Summary
Publication
Chen, J., Hao, Z., Guang, X., Zhao, C., Wang, P., Xue, L., ... & Xu, H. (2018). Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation. Nature Plants, 1.
Name
Liriodendron chinense - Reference Genome
Resource Type
Genome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Liriodendron chinense

For genome sequencing fresh leaves were collected from an adult plant that was located in the Jiangxi province of China. For Illumina sequencing, four series of paired-end sequencing libraries were constructed and sequenced on the Illumina HiSeq 2000 platform, resulting in 327.11Gb clean read. For PacBio single-molecule real-time sequencing, sequencing libraries with 20-kb DNA inserts were constructed and subsequently sequenced, resulting in a total of 150.18 Gb subread with an N50 length of 15.96 kb for the genome assembly.

The Liriodendron genome was de novo assembled using FALCON based on PacBio long reads. The errors in the PacBio reads were corrected and the contigs were first polished based on raw PacBio data and corrected using Illumina short reads with Pilon. the corrected PacBio long reads were used for superscaffold gap filling using PBJelly. From that a reference genetic map of L. chinense was constructed based on an F1 population of 150 plants from a cross between L. chinense and L. tulipifera using JoinMap 4.0. Markers with inconsistent placement were manually screened and the collinearity of common markers was inspected using MapChart 2.2 and Markers in common were used as anchor points. Possible chimeric scaffolds were identified as those containing sequences of markers mapped to different locations in the same linkage group or different linkage groups, and these scaffolds were manually inspected. This process generated 19 Liriodendron pseudomolecules.

Downloads

Source: Chen, J., Hao, Z., Guang, X., Zhao, C., Wang, P., Xue, L., ... & Xu, H. (2018). Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation. Nature Plants, 1.

Details
Program, Pipeline, Workflow or Method Name
FALCON De novo assembly
Program Version
V0.3.0
Date Performed
Tuesday, January 15, 2019 - 10:43
Data Source
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