Transcriptome of male and female ginkgo leaves and strobilus at three stages
Accession number: T0003
Data type: Transcriptome
Updated: 2020-12-30
FTP download: https://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/
FTP download: ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/
Sexual dimorphism like dioecy (separate male and female individuals) have evolved in diverse multicellular eukaryotes while the molecular mechanisms underlying the development of such a key biological trait remains elusive. The living fossil Ginkgo biloba represents an early diverged lineage of land plants with dioecy. However, its sex-determination system and molecular basis have long been controversial or unknown. In the present research, we assembled the first and largest to date chromosome-level genome of a non-model tree species using Hi-C data. With this reference genome, we addressed both questions using genome resequencing data gathered from 97 male and 265 female trees of ginkgo, as well as transcriptome data from three developmental stages for both sexes. Our results support vertebrate-like XY chromosomes for ginkgo and five potential sex-determination genes, which may originate ~14 million years ago. This is the earliest diverged sex determination region in all reported plants as yet. The present research resolved a long-term controversy, lay a foundation for future studies on the origin and evolution of plant sexes, and provide genetic markers for sex identification of ginkgo which will be valuable for both nurseries and field ecology of ginkgo.
Scientific name: Ginkgo biloba
Molecular data type：RNA
Geographic location (country and/or sea,region): China, Zhejiang Province, Tianmu Mountain National Nature Reserve
Sequencing method: BGISEQ-500 using RNASeq_OligodT libraries
Sex: female and male
Plant body site: strobilus buds and leaves
Collection date: 2018.03.28–2018.04.11
Collected by: Yun-peng Zhao
Pipline: The gene counts and abundance [transcripts per million (TPM)] were quantified by SALMON (v1.8.0). The whole genome were used as the decoy sequence for SALMON.
File Description:
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/./All_run_OriginalCounts.csv All_run_OriginalCounts.csv | gene expression data in counts |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/./All_run_OriginalTPM.csv All_run_OriginalTPM.csv | gene expression data in TPM |
| RNA_seq/ | |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF1-1.fq.gz FF1-1.fq.gz | female cones at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF1-2.fq.gz FF1-2.fq.gz | female cones at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF2-1.fq.gz FF2-1.fq.gz | female cones at stage 2 (full development of female cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF2-2.fq.gz FF2-2.fq.gz | female cones at stage 2 (full development of female cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF3-1.fq.gz FF3-1.fq.gz | female cones at stage 3 (appearance of pollination drops) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF3-2.fq.gz FF3-2.fq.gz | female cones at stage 3 (appearance of pollination drops) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FF3-3.fq.gz FF3-3.fq.gz | female cones at stage 3 (appearance of pollination drops) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM1-1.fq.gz FM1-1.fq.gz | male cones at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM1-2.fq.gz FM1-2.fq.gz | male cones at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM1-3.fq.gz FM1-3.fq.gz | male cones at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM2-1.fq.gz FM2-1.fq.gz | male cones at stage 2 (full development of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM2-2.fq.gz FM2-2.fq.gz | male cones at stage 2 (full development of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM2-3.fq.gz FM2-3.fq.gz | male cones at stage 2 (full development of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM3-1.fq.gz FM3-1.fq.gz | male cones at stage 3 (opening of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM3-2.fq.gz FM3-2.fq.gz | male cones at stage 3 (opening of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/FM3-3.fq.gz FM3-3.fq.gz | male cones at stage 3 (opening of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF1-1.fq.gz LF1-1.fq.gz | female leaves at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF1-2.fq.gz LF1-2.fq.gz | female leaves at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF2-1.fq.gz LF2-1.fq.gz | female leaves at stage 2 (full development of female cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF2-2.fq.gz LF2-2.fq.gz | female leaves at stage 2 (full development of female cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF3-1.fq.gz LF3-1.fq.gz | female leaves at stage 3 (appearance of pollination drops) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF3-2.fq.gz LF3-2.fq.gz | female leaves at stage 3 (appearance of pollination drops) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LF3-3.fq.gz LF3-3.fq.gz | female leaves at stage 3 (appearance of pollination drops) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM1-1.fq.gz LM1-1.fq.gz | male leafs at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM1-2.fq.gz LM1-2.fq.gz | male leafs at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM1-3.fq.gz LM1-3.fq.gz | male leafs at stage 1 (initial budburst) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM2-1.fq.gz LM2-1.fq.gz | male leafs at stage 2 (full development of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM2-2.fq.gz LM2-2.fq.gz | male leafs at stage 2 (full development of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM2-3.fq.gz LM2-3.fq.gz | male leafs at stage 2 (full development of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM3-1.fq.gz LM3-1.fq.gz | male leafs at stage 3 (opening of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM3-2.fq.gz LM3-2.fq.gz | male leafs at stage 3 (opening of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/LM3-3.fq.gz LM3-3.fq.gz | male leafs at stage 3 (opening of male cones) |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/CHECKSUMS.txt CHECKSUMS.txt | |
| ftp://ginkgo.zju.edu.cn/ftp/item/transcriptome/T0003/RNA_seq/md5sum.txt md5sum.txt | |
Sample Description:
| FF1-1 | female cones at stage 1 (initial budburst) |
| FF1-2 | female cones at stage 1 (initial budburst) |
| FF2-1 | female cones at stage 2 (full development of female cones) |
| FF2-2 | female cones at stage 2 (full development of female cones) |
| FF3-1 | female cones at stage 3 (appearance of pollination drops) |
| FF3-2 | female cones at stage 3 (appearance of pollination drops) |
| FF3-3 | female cones at stage 3 (appearance of pollination drops) |
| FM1-1 | male cones at stage 1 (initial budburst) |
| FM1-2 | male cones at stage 1 (initial budburst) |
| FM1-3 | male cones at stage 1 (initial budburst) |
| FM2-1 | male cones at stage 2 (full development of male cones) |
| FM2-2 | male cones at stage 2 (full development of male cones) |
| FM2-3 | male cones at stage 2 (full development of male cones) |
| FM3-1 | male cones at stage 3 (opening of male cones) |
| FM3-2 | male cones at stage 3 (opening of male cones) |
| FM3-3 | male cones at stage 3 (opening of male cones) |
| LF1-1 | female leaves at stage 1 (initial budburst) |
| LF1-2 | female leaves at stage 1 (initial budburst) |
| LF2-1 | female leaves at stage 2 (full development of female cones) |
| LF2-2 | female leaves at stage 2 (full development of female cones) |
| LF3-1 | female leaves at stage 3 (appearance of pollination drops) |
| LF3-2 | female leaves at stage 3 (appearance of pollination drops) |
| LF3-3 | female leaves at stage 3 (appearance of pollination drops) |
| LM1-1 | male leafs at stage 1 (initial budburst) |
| LM1-2 | male leafs at stage 1 (initial budburst) |
| LM1-3 | male leafs at stage 1 (initial budburst) |
| LM2-1 | male leafs at stage 2 (full development of male cones) |
| LM2-2 | male leafs at stage 2 (full development of male cones) |
| LM2-3 | male leafs at stage 2 (full development of male cones) |
| LM3-1 | male leafs at stage 3 (opening of male cones) |
| LM3-2 | male leafs at stage 3 (opening of male cones) |
| LM3-3 | male leafs at stage 3 (opening of male cones) |