Abstract
Rosa roxburghii Tratt is an important commercial horticultural crop in China that is recognized for its nutritional and medicinal values. In spite of the economic significance, genomic information on this rose species is currently unavailable. In the present research, a genome survey of R. roxburghii was carried out using next-generation sequencing (NGS) technologies. Total 30.29 Gb sequence data was obtained by HiSeq 2500 sequencing and an estimated genome size of R. roxburghii was 480.97 Mb, in which the guanine plus cytosine (GC) content was calculated to be 38.63%. All of these reads were technically assembled and a total of 627,554 contigs with a N50 length of 1.484 kb and furthermore 335,902 scaffolds with a total length of 409.36 Mb were obtained. Transposable elements (TE) sequence of 90.84 Mb which comprised 29.20% of the genome, and 167,859 simple sequence repeats (SSRs) were identified from the scaffolds. Among these, the mono-(66.30%), di-(25.67%), and tri-(6.64%) nucleotide repeats contributed to nearly 99% of the SSRs, and sequence motifs AG/CT (28.81%) and GAA/TTC (14.76%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. Genome analysis predicted a total of 22,721 genes which have an average length of 2311.52 bp, an average exon length of 228.15 bp, and average intron length of 401.18 bp. Eleven genes putatively involved in ascorbate metabolism were identified and its expression in R. roxburghii leaves was validated by quantitative real-time PCR (qRT-PCR). This is the first report of genome-wide characterization of this rose species.
Highlights
About 100–250 species have been described in the genus Rosa, many of which are recognized for their ornamental horticultural use [1]
After the sequence data was filtering and correction, a total of 30.29 Gb clean reads were generated from the small-insert (220 bp) library, with 95.14% Q20 bases, about 62.99× coverage (Table 1), much greater than 30× coverage, which was required for successful assembly
Such approach has been utilized in the analysis of the genomes of Gracilariopsis lemaneiformis [45], Cucumis sativus [47], and Myrica rubra [48]
Summary
About 100–250 species have been described in the genus Rosa, many of which are recognized for their ornamental horticultural use [1]. Rosa roxburghii Tratt (2n = 2x = 14), which is widely distributed in Southwest China, has PLOS ONE | DOI:10.1371/journal.pone.0147530. Genome Survey Sequencing for Rosa roxburghii and Ascorbate Metabolism. Gzst.gov.cn; and the natural science foundation in Guizhou Province, P. The funders provided support in the form of salaries for authors [AMH and LM], but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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