Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China.
BMC Genomics. 2022 Sep 8;23(1):638. doi: 10.1186/s12864-022-08864-3.
The strawberry fleshy fruit is actually enlarged receptacle tissue, and the successful development of the embryo and endosperm is essential for receptacle fruit set. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play indispensable regulatory roles in plant growth and development. However, miRNAs and phasiRNAs participating in the regulation of strawberry embryo and endosperm development have yet to be explored.
Here, we performed genome-wide identification of miRNA and phasiRNA-producing loci (PHAS) in strawberry seeds with a focus on those involved in the development of the early embryo and endosperm. We found that embryos and endosperm have different levels of small RNAs. After bioinformatics analysis, the results showed that a total of 404 miRNAs (352 known and 52 novel) and 156 PHAS genes (81 21-nt and 75 24-nt genes) could be found in strawberry seed-related tissues, of which four and nine conserved miRNA families displayed conserved expression in the endosperm and embryo, respectively. Based on refined putative annotation of PHAS loci, some auxin signal-related genes, such as CM3, TAR2, AFB2, ASA1, NAC and TAS3, were found, which demonstrates that IAA biosynthesis is important for endosperm and embryo development during early fruit growth. Additionally, some auxin signal-related conserved (miR390-TAS3) and novel (miR156-ASA1) trigger-PHAS pairs were identified.
Taken together, these results expand our understanding of sRNAs in strawberry embryo and endosperm development and provide a genomic resource for early-stage fruit development.
草莓肉质果实实际上是扩大的受体组织，胚胎和胚乳的成功发育对于受体果实的形成至关重要。microRNAs（miRNAs）和相控小干扰 RNA（phasiRNAs）在植物生长和发育中发挥着不可或缺的调节作用。然而，参与调节草莓胚胎和胚乳发育的 miRNAs 和 phasiRNAs 尚未被探索。
在这里，我们对草莓种子中的 miRNA 和 phasiRNA 产生基因座（PHAS）进行了全基因组鉴定，重点是那些参与早期胚胎和胚乳发育的基因座。我们发现胚胎和胚乳具有不同水平的小 RNA。经过生物信息学分析，结果表明，总共可以在草莓种子相关组织中找到 404 个 miRNAs（352 个已知和 52 个新）和 156 个 PHAS 基因（81 个 21-nt 和 75 个 24-nt 基因），其中四个和九个保守 miRNA 家族分别在胚乳和胚胎中显示保守表达。基于对 PHAS 基因座的精细假定注释，发现了一些生长素信号相关基因，如 CM3、TAR2、AFB2、ASA1、NAC 和 TAS3，这表明 IAA 生物合成对于早期果实生长过程中胚乳和胚胎的发育很重要。此外，还鉴定了一些生长素信号相关的保守（miR390-TAS3）和新的（miR156-ASA1）触发-PHAS 对。
综上所述，这些结果扩展了我们对草莓胚胎和胚乳发育中 sRNAs 的理解，并为早期果实发育提供了一个基因组资源。
