Genome Survey Sequencing for the Characterization of the Genetic Background of Rosa roxburghii Tratt and Leaf Ascorbate Metabolism Genes

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.

Draft genome sequence of an inbred line ofChenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties

“…at around ∼200) is of interest, because it may contain k-mers related to allotetraploidy. However, the k-mer curve distribution for the ‘diploid’ genome is known to show a smaller peak at the doubled multiplicity of the homo-peak 67 . Thus, the smaller peak at around ∼200 in our k-mer analysis may relate to genomic sequences caused by both allotetraploidy and other simple duplications.…”

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

“…In addition, the K-mer method has been successfully applied for the estimation of genome size using NGS reads without prior knowledge of the genome size [32]. This approach has been used to analyze a number of plant genomes such as in switchgrass ( Panicum virgatum L.) [33], Chinese bayberry ( Myrica rubra Sieb.…”

“…et Zucc.) [26], Chinese jujube ( Ziziphus jujuba Mill) [34], and Rosa roxburghii Tratt [32]. Here, for the first time, we report a genome survey of P. vera using whole genome shotgun sequencing.…”

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

“…To measure the sequencing bias of S. argus, the guanine plus cytosine (GC) content and average sequencing depth were counted. The GC content is strictly controlled and moderately balanced Animals 2019, 9, 1117 4 of 11 across the genome [33,34]. Ten kb non-overlapping sliding windows were used along the assembled sequences to calculate the GC average sequencing depth.…”