Whole-Transcriptome Analysis Reveals Long Noncoding RNAs Involved in Female Floral Development of Hickory (Carya cathayensis Sarg.)

Abstract

Hickory, an endemic woody oil and fruit tree species in China, is of great economic value. However, hickory has a long juvenile period and an inconsistent flowering of males and females, thus influencing the bearing rates and further limiting fruits yield. Currently, it is reported that long noncoding RNAs (lncRNAs) play critical regulatory roles in biological processes. However, the role of lncRNAs in the development of hickory female flowers remains unclear. In this study, a total of 6,862 putative lncRNAs were identified from the female flower transcriptomes in three different growth stages of hickory. We proposed that lncRNAs might play an important role in phytohormone signaling processes for flower formation, especially in the abscisic acid and jasmonic acid pathways, according to the results of our Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Moreover, we predicted the interactions among four microRNAs (miRNAs), three lncRNAs, and four genes. We proposed that facing the changing environment, LNC_002115 competes with PHOSPHATE2 (PHO2) for the binding sites on cca-miR399f, and protects PHO2 from suppression. In addition, cis-acting LNC_002115 regulates the expression of the SHORT VEGETATIVE PHASE (SVP) by influencing ABRE-binding factor (ABF). In brief, LNC_002115 regulates hickory female floral development by impacting both PHO2 and SVP. This study was the first to identify lncRNAs involved in hickory female floral development, and provided new insight to elucidate how lncRNAs and their targets play a role in female floral development in hickory, thus unfolding the opportunities for functional characterization of blossom-related lncRNAs in further studies.

Comprehensive identification and analysis of circRNAs during hickory (Carya cathayensis Sarg.) flower bud differentiation

“…We hypothesized that novel_circ_0005823 and novrl_circ_0005105 may act as sponges for miR167, thereby contributing to the abundance of CCA1519S0026. We proposed that novel_circ_0003968 and novel_circ_0011186 promote the expression of ptc-miR399, which regulates LNC_02115 in the female hickory bud during temperature changes ( Li et al., 2022 ). Nevertheless, more detailed mechanisms may also exist that need further experimental exploration.…”

“…A total of 3 μg of total RNA per sample was used as the starting material for the RNA sequencing (RNA-seq) libraries preparation. Ribosomal RNA depletion and RNA-seq library preparation were performed as described in Li and colleagues ( Li et al., 2022 ).…”

Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation in Melastoma candidum

“…In some cases, lncRNAs are found to enhance the binding rate of transcription factors to nearby binding sites (de la Fuente, 2010; Yang et al, 2019). A study by Li et al (2022) found that cis-acting LNC_002115 regulates hickory female floral development by influencing both PHO2 and SVP. Kang and Liu (2015) identified a significant number of lncRNAs from 35 different flower and fruit tissues of diploid strawberries.…”