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

Abstract

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.

Emerging roles and mechanisms of lncRNAs in fruit and vegetables

“…The presence of transposons significantly contributes to genome formation and evolution. In strawberries, a total of 14 552 lncRNAs have been identified, with 59.2% derived from transposon elements [ 45 ].…”

“…3B ). For example, 382 and 78 lncRNAs were identified in response to ABA treatment in strawberries [ 45 ]. In kiwifruit, 78 lncRNAs were identified in response to ABA treatment, and the upregulation of these lncRNAs induced by ABA treatment led to increased ET biosynthesis and fruit softening [ 13 ].…”

Phosphorus solubilizing microorganisms: potential promoters of agricultural and environmental engineering

“…The most well-known uses of PMSs are in agricultural and environmental engineering. For their outstanding nature described above, PMS are used for improving soil fertility in agriculture, enhancing plant growth and tolerance against stress of instance salinity (Luo et al, 2022), nutrient deficiency (He et al, 2022;2021;Chen et al, 2022a) etc.,; and hence increasing crop yields (Chen et al, 2022b); they can also be used for bioremediation along or combining with plants, to remove for instance heavy metals from contaminated soil and water (Pinilla et al, 2008;Chen et al, 2019a).…”

GIFTdb: a useful gene database for plant fruit traits improving

“…Similarly, the Strawberry Genome Database focuses on strawberry genome data rather than strawberry fruit trait genetic data. Despite these limitations, the availability of these data sources has significantly contributed to the analysis of gene function and the improvement of fruit traits in crops such as strawberries, blueberries, and tomatoes (Chen, Wang, He, Wan, et al, 2022;L opez-Casado et al, 2023;Rey-Serra et al, 2022;S unico et al, 2021;Yue et al, 2016Yue et al, , 2017. Therefore, more efforts are needed to consolidate and integrate such dispersed gene data related to fruit traits in a comprehensive database to facilitate further research and application.…”