GSE122014
Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes
Rosa roxburghii Tratt belongs to the Rosaceae family, and the fruit is flavorful, economic, and high nutritious, providing health benefits. MYB proteins play key roles in R. roxburghii' development and fruit quality. However, the available genomic and transcriptomic information are extremely deficient. Here, a normalized cDNA library was constructed using five tissues, stem, leaf, flower, young fruit, and mature fruit, with three repetitions, and sequenced using the Illumina HiSeq 3000 platform. De novo assembly was performed, and 470.66 million clean reads were obtained. In total, 63,727 unigenes, with an average GC content of 42.08%, were determined and 59,358 were annotated. In addition, 9,354 unigenes were assigned the Gene Ontology category, and 20,202 unigenes were assigned to 25 Eukaryotic Ortholog Groups. Additionally, 19,507 unigenes were classified into 140 pathways of the Kyoto Encyclopedia of Genes and Genomes database. Using the transcriptome, 163 unigenes associated with MYB were detected. Among these genes, there were total 75 genes which strikingly expressed in various tissues, including 10 R1 MYB, 42 R2R3 MYB, 1 R1R2R3 MYB, 3 MYB and 19 atypical MYB-like proteins. The expression levels of 12 MYB genes randomly selected for qRT-PCR analysis were consistent with the RNA-seq results. A total of 37,545 microsatellites were detected, with an average EST-SSR frequency of 0.59 (37,545/63,727). This transcriptome data will be valuable for identifying genes of interest and studying their expression and evolution. Overall design: Five tissues, including stem, leaf, flower, young fruit (50 days after flowering) and mature fruit (120 days after flowering) from wild Rosa roxburghii Tratt were collected and immediately stored in liquid nitrogen for RNA extraction. Three samples with three replicates were sequenced via Illumina HiSeqTM 3000.