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Ginkgo genome version-2019

Accession number: G0001

Title: 
Updated genome assembly of Ginkgo biloba
Published: 2019-06-04
Author:
Guan R; Zhao Y; Zhang H; Fan G; Liu X; Zhou W; Shi C; Wang J; Liu W; Liang X; Fu Y; Ma K; Zhao L; Zhang F; Lu Z; Lee SM; Xu X; Wang J; Yang H; Fu C; Ge S; Chen W
Abstract:

Ginkgo biloba is one of the world’s most ancient plants, a living fossil that has remained essentially unchanged in terms of gross morphology for more than 200 million years. Representing one of the four extant gymnosperm lineages and having no living relatives, it possesses a suite of fascinating characteristics including including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies.

Here we present an updated chromosome-level genome assembly using HiC technology as a major improvement of the ginkgo draft assembly. A chromosome-level reference represents a valuable resource to facilitate of studies of biologic diversity, evolutionary history, and population genetics. With technological advances, we constructed to update the existing draft assembly to the chromosome-level using Hi-C, which has been proven to be a fast, inexpensive, and accurate technology that can be applied to many species. The fresh plant leaves of two-years seedling (TM301S) were crosslinked with 1% formaldehyde. To destroy the cell wall, formaldehyde fixed powder was added to Buffer solution. The restriction endonuclease MboI was used to digest DNA, followed by biotinylated residue labeling. The Hi-C library was then sequenced on BGISEQ-500 platform with 50 bp pair-end sequencing. HiC-Pro pipeline (v2.11.1) was implemented in quality control. Of all 653,202,535 raw pair-end reads, there are 32% (207,324,555) paired Hi-C reads are valid and suitable for following analysis. Basing on these valid Hi-C reads, we used Juicer (v1.6.2) and Aiden lab’s Hi-C assembly pipeline (v180922) to assemble the genome with the main parameter "-m haploid -s 4 -c 12", generating 12 chromosomes spanning 9.03 Gb (~94% of the whole genome).

Keywords:
hic; chromosome-level; assembly
Citation:
Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee, Xun Xu, Jian Wang, Huanming Yang, Chengxin Fu*, Song Ge* & Wenbin Chen* (2019) Updated genome assembly of Ginkgo biloba. GigaScience Database

Scientific name: Ginkgo biloba

Sample description: 
DNA extracted from the leaf of seedling (of TM301) from a Gingko (Maidenhair) tree growing on Tianmu Mountain
Sample attribute:

Molecular data type: DNA

Alternative accession-BioSample: SAMN11919598

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

Geographic location (latitude and longitude): 30.350000, 119.433333

Sequencing method: BGISEQ-500

Estimated size: 1.1E10

Assembly: 3D-DNA pipeline (version: 180922)

Sex: female

Plant body site: leaf [PO: 0025034]

Collection date: 2017-06-01

Life stage: two years seedling

Ploidy: Diploid

Family relationship: isProgenyOf: TM301

Collected by: Yun-peng Zhao

File Description:

