Supporting data for "The draft genome assembly of Rhododendron delavayi Franch. var. delavayi"

Dataset type: Genomic, Transcriptomic
Data released on August 01, 2017

Cai Y; Gao Q; Li S; Li S; Ma L; Ma Y; Peng L; Song J; Wang J; Xie W; Xu P; Yan H; Zhang C; Zhang L; Zou L (2017): Supporting data for "The draft genome assembly of Rhododendron delavayi Franch. var. delavayi" GigaScience Database. http://dx.doi.org/10.5524/100331

DOI10.5524/100331

Rhododendron delavayi Franch is globally famous as an ornamental. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at molecular level, which hinders understanding of the nature of its wide adaptability to different environments, evolution, speciation and synthesis of secondary metabolites. Here, we report genome assembly and gene annotation of R. delavayi var. delavayi (the second genome sequenced in the Ericaceae), which will facilitate the study of the family, and have further applications in genome-assisted cultivar breeding.
The final size of the assembled R. delavayi var. delavayi genome (695.09 Mb) was close to the 697.94 Mb estimated by k-mer analysis. A total of 336.83 gigabases (Gb) of raw Illumina HiSeq 2000 reads were generated from nine libraries (with insert sizes ranging from 170bp to 40kb), achieving a raw sequencing depth of 482.61×. After quality filtering, 246.06 Gb of clean reads were obtained, giving 352.55× coverage depth. Assembly using Platanus gave a total scaffold length of 695.09 Mb, with a contig N50 of 61.8 kb and a scaffold N50 of 637.83kb. Gene prediction resulted in the annotation of 32,938 protein-coding genes. The genome completeness was evaluated by CEGMA and BUSCO, and reached 95.97 % and 92.8 % respectively. The Gene annotation completeness was also evaluated by CEGMA and BUSCO, and reached 97.01 % and 87.4 %. Genome annotation revealed that 51.77 % of the R. delavayi genome is composed of transposable elements, and 37.48 % of long terminal repeat elements (LTRs).
The de novo assembled genome of R. delavayi var. delavayi (hereinafter referred to as R. delavayi) is the second genomic resource of the family Ericaceae, and will provide a valuable resource for research on future comparative genomic studies in Rhododendron species. The availability of the R. delavayi genome sequence will hopefully provide a tool for scientists to tackle open questions regarding molecular mechanisms underlying environmental interactions in the genus Rhododendron, more accurately understand the evolutionary processes and systematics of the genus, facilitate the identification of genes encoding pharmaceutically important compounds, and accelerate molecular breeding to release elite varieties.

Additional details

Read the peer-reviewed publication(s):

Zhang, L., Xu, P., Cai, Y., Ma, L., Li, S., Li, S., … Wang, J. (2017). The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. GigaScience, 6(10), 1–11. doi:10.1093/gigascience/gix076

Additional information:

https://github.com/gigascience/rabbit-genome-assembler

Accessions (data included in GigaDB):

BioProject: PRJNA361437
BioProject: PRJNA358123





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
leaf321363Rhododendron delavayi Description:DNA extracted from leaf tissue of 50yr...
Analyte type:DNA
Age:50 years
...
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WHYR14030800_B_l1321363Rhododendron delavayi Description:Mixed total RNA extracted from five di...
Analyte type:RNA
Age:50 years
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherUNKNOWN0.15 KB2017-07-25
Tabular DataCSV0.21 KB2017-07-25
Phylogenetic treeUNKNOWN0.27 KB2017-07-25
Phylogenetic treeUNKNOWN0.31 KB2017-07-25
Phylogenetic treeUNKNOWN0.37 KB2017-07-25
Phylogenetic treeUNKNOWN0.42 KB2017-07-25
Phylogenetic treeUNKNOWN0.62 KB2017-07-25
Tabular DataCSV0.64 KB2017-07-25
Tabular DataCSV0.82 KB2017-07-25
Tabular DataCSV0.87 KB2017-07-25
Displaying 1-10 of 41 File(s).
Funding body Awardee Award ID Comments
Yunnan Provincial Science and Technology Department JH Wang 2016HA005 Science and Technology Talents Training Program
Yunnan Provincial Science and Technology Department JH Wang 2014HE002 Innovative Talents Promotion Program
Yunnan Provincial Science and Technology Department L Zhang 2016FB058 Applied Basic Research Project of Yunnan Province
National Natural Science Foundation of China WJ Xie 31560225 District science fund project
National Natural Science Foundation of China YF Cai 31460217 District science fund project
Date Action
August 1, 2017 Dataset publish
August 14, 2017 External Link added : https://github.com/gigascience/rabbit-genome-assembler
August 14, 2017 External Link added : https://github.com/gigascience/rabbit-genome-assembler
August 14, 2017 External Link removed : https://github.com/gigascience/rabbit-genome-assembler
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix076