De novo sequencing of Ginkgo biloba L. ====================================== 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, S, M; Xu, X; Wang, J; Yang, H; Fu, C; Ge, S; Chen1, W 2016 GigaScience Database. http://dx.doi.org/10.5524/100209 Summary ------- Ginkgo biloba L. is one of the world.s most ancient plants with huge genome size and enjoys particular phenotype like dioecism, and resistant to biotic and abiotic stress. Insufficient genome information has been a key factor which impedes our understanding towards gymnosperm species. Here, we assembled and annotated the first complete genome sequence of ginkgo, which will dramatically promote related research area. Files ----- Ginkgo_biloba.scaf.fa.gz - Genome assembly result of Ginkgo Gb.gene.gff - Protein-coding gene annotation in GFF3 file format Gb.cds.fa - Coding sequence in FASTA format Gb.pep.fa - Translated protein sequence in FASTA format Ginkgo.divtree.newick - newick format tree of the tree file Ginkgo.philip.phase1.gz - all phase1 site of sequence alignment in tree all.gene.FPKM.csv - FPKM of each gene in different samples trans_leaf.fa.gz - assembled transcriptome of leaf data downloaded from NCBI, source="Nanjing Forestry University" trans_seed.fa.gz - assembled transcriptome of seed data downloaded from NCBI, source="Nanjing Forestry University" S_figure1_17mer.freq.csv.gz - kmer analysis table S_figure3.tar.gz - gene set statistic of different species S_figure4.csv - gene families number of each type statistics S_figure5.csv - repeat length distribution of intron and intergenic regions S_figure6.csv - Ks distribution of ginkgo and other angiosperm plants S_figure7.csv - FPKM of gene family alpha-bisabolene synthase repeat.gff.gz - repeat annotation of genome repeat_stat.tar.gz - Perl scripts used in statistic of repeat annotation result, all needed files and scripts were included TM010.scaf.fa.gz - Genome survey assembly result of Ginkgo TM010 TM2217.scaf.fa.gz - Genome survey assembly result of Ginkgo TM2217 Ty1-copia.Final-Pta.pep.gz - Ty1 sequences of loblolly pine Ty3-gypsy.Final-Pta.pep.gz - Ty3 sequences of loblolly pine Ty1.muscle.out.gz - Muscle alignment result of Ty1 of G. biloba, P. patens, P. abies, P. trichocarpa and Z.mays Ty1.muscle.tre.gz - Phylogenetic tree of Ty1 of G. biloba, P. patens, P. abies, P. trichocarpa and Z.mays Ty3.muscle.out.gz - Muscle alignment result of Ty3 of G. biloba, P. patens, P. abies, P. trichocarpa and Z.mays Tye3.muscle.tre.gz - Phylogenetic tree of Ty3 of G. biloba, P. patens, P. abies, P. trichocarpa and Z.mays completed_LTR.fa.gz - Completed LTR sequences of ginkgo. Repeat_lib_identified_by_LTRfinder_and_Repeatmodeler.gz - The repeat library of ginkgo annotated by LTRfinder and Repeatmodeler all_orthomcl.out.gz - Orthomcl results of ginkgo and P. abies, S. moellendorffii, A.thaliana and O. sativa