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Ginkgo genome version-2021

Accession number: G0002

Title: 
The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution
Published: 2021-06-14
Author:
Hailin Liu; Xiaobo Wang; Guibin Wang; Peng Cui; Shigang Wu; Cheng Ai; Nan Hu; Alun Li; Bing He; Xiujuan Shao; Zhichao Wu; Hu Feng; Yuxiao Chang; Desheng Mu; Jing Hou; Xiaogang Dai; Tongming Yin; Jue Ruan; Fuliang Cao
Abstract:

Gymnosperms are a unique lineage of plants that currently lack a high-quality reference genome due to their large genome size and high repetitive sequence content. Here, we report a nearly complete genome assembly for Ginkgo biloba with a genome size of 9.87 Gb, an N50 contig size of 1.58 Mb and an N50 scaffold size of 775 Mb. We were able to accurately annotate 27,832 protein-coding genes in total, superseding the inaccurate annotation of 41,840 genes in a previous draft genome assembly. We found that expansion of the G. biloba genome, accompanied by the notable extension of introns, was mainly caused by the insertion of long terminal repeats rather than the recent occurrence of whole-genome duplication events, in contrast to the findings of a previous report. We also identified candidate genes in the central pair, intraflagellar transport and dynein protein families that are associated with the formation of the spermatophore flagellum, which has been lost in all seed plants except ginkgo and cycads. The newly obtained Ginkgo genome provides new insights into the evolution of the gymnosperm genome.

Citation:
Hailin Liu, Xiaobo Wang, Guibin Wang, Peng Cui, Shigang Wu, Cheng Ai, Nan Hu, Alun Li, Bing He, Xiujuan Shao, Zhichao Wu, Hu Feng, Yuxiao Chang, Desheng Mu, Jing Hou, Xiaogang Dai, Tongming Yin*, Jue Ruan* & Fuliang Cao* (2021) The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. Nature Plants 7, 748-756

Scientific name: Ginkgo biloba

Sample description: 
Fresh young leaves, collected in Nanjing Forestry University
Sample attribute:

Molecular data type: DNA

Sequencing method: PacBio RS II

Sex: female

Plant body site: leaf

Collection date: 2015-06-16

Ploidy: Diploid

File Description:

genome/
Ginkgo_biloba.dna.genome.0.v2.fa.gzFASTA sequences for Ginkgo genome sequence
Ginkgo_biloba.dna.chromsome.1.v2.fa.gzFASTA sequence for chromosome 1
Ginkgo_biloba.dna.chromsome.2.v2.fa.gzFASTA sequence for chromosome 2
Ginkgo_biloba.dna.chromsome.3.v2.fa.gzFASTA sequence for chromosome 3
Ginkgo_biloba.dna.chromsome.4.v2.fa.gzFASTA sequence for chromosome 4
Ginkgo_biloba.dna.chromsome.5.v2.fa.gzFASTA sequence for chromosome 5
Ginkgo_biloba.dna.chromsome.6.v2.fa.gzFASTA sequence for chromosome 6
Ginkgo_biloba.dna.chromsome.7.v2.fa.gzFASTA sequence for chromosome 7
Ginkgo_biloba.dna.chromsome.8.v2.fa.gzFASTA sequence for chromosome 8
Ginkgo_biloba.dna.chromsome.9.v2.fa.gzFASTA sequence for chromosome 9
Ginkgo_biloba.dna.chromsome.10.v2.fa.gzFASTA sequence for chromosome 10
Ginkgo_biloba.dna.chromsome.11.v2.fa.gzFASTA sequence for chromosome 11
Ginkgo_biloba.dna.chromsome.12.v2.fa.gzFASTA sequence for chromosome 12
md5sum.txt
README.txt
CHECKSUMS.txt
annotation/
Ginkgo_biloba.all.v2.gff3.gzGenome annotation file in GFF3
Ginkgo_biloba.chrom1.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 1)
Ginkgo_biloba.chrom2.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 2)
Ginkgo_biloba.chrom3.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 3)
Ginkgo_biloba.chrom4.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 4)
Ginkgo_biloba.chrom5.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 5)
Ginkgo_biloba.chrom6.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 6)
Ginkgo_biloba.chrom7.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 7)
Ginkgo_biloba.chrom8.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 8)
Ginkgo_biloba.chrom9.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 9)
Ginkgo_biloba.chrom10.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 10)
Ginkgo_biloba.chrom11.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 11)
Ginkgo_biloba.chrom12.v2.gff3.gzGenome annotation file in GFF3 (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt
cds/
Ginkgo_biloba.cds.all.v2.fa.gzGene coding sequences
Ginkgo_biloba.cds.chrom1.v2.fa.gzGene coding sequences (Chromosome 1)
Ginkgo_biloba.cds.chrom2.v2.fa.gzGene coding sequences (Chromosome 2)
Ginkgo_biloba.cds.chrom3.v2.fa.gzGene coding sequences (Chromosome 3)
Ginkgo_biloba.cds.chrom4.v2.fa.gzGene coding sequences (Chromosome 4)
Ginkgo_biloba.cds.chrom5.v2.fa.gzGene coding sequences (Chromosome 5)
Ginkgo_biloba.cds.chrom6.v2.fa.gzGene coding sequences (Chromosome 6)
Ginkgo_biloba.cds.chrom7.v2.fa.gzGene coding sequences (Chromosome 7)
Ginkgo_biloba.cds.chrom8.v2.fa.gzGene coding sequences (Chromosome 8)
Ginkgo_biloba.cds.chrom9.v2.fa.gzGene coding sequences (Chromosome 9)
Ginkgo_biloba.cds.chrom10.v2.fa.gzGene coding sequences (Chromosome 10)
Ginkgo_biloba.cds.chrom11.v2.fa.gzGene coding sequences (Chromosome 11)
Ginkgo_biloba.cds.chrom12.v2.fa.gzGene coding sequences (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt
protein/
Ginkgo_biloba.pep.all.v2.fa.gzProtein sequences
Ginkgo_biloba.pep.chrom1.v2.fa.gzProtein sequences (Chromosome 1)
Ginkgo_biloba.pep.chrom2.v2.fa.gzProtein sequences (Chromosome 2)
Ginkgo_biloba.pep.chrom3.v2.fa.gzProtein sequences (Chromosome 3)
Ginkgo_biloba.pep.chrom4.v2.fa.gzProtein sequences (Chromosome 4)
Ginkgo_biloba.pep.chrom5.v2.fa.gzProtein sequences (Chromosome 5)
Ginkgo_biloba.pep.chrom6.v2.fa.gzProtein sequences (Chromosome 6)
Ginkgo_biloba.pep.chrom7.v2.fa.gzProtein sequences (Chromosome 7)
Ginkgo_biloba.pep.chrom8.v2.fa.gzProtein sequences (Chromosome 8)
Ginkgo_biloba.pep.chrom9.v2.fa.gzProtein sequences (Chromosome 9)
Ginkgo_biloba.pep.chrom10.v2.fa.gzProtein sequences (Chromosome 10)
Ginkgo_biloba.pep.chrom11.v2.fa.gzProtein sequences (Chromosome 11)
Ginkgo_biloba.pep.chrom12.v2.fa.gzProtein sequences (Chromosome 12)
md5sum.txt
README.txt
CHECKSUMS.txt