Department of Biotechnology, University of Verona, Verona, 37134, Italy.
BMC Res Notes. 2023 Sep 30;16(1):242. doi: 10.1186/s13104-023-06510-z.
Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). In a recent work, we developed a method to silence IAA9 and AGL6 in tomato ovaries using exogenous dsRNAs. We also produced small RNA libraries from IAA9- and AGL6-silenced ovaries to confirm the presence of siRNAs, derived from exogenous dsRNA, targeting IAA9 and AGL6. The objective of this work is to exploit these sRNA libraries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries.
We identified by RNA sequencing 125 and 104 known and 509 and 516 novel miRNAs from reads mapped to mature or hairpin sequences, respectively. Of the known miRNAs, 7 and 45 were differentially expressed in IAA9- and AGL6-silenced ovaries compared to control ones, respectively. Six miRNAs were common to both datasets, suggesting their importance in the fruit set process. The expression pattern of two of these (miR393 and miR482e-5p) was verified by stem-loop qRT-PCR. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.
授粉后胚珠受精会触发果实的形成，这是由于下调了卵巢生长抑制剂，如番茄转录因子生长素/吲哚-3-乙酸 9（IAA9）和类 AGAMOUS 6（AGL6）。在最近的一项工作中，我们开发了一种使用外源 dsRNA 沉默番茄卵巢中 IAA9 和 AGL6 的方法。我们还从 IAA9 和 AGL6 沉默的卵巢中产生了小 RNA 文库，以确认存在靶向 IAA9 和 AGL6 的 siRNAs，这些 siRNAs 来源于外源 dsRNA。这项工作的目的是利用这些 sRNA 文库来鉴定与未授粉对照卵巢相比，在 IAA9 和 AGL6 沉默的卵巢中差异表达的 miRNAs。
我们通过 RNA 测序，从分别映射到成熟或发夹序列的读取中鉴定出 125 个和 104 个已知以及 509 个和 516 个新的 miRNAs。在已知的 miRNAs 中，7 个和 45 个在 IAA9 和 AGL6 沉默的卵巢中与对照卵巢相比差异表达。这两个数据集有 6 个 miRNAs 是共同的，这表明它们在果实形成过程中的重要性。其中两个（miR393 和 miR482e-5p）的表达模式通过茎环 qRT-PCR 进行了验证。鉴定出的 miRNAs 代表了一组潜在参与番茄果实起始的调节性 sRNAs。
