig 1)

Summary

Introduction

Commonly called woodland strawberry, is emerging as an advantageous alternative system for the cultivated octoploids as well as the Rosaceae family due to its small. RNA-Seq of Red and Yellow Woodland Strawberry genome size (240 Mb), diploidy (2n = 2x = 14), small herbaceous stature, ease of propagation, short reproductive cycle, and facile transformation [1]. Woodland strawberry fruits are strongly flavored and have a wide variety of colors, such as red, yellow, white, and pink. Ruegen (RG) and Yellow Wonder (YW) are two botanical forms of F. vesca, both of which produce small-sized plants and propagate without runners. The availability of the F. vesca genomics resource affords opportunities to conduct comparative gene studies within the Rosaceae and identify important genes involved in flavonoid biosynthesis in strawberry [1]

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