Genome survey sequencing and identification of genomic SSR markers for Rhododendron micranthum.

Xiao-Jun Zhou,Xiao-Yu Lu,Shan-Shan Sun,Yan-Wei Cheng,Meng-Xue Liu,Hui-Yuan Ya

doi:10.1042/bsr20200988

Abstract

Rhododendron micranthum is an evergreen shrub species widely distributed in China that has high ornamental and medicinal value. However, there is a lack of molecular and genomic data for this plant, which severely restricts the development of its relevant research. The objective of the present study was to conduct a first genomic survey of R. micranthum and determine its whole-genome sequencing scheme. Next-generation sequencing (Illumina Hi-Seq Xten) was used to measure the genome size of R. micranthum, K-mer analysis were employed to investigate its genomic profile. Finally, we conducted bioinformatics methods to performed SSR (simple sequence repeat) prediction based on the genomic data. The genome size of R. micranthum was estimated to be 554.22 Mb. The heterozygosity ratio was 0.93%, and the sequence repeat ratio was calculated to be 49.17%. The clean reads of R. micranthum were assembled into 2281551 scaffolds with a N50 value of 916 bp. A total of 479724 SSR molecular markers were identified in the R. micranthum genome, and 871656 pairs of primers designed for application. Among of them, 100 primer pairs were validated, and 71 primer pairs were successfully amplified. In summary, the R. micranthum genome is complex with high heterozygosity and low repeated sequences. In future whole-genome research in R. micranthum, higher-depth ‘2+3’ (Illumina+PacBio) sequencing may yield better assembly results.

Highlights

Rhododendron micranthum is an evergreen shrub species belonging to the genus Rhododendron in the family Ericaceae (Figure 1)
The results demonstrated that the sequencing quality was good
The results showed that there was no contamination from other species

Summary

Introduction

Rhododendron micranthum is an evergreen shrub species belonging to the genus Rhododendron in the family Ericaceae (Figure 1). It is widely distributed in China, growing on the hillsides of thickets, valleys, cliffs, and rocks at an elevation of 1000–3000 m [1]. To explore the genes related to the effective components and excellent agronomic characters of plants, and analyze the metabolic pathway and regulatory mechanism from the genome-wide level can lay the foundation for the improvement of medicinal plant varieties and the protection of genetic resources [7]. Illumina Hi-Seq technology combined with K-mer analysis was used to evaluate the genome size and characteristics of R. micranthum, which laid the foundation for fine sequencing of the whole genome and will be conducive to further understand its pharmacological effect.

Objectives

Methods

Results

Conclusion