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

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.

Genome Survey Sequencing and Genetic Background Characterization of Ilex chinensis Sims (Aquifoliaceae) Based on Next-Generation Sequencing

“…Though flow cytometry has become a well-recognized technique for predicting genome size before plant genome sequencing due to its low material requirements, short analysis time, and high accuracy, there is still some technical error that will hinder exact quantification [ 21 , 31 ]. With the rapid development of NGS technology, k-mer analysis, which is based on whole-genome sequencing reads, has become an effective and economical method to obtain genome sizes of non-model or emerging species [ 32 ], which has been proven successful for many plant species, such as Metroxylon sagu Rottboll [ 19 ], Rhododendron micranthum [ 14 ], Pistacia vera [ 15 ], and Akebia trifoliata [ 33 ]. Therefore, using both methods to measure genome size can improve the reliability of the results.…”

“…The genome contains all the information controlling biological characters and ultimately determining the transmission of genetic material [ 12 , 13 , 14 ]. Genome sequencing has been an important step to decipher the genetic structure and accelerate genetic improvements in traits of interest in eukaryotes [ 15 , 16 ].…”

“…Genome sequencing has been an important step to decipher the genetic structure and accelerate genetic improvements in traits of interest in eukaryotes [ 15 , 16 ]. Exploring the genes related to the effective components and excellent agronomic characters of plants, and analyzing the metabolic pathways and regulatory mechanisms from the genome-wide level, can lay the foundation for the improvement of medicinal plant varieties and the protection of genetic resources [ 14 , 17 ]. Owing to recent advances in DNA sequencing techniques, draft genomes have been assembled for many plant species as resources for genomic and genetic research efforts [ 18 , 19 , 20 ].…”

Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets of Mikania cordata

“…As plant genomes are generally giant, genome survey by next-generation sequencing offers an affordable way to characterize the genome before conducting costly long-read genome sequencing [46]. Similar strategies have been applied to Betula platyphylla [47], Pistacia vera [48], and Rhododendron micranthum [49]. Genome survey sequencing has been shown that it enables to provide a preliminary understanding of such genomic characteristics as genome size, heterozygosity, and repetitive rate.…”

Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers

“…For species without reference sequenced genomes, developing SSR molecular markers based on a genomic survey is considered as an efficient strategy (Zhou et al, 2013). SSR markers are particularly useful in plant genetics and breeding because of their reproducibility, multiple alleles, codominant inheritance, relative abundance, and good genome coverage (Chen et al, 2017, Zhou et al, 2020. A genome survey includes information on the structure of an organism's genome, such as genome size, heterozygosity ratio, GC content, and repeated sequences.…”