Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, RNA, and degradome sequencing

Abstract

Background: Ginkgo biloba, a typical dioecious plant, is a traditional medicinal plant widely planted. However, it has a long juvenile period, which severely affected the breeding and cultivation of superior ginkgo varieties. Results: In order to clarify the complex mechanism of sexual differentiation in G. biloba strobili. Here, a total of 3293 miRNAs were identified in buds and strobili of G. biloba, including 1085 known miRNAs and 2208 novel miRNAs using the three sequencing approaches of transcriptome, small RNA, and degradome. Comparative transcriptome analysis screened 4346 and 7087 differentially expressed genes (DEGs) in male buds (MB) _vs_ female buds (FB) and microstrobilus (MS) _vs_ ovulate strobilus (OS), respectively. A total of 6032 target genes were predicted for differentially expressed miRNA. The combined analysis of both small RNA and transcriptome datasets identified 51 miRNA-mRNA interaction pairs that may be involved in the process of G. biloba strobili sexual differentiation, of which 15 pairs were verified in the analysis of degradome sequencing. Conclusions: The comprehensive analysis of the small RNA, RNA and degradome sequencing data in this study provided candidate genes and clarified the regulatory mechanism of sexual differentiation of G. biloba strobili from multiple perspectives.

The emerging role of small RNAs in ovule development, a kind of magic

“…analysis, miRNA targets pred. Liu et al ( 2020b ) Gossypium hirsutum sRNA-seq Abdurakhmonov et al ( 2008 ) Gossypium hirsutum sRNA-seq, miRNA analysis and targets pred. Pang et al 2009 ) Gossypium hirsutum sRNA-seq, degrad.…”

Genome-wide identification and expression pattern analysis of the TCP transcription factor family in Ginkgo biloba

“… 6 , 7 Besides, Liu et al confirmed that CYC is recent and originated from CIN in angiosperms while G. biloba belong to ancient gymnosperms. 54 , 55 Therefore, we speculated that the difference in evolutionary time may cause this result. In addition, GbTCP09-12 was found to distribute in the same chromosome and adjacent to each other.…”

Significance of miRNA in enhancement of flavonoid biosynthesis

“…miRNA has a complex regulatory network in cells, which can regulate the expression of many genes through a miRNA and the expression of a specific gene by the combination of several miRNAs (Liu et al 2020). miRNAs have the characteristic of being highly matched with target genes, having strong targeting preference for transcription factors or other genes controlling development, and high diversity of species.…”

“…microRNA (miRNA) is a form of single-strand endogenous RNA with a length of 20-25 nt. It does not have a coding region and is highly conservative, tissue specific and stage specific (Du et al 2018;Liu et al 2020). The main function of miRNA is to downregulate the expression of target genes at the post-transcriptional level through translation suppression, as well as to target mRNA cleavage and epigenetic modification (Bartel 2004;Yu et al 2015).…”