Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria x ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway
Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria x ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway
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DOI：
10.1093/pcp/pcy098
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发表时间：
2018-09-01
影响因子：
4.9
通讯作者：
Tang, Haoru
中科院分区：
文献类型：
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作者：
Lin, Yuanxiu;Jiang, Leiyu;Tang, Haoru
花青素是植物中的水溶性色素。它们为人类带来了经济和健康的利润。为了更深入地了解花色苷生物合成的调节在四倍体草莓（草莓x ananassa; Fa），广泛消费的经济上重要的水果，我们进行了比较转录组学分析的红色和白色果肉草莓品种在两个成熟阶段。总共有365，455个非冗余转录物从RNA测序（RNAseq）数据组装。在这些集合中，377个被注释为推定的花青素相关转录本。差异表达分析显示，57花青素的生物合成转录本下调，89转录因子（TF）的下调或上调花青素缺乏。此外，在这里鉴定的50，601个推定的长非编码RNA（lncRNA）中，68个lncRNA差异表达并与差异表达的花青素苷相关mRNA共表达;产生了2，070个共表达lncRNA-mRNA对。表达谱分析表明，两个草莓品种中类黄酮3 '-羟化酶（FaF 3' H）的有限表达抑制了花青素3-葡萄糖苷的积累。这进一步得到了FaMYB 10瞬时过表达实验的支持。下调的lncRNA可能通过作为microRNA（miRNAs）的靶标参与花青素的调控。白肉草莓中miRNA和lncRNA对同一mRNA靶点的竞争强度可能较低，从而解除了红肉草莓中miRNA和lncRNA的抑制作用。该研究首次展示了草莓中与花色苷相关的lncRNA，为花色苷调节网络提供了新的见解，也为鉴定草莓中新的花色苷调节剂奠定了基础。
Anthocyanins are water-soluble pigments in plants. They confer both economic and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanin biosynthesis in octoploid strawberry (Fragaria x ananassa; Fa), a widely consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanin-related transcripts. Differential expression analysis revealed that 57 anthocyanin biosynthesis transcripts were down-regulated, and 89 transcription factors (TFs) were either down- or upregulated under anthocyanin deficiency. Additionally, amongst the 50,601 putative long non-coding RNAs (lncRNAs) identified here, 68 lncRNAs were differentially expressed and co-expressed with differentially expressed anthocyanin-related mRNAs; 2,070 co-expressing lncRNA-mRNA pairs were generated. Expression profile analysis revealed that it was the limited expression of FaF3'H (flavonoid 3'-hydroxylase) that blocked the cyanidin 3-glucoside accumulation in the two investigated strawberry cultivars. This was further supported by a transient overexpression experiment with FaMYB10. The down-regulated lncRNAs might participate in anthocyanin regulation by acting as targets for microRNAs (miRNAs). The level of competitive intensity in miRNA and lncRNA for the same mRNA targets was probably lower in the white-fleshed strawberries, which can release the repression effect of the mRNAs in red-fleshed strawberry as a result. This study for the first time presents lncRNAs related to anthocyanins in strawberries, provides new insights into the anthocyanin regulatory network and also lays the foundation for identifying new anthocyanin regulators in strawberry.