Analysis Of Genes Differentially Expressed In Watermelon Rind Color Based On RNA-seq

Watermelon(Citrullus lanatus), belongs to the Cucurbitaceae Citrullus trailing annual herb, native to Africa. Watermelon is one of the world’s most important fruit. Improvement of living standards, people are demanding higher quality of watermelon. Watermelon quality including appearance, taste and nutrition. Watermelon rind color is watermelon fruit germplasm evaluation and improvement of the quality of important economic traits in modern society people consume watermelon important reference product features,therefore, high-quality, high yield and appearance of the beautiful new varieties of watermelon watermelon varieties conducive structure enrich and improve the quality of goods, but also has a great impact on the marketability of watermelon.The test material from watermelon yellow mutant Green Paper wild-type material of the fruits fruit set, enlargement and maturity of six samples extracted from skin color genes related to the use of the biological function of transcriptome gene sequencing research.Transcription based sequencing data, we evaluated the transcriptome libraries, analysis of new genes differentially expressed gene analysis conclusion of each period are as follows:(1) After electrophoresis, quantitative detection of trace UV spectrophotometer to obtain a total RNA watermelon rind in line with building a database standard. Use Qubit2.0,Aglient2100 concentration library and insert size were detected by qPCR method for the effective concentration of the library for accurate quantification, detection and quantification determine library quality standards. After six samples transcriptome sequencing completed remove the linker sequence and low quality Reads won 34.27 Gb Clean Data, and each sample Clean Data are up to 4.67 Gb, Q30 base ratio were 86.85%and above, transcriptome sequencing data quality better. The Clean Reads each sample and the reference genome sequence enacted by contrast, the ratio of the efficiency of 83.75% to88.11% range, the transcriptome data to meet the needs of data analysis and post-analysis of the reliability of the results is ideal.(2) Based on the reference genome sequence alignment results were predicted alternative splicing analysis of 10,550 genes structure has been optimized gene structure analysis, 958 genes were found, of which 678 have been functional annotation.(3)During the same period the gene expression differences between different colors COG functional classification, general function prediction, transcription, replication,recombination and repair, transport and metabolism of amino acid transport andmetabolism of carbohydrates genes large number of these five functions, includingnuclear structure,cell motility, extracellular structural differences in the three periodincontrast no corresponding genes.GO annotation, the annotation to the main part ofthe cellular components of the extracellular matrix composition, extracellular domainportion, the outerzone, the extracellular matrix, the activity of transcription factor binding to a nucleic acid molecule in the functional part, the electron carrier activity, biological processes section development, more biological processes, extracellular matrix protein binding transcription factor activity and other functions. KEGG annotations, comments focused on the plant hormone signal transduction, styrene anabolic section, part of photosynthesis, metabolism,metabolic part of starch and sucrose metabolism of these environmental information processing pathway.(4)Same period differentially expressed genes in different colors COG functional categories, the differences are mainly common gene function prediction, transcription,replication, recombination and repair, carbohydrate transport and metabolism, signal transduction mechanisms, such as expression, and nuclear structure, cell in COG functional classification no corresponding gene motion, extracellular structure.GO annotation, the performance in several main components and cell fraction, molecularfunctionof the protein tags and transcriptional factor activity in cell extracellular matrix components, biological processes and cell killing more biological processes.KEGG annotations, comments focused on plant hormone signal transduction in environmental information processing section, part of the metabolism of starch and sucrose metabolism, photosynthesis metabolism part,styrene anabolic section, geneticinformation processing section ribose body, metabolism portion pheny alanine metabolism.(5)Based TopHat2 alignment score greater than or equal to 50; the single basemismatch sites at intervals of not less than 5 bases; variant recognition quality value is not less than 20; sequencing depth, of not less than 5x and not higher than the SNP screening 100 x conditions.T01, T02, T03, T04, T05, T06, respectively, won the 13853,15617, 14163, 12155, 15108, 18297 and reliable SNP loci.SNP analysis of six samples transcriptome there in the 13852 T01 reliable SNP loci, there are 15617 reliable SNP loci in T02, there are 14163 reliable SNP loci in T03, there are 12,155 in the T04 a reliable SNP loci, there are 15108 reliable SNP loci in T05, there are 18279 reliable SNP loci in the T06.