Table_9_Transcriptome Profiling of Transposon-Derived Long Non-coding RNAs Response to Hormone in Strawberry Fruit Development.XLSX

Strawberry is an economically grown horticulture crop required for fruit consumption. The ripening of its fruit is a complex biological process regulated by various hormones. Abscisic acid (ABA) is a critical phytohormone involved in fruit ripening. However, little is known about the long non-coding RNAs (LncRNAs), especially transposon-derived LncRNA (TE-lncRNA), response to hormones during fruit ripening in octoploid strawberry. In the study, the transcriptome data of developing strawberry fruits treated with ABA and its inhibitor Nordihydroguaiaretic acid (NGDA) were analyzed to identify responsive LncRNAs and coding genes. A total of 14,552 LncRNAs were identified, including 8,617 transposon-derived LncRNAs (TE-LncRNAs), 412 LncRNAs (282 TE-LncRNAs), and 382 ABA-sensitive LncRNAs (231 TE-LncRNAs). Additionally, a weighted co-expression network analysis constructed 27 modules containing coding RNAs and LncRNAs. Seven modules, including “MEdarkorange” and “MElightyellow” were significantly correlated with ABA/NDGA treatments, resulting in 247 hub genes, including 21 transcription factors and 22 LncRNAs (15 TE-LncRNAs). Gene ontology enrichment analysis further revealed that ABA/NDGA-responsive modules, including LncRNAs, were associated with various metabolic pathways involved in strawberry fruit development and ripening, including lipid metabolism, organic acid metabolism, and phenylpropanoid metabolism. The current study identifies many high-confidence LncRNAs in strawberry, with a percentage of them being ABA pathway-specific and 22 hub-responsive LncRNAs, providing new insight into strawberry or other Rosaceae crop fruit ripening.草莓是一种用于鲜食果品的经济栽培园艺作物。其果实的成熟是受多种激素调控的复杂生物学过程。脱落酸（Abscisic acid，ABA）是参与果实成熟的关键植物激素。然而，对于八倍体草莓果实成熟过程中响应激素的长链非编码RNA（long non-coding RNAs，LncRNAs），尤其是转座子衍生长链非编码RNA（transposon-derived LncRNA，TE-lncRNA）的相关研究仍较为匮乏。本研究对经脱落酸及其抑制剂去二氢愈创木酸（Nordihydroguaiaretic acid，NGDA）处理的发育中草莓果实的转录组数据进行分析，以鉴定响应相关的长链非编码RNA及编码基因。本研究共鉴定得到14552条长链非编码RNA，其中包括8617条转座子衍生长链非编码RNA（TE-LncRNAs）、412条响应相关长链非编码RNA（其中282条为转座子衍生长链非编码RNA）以及382个脱落酸敏感型长链非编码RNA（其中231条为转座子衍生长链非编码RNA）。此外，通过加权共表达网络分析构建了包含编码RNA与长链非编码RNA的27个共表达模块。其中"MEdarkorange"与"MElightyellow"等7个模块与脱落酸/去二氢愈创木酸处理显著相关，筛选得到247个枢纽基因，包括21个转录因子与22个长链非编码RNA（其中15条为转座子衍生长链非编码RNA）。基因本体富集分析进一步显示，包含长链非编码RNA的脱落酸/去二氢愈创木酸响应模块与草莓果实发育及成熟相关的多种代谢通路密切相关，包括脂质代谢、有机酸代谢及苯丙烷代谢。本研究鉴定得到草莓中大量高可信度长链非编码RNA，其中部分为脱落酸信号通路特异性的长链非编码RNA，同时筛选得到22个枢纽响应型长链非编码RNA，为草莓或其他蔷薇科作物的果实成熟研究提供了新的视角。