11Impatiens downy mildew is a highly destructive disease of Impatiens walleriana, and economically 12 important bedding ornamental crop. This disease is caused by a recently emerged pathogen 13 Plasmopara obducens. Since both the host and pathogen are relatively less studied, there are only a 14 few genomic resources available for both I. walleriana and P. obducens. In this study, we have 15 analyzed transcriptional changes in I. walleriana in response to P. obducens infection during 16 different stages of disease development. Our main goal was to identify candidate genes that may be 17 involved in I. walleriana susceptibility to P. obducens. Since the genome of I. walleriana is not 18 available publicly, we constructed and optimized a de novo transcriptome assembly consisting of 19 73,022 transcripts. Differential expression analysis based on this optimized de novo transcriptome 20 assembly revealed 3,000 to 4,500 differentially expressed transcripts (DETs) at 0 hr, 12 hr, 48 hr, 21 120 hr, and 240 hr time points after infection. Functional annotation of these DETs revealed that 22 numerous plant stress responsive genes are activated and deactivated throughout the infection cycle. 23Genes in the calcium signaling pathways, receptor-like kinases (RLKs) including 10 disease 24 resistance associated RLK transcripts, powdery mildew resistance genes (MLO), and many other 25 plant stress related genes were predominantly differentially expressed in I. walleriana in response to 26 P. obducens. Analyses reported here provides molecular insights into the disease susceptibility 27 mechanism of the Impatiens downy mildew, and lays out a strong foundation for future studies aimed 28 at improving downy mildew resistance in I. walleriana. 29 CLC Genomics workbench which resulted in 91,164 contigs with an N50 value of 1650 bp (50% of 126 transcripts greater than or equal to 1650bp long) ( Table 1). These contigs were fed into the cd-hit-est 127 cluster analysis based on similarity, producing 89,987 contigs. Filtering through BLASTx to remove 128 P. obducens contigs resulted in 73,022 contigs. This optimized assembly was used as a reference and 129 reads from all the samples were mapped back to this optimized pooled reference assembly and a read 130 count table was generated. Differential expression analysis was done on this table using DEseq2. 131Only those transcripts were considered as differentially expressed genes that have log2fold > |2| and 132 padj < 0.001. According to this criterion, the number of DETs between infected and control samples

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