Sequencing analysis of transcriptome of Vitis amurensis during different periods of coloration

Abstract:【Objective】Vitis amurensis is one of the most cold-resistant Vitis plants, therefore, it is a value⁃able resourse for cold-resistant breeding in Vitis plants. The fruits of V. amurensis are rich in proteins, carbohydrates, minerals and many kinds of vitamins. The fruit color is an important character influencingfruit quality. The fruit color is mainly decided by content and composition of anthocyanins. The biosynthe⁃sis process of anthocyanin is very complicated is influenced by many genes. Therefore the study of the expression of related genes during color transformation of the fruits is of great value.【Methods】The fruitskins of V. amurensis were collected during different ripening stages, before color-changed, 50% colorchangedand full ripe stage as experimental materials and high-throughput sequencing technology Illumi⁃naHiSeq was used to conduct sequencing. After data filtering, we got Clean Data and run sequence comparison with designated reference genome to obtain Mapped Data and then we did transcriptome analysis.【Results】Through transcriptome sequencing and analysis of the related genes in the skins toward threedifferent ripening stages, clean reads were obtained and they were 20 157 930 for before color-changed,16 197 432 for 50% color-changed and 16 410 824 for full ripe stage, the GC contents were 48.41%、48.04% and 49.54% respectively. The Q30 contents of three different maturation periods were or wereover 94.73%, indicating the high quality of transcriptome sequencing and the high accuracy of the data.TopHat2 was adopted to do sequence alignment between Clean Reads and reference genome to obtain theposition information of maturation related genes on reference genome or genes. The sequence alignment efficiency between reads of three different maturation periods and reference genome was from 60.57% to 67.77%, for unique alignment position the sequence alignment efficiency between reads of all samplesand reference genome was over 58.99%. Most sequences that aligned with reference genome were on ex⁃ons and the efficiency was over 96.3%. For these aligned genes in three samples, we used FPKM methodto get the standard measure. According to FPKM value, we calculated differential expression multiple ofthe genes in different samples. When the FDR value became smaller, the differential expression multiplebecame bigger, implying that the differential expression was much more remarkable. We ran differentialexpression screening under the situation of FDR≤0.001 and differential expression multiple no less than2 times (log2Ratio≥1). The gene differential expressions of before color-changed samples were analyzedand compared with those of 50% color-changed samples and full ripe stage samples. The results showedthat between before color-changed samples and 50% color-changed samples, the number of all differen⁃tial expression genes were 2 986, the number of up-regulated expression genes were 1 849, the number ofdown-regulated expression genes were 1 137. Up-regulated expression genes were more than down-regulated expression genes. Between before color-changed samples and full ripe stage samples, the number ofall differential expression genes were 3 841, the number of up-regulated expression genes were 1 567, thenumber of down-regulated expression genes were 2 274. Up-regulated expression genes were much lessthan down-regulated expression genes. The number of COG function annotation were 1 305 and 1 602 respectively.【Conclusion】This study enriched V. amurensis transcriptome database through transcriptomesequencing of the fruit skins during three different maturation periods. This study clarified the changes ofripening related genes in V. amurensis transformation process and provided a good basis for further exploration for essential expression genes in the process of the husk transformation.