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Whole-transcriptome of female strobilus buds during the early differentiation in Ginkgo biloba

Accession number: T0001

Data type: Transcriptome

Updated: 2021-12-24

FTP download: https://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0001/

FTP download: ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0001/

Title: 
Temporal dynamic transcriptome landscape reveals regulatory network during the early differentiation of female strobilus buds in Ginkgo biloba
Published: 2022-03-31
Author:
Pan-Pan Bai; Han-Yang Lin; Yue Sun; Jun-Jie Wu; Kai-Jie Gu; Yun-Peng Zhao
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.

Keywords:
flower bud differentiation; Ginkgo biloba; lncRNA; miRNA; ceRNA network
Citation:
Pan-Pan Bai, Han-Yang Lin, Yue Sun, Jun-Jie Wu, Kai-Jie Gu & Yun-Peng Zhao* (2022) Temporal dynamic transcriptome landscape reveals regulatory network during the early differentiation of female strobilus buds in Ginkgo biloba. Frontiers in Plant Science 13,863330.

Scientific name: Ginkgo biloba

Sample description: 
Female strobilus buds at vegetative, initial differentiation, and exuberant differentiation stages
Sample attribute:

Molecular data type:RNA

Geographic location (country and/or sea,region): China, Zhejiang Province

Sequencing method: Hiseq 4000 for strand-specific libraries, and BGISEQ-500 for small RNA libraries

Sex: female

Plant body site: strobilus buds

Collection date: 2020.06.19–2021.05.26

Collected by: Pan-Pan Bai

File Description:

all_sample_gene_TPM.txt gene expression data in TPM
lncRNA-seq/
ST1F1_1.fq.gzfemale strobilus buds at vegetative stage
ST1F1_2.fq.gzfemale strobilus buds at vegetative stage
ST1F2_1.fq.gzfemale strobilus buds at vegetative stage
ST1F2_2.fq.gzfemale strobilus buds at vegetative stage
ST1F3_1.fq.gzfemale strobilus buds at vegetative stage
ST1F3_2.fq.gzfemale strobilus buds at vegetative stage
ST2F1_1.fq.gzfemale strobilus buds at initial differentiation stage
ST2F1_2.fq.gzfemale strobilus buds at initial differentiation stage
ST2F2_1.fq.gzfemale strobilus buds at initial differentiation stage
ST2F2_2.fq.gzfemale strobilus buds at initial differentiation stage
ST2F3_1.fq.gzfemale strobilus buds at initial differentiation stage
ST2F3_2.fq.gzfemale strobilus buds at initial differentiation stage
ST3-1F1_1.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F1_2.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F2_1.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F2_2.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F3_1.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F3_2.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-2F1_1.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F1_2.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F2_1.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F2_2.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F3_1.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F3_2.fq.gzfemale strobilus buds at late exuberant differentiation stage
CHECKSUMS.txt
md5sum.txt
sRNA-seq/
ST1F1.fq.gzfemale strobilus buds at vegetative stage
ST1F2.fq.gzfemale strobilus buds at vegetative stage
ST1F3.fq.gzfemale strobilus buds at vegetative stage
ST2F1.fq.gzfemale strobilus buds at initial differentiation stage
ST2F2.fq.gzfemale strobilus buds at initial differentiation stage
ST2F3.fq.gzfemale strobilus buds at initial differentiation stage
ST3-1F1.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F2.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-1F3.fq.gzfemale strobilus buds at early exuberant differentiation stage
ST3-2F1.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F2.fq.gzfemale strobilus buds at late exuberant differentiation stage
ST3-2F3.fq.gzfemale strobilus buds at late exuberant differentiation stage
CHECKSUMS.txt
md5sum.txt

Sample Description:

ST1F1female strobilus buds at vegetative stage
ST1F2female strobilus buds at vegetative stage
ST1F3female strobilus buds at vegetative stage
ST2F1female strobilus buds at initial differentiation stage
ST2F2female strobilus buds at initial differentiation stage
ST2F3female strobilus buds at initial differentiation stage
ST3-1F1female strobilus buds at early exuberant differentiation stage
ST3-1F2female strobilus buds at early exuberant differentiation stage
ST3-1F3female strobilus buds at early exuberant differentiation stage
ST3-2F1female strobilus buds at late exuberant differentiation stage
ST3-2F2female strobilus buds at late exuberant differentiation stage
ST3-2F3female strobilus buds at late exuberant differentiation stage