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. 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.

缫丝花（Rosa roxburghii Tratt）隶属于蔷薇科（Rosaceae），其果实风味佳美、经济价值显著且营养丰富，兼具保健益处。MYB蛋白在缫丝花的生长发育与果实品质调控中发挥关键作用，但当前已有的缫丝花基因组与转录组信息极度匮乏。本研究选取茎、叶、花、幼果、成熟果5种组织作为材料，设置3次生物学重复，构建归一化cDNA文库，并采用Illumina HiSeq 3000平台进行测序。经de novo从头组装后，共获得4.7066亿条clean reads（干净读数）。最终注释得到63727条unigene（非重复基因），平均GC含量为42.08%，其中59358条获得功能注释。另有9354条unigene被归入基因本体论（Gene Ontology, GO）分类体系，20202条unigene被注释至25个真核生物直系同源簇（Eukaryotic Ortholog Groups, KOG）数据库。此外，19507条unigene被富集到京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）的140条代谢通路中。基于该转录组数据，共检测到163个与MYB相关的unigene。其中，在不同组织中显著表达的共有75个，包括10个R1型MYB、42个R2R3型MYB、1个R1R2R3型MYB、3个常规MYB以及19个非典型MYB类蛋白。随机选取12个MYB基因进行qRT-PCR（实时定量荧光PCR）验证，其表达模式与RNA-seq测序结果高度一致。本研究共检测到37545个微卫星（microsatellite）位点，平均EST-SSR（表达序列标签-简单序列重复）频率为0.59（37545/63727）。该转录组数据将为目标功能基因的挖掘以及基因表达与进化研究提供重要支撑。本研究采集野生缫丝花（Rosa roxburghii Tratt）的茎、叶、花、花后50天幼果及花后120天成熟果共5种组织，采集后立即置于液氮中保存以用于RNA提取。设置3次生物学重复，通过Illumina HiSeq™ 3000平台完成测序。