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The draft genome assembly of Rhododendron delavayi Franch. var. delavayi
Zhang, Lu1,2; Xu, Pengwei3; Cai, Yanfei1,2; Ma, Lulin1,2; Li, Shifeng1,2; Li, Shufa1,2; Xie, Weijia1,2; Song, Jie1,2; Peng, Lvchun1,2; Yan, Huijun1,2; Zou, Ling1,2; Ma, Yongpeng4; Zhang, Chengjun5; Gao, Qiang; Wang, Jihua1,2
2017-08-23
发表期刊GIGASCIENCE
ISSN2047-217X
卷号6期号:10页码:1
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.
关键词Rhododendron Delavayi Genomics Genome Assembly Annotation
收录类别SCI
语种英语
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文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/54875
专题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
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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.
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