Temporal Dynamic Transcriptome Landscape Reveals Regulatory Network During the Early Differentiation of Female Strobilus Buds in Ginkgo biloba

Abstract

Reproductive bud differentiation is one of the most critical events for the reproductive success of seed plants. Yet, our understanding of genetic basis remains limited for the development of the reproductive organ of gymnosperms, namely, unisexual strobilus or cone, leaving its regulatory network largely unknown for strobilus bud differentiation. In this study, we analyzed the temporal dynamic landscapes of genes, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) during the early differentiation of female strobilus buds in Ginkgo biloba based on the whole transcriptome sequencing. Results suggested that the functions of three genes, i.e., Gb_19790 (GbFT), Gb_13989 (GinNdly), and Gb_16301 (AG), were conserved in both angiosperms and gymnosperms at the initial differentiation stage. The expression of genes, lncRNAs, and miRNAs underwent substantial changes from the initial differentiation to the enlargement of ovule stalk primordia. Besides protein-coding genes, 364 lncRNAs and 15 miRNAs were determined to be functional. Moreover, a competing endogenous RNA (ceRNA) network comprising 10,248 lncRNA-miRNA-mRNA pairs was identified, which was highly correlated with the development of ovulate stalk primordia. Using the living fossil ginkgo as the study system, this study not only reveals the expression patterns of genes related to flowering but also provides novel insights into the regulatory networks of lncRNAs and miRNAs, especially the ceRNA network, paving the way for future studies concerning the underlying regulation mechanisms of strobilus bud differentiation.

Identification and analysis of key miRNA for sex differentiation in hermaphroditic Juglans mandshurica Maxim.

“…The present sequencing showed that TCP4 and MYB33 could be targeted by miR159 and miR319, while miR167 was repressed in expression by TCP4 and MYB33 [29], thereby promoting the expression of ARF6 and ARF8, two key genes for ower formation. miR167 and miR319 affect FT gene expression by targeting FTIP1 [30][31][32][33]. miR319 and miR159 are highly expressed in the pistil and relatively low in the stamen, while miR167 is expressed in the opposite direction, suggesting that these three miRNA families play a key role in the sexual differentiation of Juglans mandshurica.…”

“…There were 46 differentially expressed miRNA targeting 416 mRNA loci in T1vsM1, with an average of 9.04 mRNAs/miRNA. Among these miRNA, miR159b-3p.1 and miR159c targeted the most mRNAs (34), followed by miR159a (33). A total of 247 mRNAs could be targeted by more than 1 miRNA.…”

Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development

“…The gene expression data of Physcomitrella patens (E-MTAB-3069) (http://www.ebi.ac.uk/arrayexpress) (Ortiz-Ramirez et al, 2016), Adiantum capillus (PRJNA593361) (https://www.ncbi.nlm.nih.gov/ sra) (Fang et al, 2021), Ginkgo biloba (T0001) (https://ginkgo.zju.edu. cn/project/T0001) (Bai et al, 2022), and rice (PRJNA591969) (https:// www.ncbi.nlm.nih.gov/sra) (Zhao et al, 2020) were collected to investigate the spectrum of expression variation of key integument regulatory genes in various organs across species. The reference genome of A. capillus was downloaded from the NCBI database (https://www.…”