The draft genome assembly of Rhododendron delavayi Franch. var. delavayi

doi:10.1093/gigascience/gix076

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	The draft genome assembly of Rhododendron delavayi Franch. var. delavayi
	Zhang, Lu 1,2; Xu, Pengwei 3; Cai, Yanfei 1,2; Ma, Lulin 1,2; Li, Shifeng 1,2; Li, Shufa 1,2; Xie, Weijia 1,2; Song, Jie 1,2; Peng, Lvchun 1,2; Yan, Huijun 1,2
刊名	GIGASCIENCE
	2017-08-23
卷号	6 期号:10 页码:1
关键词	Rhododendron Delavayi Genomics Genome Assembly Annotation
ISSN号	2047-217X
DOI	10.1093/gigascience/gix076
英文摘要	Rhododendron delavayi Franch. is globally famous as an ornamental plant. Its distribution in southwest China covers several different habitats and environments. However, not much research had been conducted on Rhododendron spp. at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to different environments. Here, we report the 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. The genome assembly will 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 9 libraries (with insert sizes ranging from 170 bp to 40 kb), achieving a raw sequencing depth of x482.6. After quality filtering, 246.06 Gb of clean reads were obtained, giving x352.55 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 637.83 kb. 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%, respectively. 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.
学科主题	Multidisciplinary Sciences
语种	英语
WOS记录号	WOS:000412397500001
内容类型	期刊论文
源URL	[http://ir.kib.ac.cn/handle/151853/54875]
专题	昆明植物研究所_中国西南野生生物种质资源库
作者单位	1.Yunnan Acad Agr Sci, Natl Engn Res Ctr Ornamental Hort, Flower Res Inst, 2238 Beijing Rd, Kunming 650205, Yunnan, Peoples R China 2.Key Lab Yunnan Flower Breeding, 2238 Beijing Rd, Kunming 650205, Yunnan, Peoples R China 3.BGI Shenzhen, BGI Pk,21 Hongan 3rd St, Shenzhen 518083, Peoples R China 4.Chinese Acad Sci, Kunming Inst Bot, Kunming Bot Garden, 132 Lanhei Rd, Kunming 650201, Yunnan, Peoples R China 5.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, 132 Lanhei Rd, Kunming 650201, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Lu,Xu, Pengwei,Cai, Yanfei,et al. The draft genome assembly of Rhododendron delavayi Franch. var. delavayi[J]. GIGASCIENCE,2017,6(10):1.
APA	Zhang, Lu.,Xu, Pengwei.,Cai, Yanfei.,Ma, Lulin.,Li, Shifeng.,...&Wang, Jihua.(2017).The draft genome assembly of Rhododendron delavayi Franch. var. delavayi.GIGASCIENCE,6(10),1.
MLA	Zhang, Lu,et al."The draft genome assembly of Rhododendron delavayi Franch. var. delavayi".GIGASCIENCE 6.10(2017):1.