Summary
Publication
Peng Cui, Qiang Lin, Dongming Fang, Lingling Zhang, Rongjun Li, Junyong Cheng, Fei Gao, Jay Shockey, Songnian Hu, Shiyou Lü, Tung Tree (Vernicia fordii, Hemsl.) Genome and Transcriptome Sequencing Reveals Co-Ordinate Up-Regulation of Fatty Acid β-Oxidation and Triacylglycerol Biosynthesis Pathways During Eleostearic Acid Accumulation in Seeds, Plant and Cell Physiology, Volume 59, Issue 10, October 2018, Pages 1990–2003, https://doi.org/10.1093/pcp/pcy117
Name
Vernicia fordii - Reference Genome
Resource Type
Genome Assembly
Organism
Details
Program, Pipeline, Workflow or Method Name
SOAPdenovo2
Program Version
r240
Date Performed
Thursday, April 18, 2019 - 12:35
Data Source
Description and Download
The genome DNA was isolated in young leaves using modified recycling CTAB and stored at low temperatures. The raw data was then filtered using Trimmomatic (3.3) and SOAPdenovo2 was then used to assemble the high quality reads into a draft assembly with default insert size and parameters. Then 40,000 paired reads of each library were mapped to the first version contigs and scaffoldings for library quality control and accurate estimation of average insert size. The insert size of each set of data was then carefully adjusted in configure file for final SOAPdenovo2 (r240) running with a multi-K-mer of 51–85. The scaffolds were further connected by SSPACE (v2.0) and scaffold gaps were closed by Gapfiller (1.12) with pair-end reads.

Downloads

Genomic scaffolds
All Gene Models CDS (fasta format)
All Gene Models Protein (fasta format)
All Gene Models GFF (Fasta format)
Source: https://academic.oup.com/pcp/article/59/10/1990/5077255
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