Summary
Publication
De-Lu Ning, Tao Wu, Liang-Jun Xiao, Ting Ma, Wen-Liang Fang, Run-Quan Dong, Fu-Liang Cao, Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis, GigaScience, Volume 9, Issue 2, February 2020, giaa006, https://doi.org/10.1093/gigascience/giaa006
Name
Juglans sigillata - Reference Genome V2.0
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
Nanopore, BioNano, and Hi-C analysis
Program Version
n/a
Date Performed
Tuesday, June 9, 2020 - 16:08
Data Source
Cross Reference
Description and Download
All samples at the vegetative growth stage were collected from a J. sigillata specimen collected in Guangming town, Yangbi Yi autonomous county, Yunnan province, China. For sequencing on the Oxford Nanopore GridION X5, genomic DNA was isolated and extracted from leaves of a single plant using the Plant Genomic DNA kit (Qiagen, Hilden, Germany) based on the manufacturer's instructions. The genome size of J. sigillata was estimated by the k-mer method using sequencing data from the Illumina DNA library. Quality-filtered reads were subjected to 17-mer frequency distribution analysis using the Jellyfish program (Jellyfish, RRID:SCR_005491). The genome size (G) of J. sigillata was estimated using the following formula: G = (Nk-mer−Nerror_k-mer)/D, where Nk-mer is the number of k-mers, Nerror_k-mer is the number of k-mers with the depth of 1, and D is the k-mer depth.
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