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Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis

Mao Weitao Yao Guoxin Wang Shangde Zhou Lei Chen Guosong Dong Ningguang Hu Guanglong

Mao W, Yao G, Wang S, Zhou L, Chen G, et al. 2021. Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis. Forestry Research 1: 9 doi: 10.48130/FR-2021-0009
Citation: Mao W, Yao G, Wang S, Zhou L, Chen G, et al. 2021. Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis. Forestry Research 1: 9 doi: 10.48130/FR-2021-0009

Chromosome-level genomes of seeded and seedless date plum based on third-generation DNA sequencing and Hi-C analysis

doi: 10.48130/FR-2021-0009
  • Figure  1.  Fruit shapes and seed sizes of the seeded and seedless Diospyros lotus. (a) Seeded (Yz01); (b) Seedless (W01).

    Figure  2.  Hi-C interaction heat maps for Diospyros lotus genomes presenting the interactions among 15 chromosomes. (a) Seeded (Yz01); (b) Seedless (W01).

    Figure  3.  Circular genomic maps for Diospyros lotus. (a) Seeded (Yz01); (b) Seedless (W01). A. GC content distribution; B. Gene density distribution; C. Repeats density distribution; D. LTR-Copia density distribution; E. LTR-Gypsy density distribution; F. DNA transposon density distribution.

    Figure  4.  Chromosomal synteny between seedless and seeded Diospyros lotus. (a) Inter-genomic comparison. (b) Chromosomal maps of seedless and seeded Diospyros lotus.

    Figure  5.  Venn diagram presenting the number of shared and unique protein-coding genes among seedless and seeded Diospyros lotus, Malus domestica, Citrus reticulata, and Juglans regia revealed by an orthology analysis.

    Figure  6.  Phylogenetic tree of seedless and seeded Diospyros lotus and 17 other species constructed using the maximum-likelihood method. Estimated species divergence times (million years ago) and 95% confidence intervals are labeled at each branch site. Blue numbers on branches indicate the estimated divergence times. Red dots indicate the divergence times estimated based on fossil evidence.

    Figure  7.  The user interface of Diospyros Genome Database for browsing genomes, searching for homologous sequences and designing primers.

    Table  1.   Summary of the sequencing data used for assembling the Diospyros lotus genomes.

    Library typeSeedless Diospyros lotus (W01)Seeded Diospyros lotus (Yz01)
    Library size (bp)Clean data (Gb)Coverage (×)Library size (bp)Clean data (Gb)Coverage (×)
    Illumina35080.99 119.5335079.21114.98
    Pacbio20,00092.1103.2920,000133.51166.98
    Hi-C35086.96 350107.87
    下载: 导出CSV

    Table  2.   Summary of the assembled seedless and seeded Diospyros lotus genomes.

    ParameterSeedless Diospyros lotus (W01)Seeded Diospyros lotus (Yz01)
    Contig length (bp)Contig numberContig length (bp)Contig number
    N90561,232228537,928279
    N801,144,3541511,078,450194
    N701,625,0121061,450,541143
    N602,258,638732,059,392106
    N503,006,748492,463,96077
    Total length617,662,490647,313,630
    Number (≥ 100 bp)706743
    Number (≥ 2 kb)691734
    Max length16,262,24114,842,567
    下载: 导出CSV

    Table  3.   General statistics for the functional annotations of the genes in the seedless and seeded Diospyros lotus genomes.

    TypeSeedless Diospyros lotus (W01)Seeded Diospyros lotus (Yz01)
    NumberPercent (%)NumberPercent (%)
    Total21,68423,193
    Annotated20,68995.4122,84498.5
    InterPro17,47380.5820,03786.39
    GO12,16156.0814,06660.65
    KEGG ALL20,54794.7622,75098.09
    KEGG KO8,43538.909,81242.31
    Swissprot15,05769.4416,89672.85
    TrEMBL20,58794.9422,79098.26
    TF1,5607.191,5726.78
    Pfam17,06478.6919,70984.98
    NR20,60795.0322,79498.28
    KOG17,99082.9620,20887.13
    Unannotated9954.593491.50
    下载: 导出CSV
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出版历程
  • 收稿日期:  2021-03-25
  • 录用日期:  2021-05-14
  • 网络出版日期:  2021-12-15
  • 发布日期:  2021-05-27
  • 刊出日期:  2021-01-16

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