Comparative transcriptome analysis of Powdery mildew Resistance between two Melon (Cucumis melo L) with Different Thickness Peel

Abstract

8Melon (Cucumis melo L.) is wildly planted in the world and China is a major producer of muskmelon. 9Powdery mildew is one of the most common fungal diseases in the world and this disease frequently 1 7 materials were identified. All the DEGs were annotated with several database and the transcript factors 1 8 (TFs) that related to disease resistance such as MYB, ERF and WRKY among the DEGs were also 1 9identified. This research could not only provide the information about understanding the mechanism of 2 0 powdery mildew infection but also help researchers breed the varieties with powdery mildew 2 1 resistance. 2Key words Melon (Cucumis melo L.). powdery mildew. Transcript sequencing. Candidate genes. 2 3 Transcript factors 2 4 4 1 were selected. After inoculating the powdery mildew, both materials were used to do the RNA-Seq. In 4 2 total, two RNA-seq libraries were constructed and sequenced separately; generating 47,462,015 mean 4 3 clean reads with mean GC content of 49.32 and mean Q30 of 85.89%. Among all the genes in the 4 4 genome of melon, 13828 genes were expressed in the material G and 13944 genes were expressed in 4 5 the material S (RPKM>1). Through multiple comparisons between libraries, 769 DEGs were identified, 4 6 of which the 726 were up-regulated DEGs and 43 were down-regulated ones. Based on the annotation 4 7 information in gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG) and eukaryotic 4 8 orthologous groups (KOG) database, most of the DEGs were related to "nucleus", "chloroplast" and 4 9 7 7 paired-end (PE) raw reads (Personalbio, Shanghai, China). Raw data (raw reads) in FASTQ format 7 8were processed used the trimmomatic software (Bolger et al., 2014). In this step, clean data were 7 9 obtained as follows: the first, removing reads with ≥ 10% unidentified nucleotides (N); the second, 0Removing reads with > 50% bases having phred quality < 5; the third, Removing reads with > 10 nt 8 1 aligned to the adapter, allowing ≤ 10% mismatches; the fourth, removing putative PCR duplicates 8 2 generated by PCR amplification in the library construction process. After trimmomatic, the quality of the clean data was checked by the software FASTQC 3 0 8 3 0 9

Characterization, identification and expression profiling of genome-wide R-genes in melon and their putative roles in bacterial fruit blotch resistance

“…Several comparative transcriptomic studies have been reported in melon [75][76][77], but few studies have focused exclusively on expression profiling of R-genes against phytopathogenic agents in melon. For example, RNA-seq assessment of the changes in transcript levels at different time points in Phytophthora capsici-inoculated tissues of resistant and susceptible melon genotypes provided a basis for identifying candidate resistant genes [78].…”

Characterization, Identification and Expression Profiling of Genome-Wide R-Genes in Melon and Their Putative Roles in Bacterial Fruit Blotch Resistance

“…5) in the resistant vs. the susceptible accession, indicates their potential involvement in BFB resistance in melon. Several comparative transcriptomic studies have been reported in melon [71][72][73], but few studies have focused exclusively on expression profiling of R-genes against phytopathogenic agents in melon. A study of the MLO (mildew resistance locus o) gene family in melon revealed candidate genes that might play roles in susceptibility to powdery mildew [74].…”

Characterization, Identification and Expression Profiling of Genome-Wide R-Genes in Melon and Their Putative Roles in Bacterial Fruit Blotch Resistance

“…Several comparative transcriptomic studies have been reported in melon [75][76][77], but few studies have focused exclusively on expression pro ling of R-genes against phytopathogenic agents in melon. For example, RNA-seq assessment of the changes in transcript levels at different time points in Phytophthora capsici-inoculated tissues of resistant and susceptible melon genotypes provided a basis for identifying candidate resistant genes [78].…”