Summary
Publication
Zhu, Q. G., Xu, Y., Yang, Y., Guan, C. F., Zhang, Q. Y., Huang, J. W., ... & Yin, X. R. (2019). The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. Horticulture Research, 6(1), 1-15
Name
Diospyros oleifera - Reference Genome
Resource Type
Genome Assembly
Organism

Young leaves of D. oleifera from three branches were collected from the National Persimmon Germplasm Resources Nursery were used as the sample for genome sequencing and Nuclear DNA was isolated from fresh leaf tissue. Two paired-end (PE) libraries with insert sizes of 220 and 500 bp and 14 mate-pair (MP) libraries with insert sizes of 3, 4, 5, 8, 10, 15, and 17 kb were constructed using. The Illumina HiSeq 2500 platform (Illumina, San Diego, CA, USA) was used to sequence these libraries and produced 88.35 Gb of raw sequencing data, representing 100X genome coverage. Reads were trimmed for adaptor removal and quality enhancement. PacBio library construction included DNA purification, damage repair, hairpin adaptor ligation, and digestion with exonucleases to remove damaged DNA and fragments without adaptors. Another assembly method for scaffold anchoring using Hi-C sequencing technology was applied. To improve the persimmon genome assembly and chromosome anchoring accuracy, the Illumina data, PacBio long reads and Hi-C data were combined and mutually corrected. Finally, the persimmon genome was assembled into 856.41 Mb of scaffold sequences with 99.99% (856.35 Mb) of the genome consisting of the contig sequences.

Source:

Zhu, Q. G., Xu, Y., Yang, Y., Guan, C. F., Zhang, Q. Y., Huang, J. W., ... & Yin, X. R. (2019). The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. Horticulture Research, 6(1), 1-15. https://www.nature.com/articles/s41438-019-0227-2#Sec9

Details
Program, Pipeline, Workflow or Method Name
De novo assembly
Program Version
Illumina HiSeq 2500 platform
Date Performed
Wednesday, January 29, 2020 - 11:06
Data Source
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