genome/
Ginkgo_biloba.dna.genome.0.v1.fa.gzFASTA sequences for Ginkgo genome sequence
Ginkgo_biloba.dna.chromsome.1.v1.fa.gzFASTA sequence for chromosome 1
Ginkgo_biloba.dna.chromsome.2.v1.fa.gzFASTA sequence for chromosome 2
Ginkgo_biloba.dna.chromsome.3.v1.fa.gzFASTA sequence for chromosome 3
Ginkgo_biloba.dna.chromsome.4.v1.fa.gzFASTA sequence for chromosome 4
Ginkgo_biloba.dna.chromsome.5.v1.fa.gzFASTA sequence for chromosome 5
Ginkgo_biloba.dna.chromsome.6.v1.fa.gzFASTA sequence for chromosome 6
Ginkgo_biloba.dna.chromsome.7.v1.fa.gzFASTA sequence for chromosome 7
Ginkgo_biloba.dna.chromsome.8.v1.fa.gzFASTA sequence for chromosome 8
Ginkgo_biloba.dna.chromsome.9.v1.fa.gzFASTA sequence for chromosome 9
Ginkgo_biloba.dna.chromsome.10.v1.fa.gzFASTA sequence for chromosome 10
Ginkgo_biloba.dna.chromsome.11.v1.fa.gzFASTA sequence for chromosome 11
Ginkgo_biloba.dna.chromsome.12.v1.fa.gzFASTA sequence for chromosome 12
md5sum.txt
README.txt
CHECKSUMS.txt
annotation/
Ginkgo_biloba.all.v1.gff3.gzGenome annotation file in GFF3
Ginkgo_biloba.chrom1.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 1)
Ginkgo_biloba.chrom2.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 2)
Ginkgo_biloba.chrom3.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 3)
Ginkgo_biloba.chrom4.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 4)
Ginkgo_biloba.chrom5.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 5)
Ginkgo_biloba.chrom6.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 6)
Ginkgo_biloba.chrom7.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 7)
Ginkgo_biloba.chrom8.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 8)
Ginkgo_biloba.chrom9.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 9)
Ginkgo_biloba.chrom10.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 10)
Ginkgo_biloba.chrom11.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 11)
Ginkgo_biloba.chrom12.v1.gff3.gzGenome annotation file in GFF3 (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt
cds/
Ginkgo_biloba.cds.all.v1.fa.gzGene coding sequences
Ginkgo_biloba.cds.chrom1.v1.fa.gzGene coding sequences (Chromosome 1)
Ginkgo_biloba.cds.chrom2.v1.fa.gzGene coding sequences (Chromosome 2)
Ginkgo_biloba.cds.chrom3.v1.fa.gzGene coding sequences (Chromosome 3)
Ginkgo_biloba.cds.chrom4.v1.fa.gzGene coding sequences (Chromosome 4)
Ginkgo_biloba.cds.chrom5.v1.fa.gzGene coding sequences (Chromosome 5)
Ginkgo_biloba.cds.chrom6.v1.fa.gzGene coding sequences (Chromosome 6)
Ginkgo_biloba.cds.chrom7.v1.fa.gzGene coding sequences (Chromosome 7)
Ginkgo_biloba.cds.chrom8.v1.fa.gzGene coding sequences (Chromosome 8)
Ginkgo_biloba.cds.chrom9.v1.fa.gzGene coding sequences (Chromosome 9)
Ginkgo_biloba.cds.chrom10.v1.fa.gzGene coding sequences (Chromosome 10)
Ginkgo_biloba.cds.chrom11.v1.fa.gzGene coding sequences (Chromosome 11)
Ginkgo_biloba.cds.chrom12.v1.fa.gzGene coding sequences (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt
protein/
Ginkgo_biloba.pep.all.v1.fa.gzProtein sequences
Ginkgo_biloba.pep.chrom1.v1.fa.gzProtein sequences (Chromosome 1)
Ginkgo_biloba.pep.chrom2.v1.fa.gzProtein sequences (Chromosome 2)
Ginkgo_biloba.pep.chrom3.v1.fa.gzProtein sequences (Chromosome 3)
Ginkgo_biloba.pep.chrom4.v1.fa.gzProtein sequences (Chromosome 4)
Ginkgo_biloba.pep.chrom5.v1.fa.gzProtein sequences (Chromosome 5)
Ginkgo_biloba.pep.chrom6.v1.fa.gzProtein sequences (Chromosome 6)
Ginkgo_biloba.pep.chrom7.v1.fa.gzProtein sequences (Chromosome 7)
Ginkgo_biloba.pep.chrom8.v1.fa.gzProtein sequences (Chromosome 8)
Ginkgo_biloba.pep.chrom9.v1.fa.gzProtein sequences (Chromosome 9)
Ginkgo_biloba.pep.chrom10.v1.fa.gzProtein sequences (Chromosome 10)
Ginkgo_biloba.pep.chrom11.v1.fa.gzProtein sequences (Chromosome 11)
Ginkgo_biloba.pep.chrom12.v1.fa.gzProtein sequences (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt
variation/
Ginkgo_biloba.all.v1.vcf.gzVariation sites data in VCF format
Ginkgo_biloba.chrom1.v1.vcf.gzVariation sites data in VCF format (Chromosome 1)
Ginkgo_biloba.chrom2.v1.vcf.gzVariation sites data in VCF format (Chromosome 2)
Ginkgo_biloba.chrom3.v1.vcf.gzVariation sites data in VCF format (Chromosome 3)
Ginkgo_biloba.chrom4.v1.vcf.gzVariation sites data in VCF format (Chromosome 4)
Ginkgo_biloba.chrom5.v1.vcf.gzVariation sites data in VCF format (Chromosome 5)
Ginkgo_biloba.chrom6.v1.vcf.gzVariation sites data in VCF format (Chromosome 6)
Ginkgo_biloba.chrom7.v1.vcf.gzVariation sites data in VCF format (Chromosome 7)
Ginkgo_biloba.chrom8.v1.vcf.gzVariation sites data in VCF format (Chromosome 8)
Ginkgo_biloba.chrom9.v1.vcf.gzVariation sites data in VCF format (Chromosome 9)
Ginkgo_biloba.chrom10.v1.vcf.gzVariation sites data in VCF format (Chromosome 10)
Ginkgo_biloba.chrom11.v1.vcf.gzVariation sites data in VCF format (Chromosome 11)
Ginkgo_biloba.chrom12.v1.vcf.gzVariation sites data in VCF format (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt