Summary
Publication
Chaw, S. M., Liu, Y. C., Wu, Y. W., Wang, H. Y., Lin, C. Y. I., Wu, C. S., ... & Sudianto, E. (2019). Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution. Nature plants, 5(1), 63.
Name
Cinnamomum micranthum - Reference Genome
Resource Type
Genome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Cinnamomum micranthum

All plant materials used in this study were collected from a 12-year-old SCT growing in Ershui Township, Changhua County, Taiwan during April–July of 2014–2016.

For genomic DNA extraction and sequencing a modified high-salt method was used to eliminate the high content of polysaccharides in SCT leaves, followed by total DNA extraction with a modified cetyltrimethylammonium bromide (CTAB) method. Paired-end and mate-pair libraries were constructed using the Illumina TruSeq DNA HT Sample Prep Kit and Illumina Nextera Mate Pair Sample Prep Kit. All obtained libraries were sequenced on an Illumina NextSeq 500 platform to generate ~278.8 Gb of raw data. SMRT libraries were constructed using the PacBio 20-kb protocol, these libraries were sequenced on a PacBio RS-II instrument using P6 polymerase and C4 sequencing reagent. A Chicago and a Hi-C library were prepared by Dovetail Genomics (Santa Cruz) and sequenced on an Illumina HiSeq 2500 to generate 150-bp read pairs.

For RNA extraction and sequencing opening flowers, flower buds (two stages), immature leaves, young leaves, mature leaves, young stems and fruits were collected from the same individual and their total RNAs were extracted. The extracted RNA was purified using poly-T oligo-attached magnetic beads and all transcriptome libraries were constructed using the Illumina TruSeq library Stranded mRNA Prep Kit and sequenced on an Illumina HiSeq 2000 platform.

De novo assembly of PacBio reads were assembled using the FALCON (version 0.5.0) assembler. The consensus sequences of the assembly were further corrected using PacBio reads using Quiver and Illumina reads using Pilon (version 1.22). The PacBio assembly was scaffolded using the HiRISE scaffolder (version July 2015_GR), and consensus sequences were further improved using Pilon with one iteration. The genome completeness was assessed using a plant data set of BUSCO (version 3.0.2). To identify putative telomeric repeats, the assembly was searched for high copy number repeats less than 10 bp using tandem repeat finder (version 4.09; options: 2 7 7 80 10 50 500).

Downloads

Details
Program, Pipeline, Workflow or Method Name
De novo assembly using FALCON
Program Version
V0.5.0
Date Performed
Friday, March 1, 2019 - 17:00
Data Source
Give Feedback!