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

Lu Zhang,Shufa Li,Qiang Gao,Weijia Xie,Jie Song,Ling Zou,Huijun Yan,Chengjun Zhang,Pengwei Xu,Jihua Wang,Shifeng Li,Yongpeng Ma,Lvchun Peng,Yanfei Cai,Lulin Ma

doi:10.1093/gigascience/gix076

Abstract

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 ×482.6. 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 637.83 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.

Highlights

Rhododendron L. is a genus in the family Ericaceae
We report the genome assembly and gene annotation of R. delavayi var. delavayi, which will facilitate the study of the family
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)

Summary

Background

Rhododendron L. is a genus in the family Ericaceae. It is 1 of the largest and most diverse genera in the family and is distributed predominantly throughout the Northern hemisphere, and reaches into the Asian tropics. We combined homology-based, de novo, and transcript alignment methods to predict protein-coding genes in the R. delavayi genome. For genes with alternative splicing variants, the longest transcript was selected to represent the gene We aligned these homologous protein sequences to the R. delavayi genome using TBLASTN As a result of these steps, a total of 32 938 non-redundant genes were predicted in the R. delavayi genome (Table 8). The BUSCO evaluation demonstrated that 87.4% and 6.4% of 1440 expected plant genes were identified as completeness and fragment, respectively (Table 9) Both assessment methods suggested that for the R. delavayi genome our current pipeline performed better than the Maker-P pipeline. OrthoMCL (OrthoMCL DB: Ortholog Groups of Protein Sequences, RRID:SCR 007839) [63] was used with default parameters to identify gene family membership based on overall gene similarity combined with Markov Chain Clustering (MCL). When using previously published calibration times (split of Oryza sativa and Arabidopsis thaliana fixed as 130∼200 Mya) [67], the divergence time between R. delavayi and Actinidia chinensis was estimated to be in the range of 56.1–120.8 million years ago (Fig. 5)

Conclusion

Findings

Availability of supporting data