Comparative Analysis of Impatiens Leaf Transcriptomes Reveal Candidate Genes for Resistance to Downy Mildew Caused by Plasmopara obducens

Bhattarai, Krishna; Wang, Weining; Cao, Zhe; Deng, Zhanao

doi:10.3390/ijms19072057

Cited by 14 publications

(14 citation statements)

References 53 publications

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“…In this study, the transcriptomes of leaf, flower, early-, mature-and postbreaker stage capsules of I. balsamina were generated and analysed. The transcriptome sequencing outputs and functional annotation results obtained (total of 94,659 unigenes obtained, 73.96% unigenes successfully annotated) are comparable to the recently reported transcriptome results of I. walleriana and I. hawheri 75 . In the I. balsamina transcriptome datasets, 26.04% of the unigenes did not possess significant similarity to sequences of other species, which is close to the percentage of 'orphans' or 'taxonomically restricted genes' (TRGs) in a given species 76 .…”

Section: Discussionsupporting

confidence: 85%

Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L.

Foong

Chai

et al. 2020

Sci Rep

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Impatiens balsamina L. is a tropical ornamental and traditional medicinal herb rich in natural compounds, especially 2-methoxy-1,4-naphthoquinone (MNQ) which is a bioactive compound with tested anticancer activities. Characterization of key genes involved in the shikimate and 1,4-dihydroxy-2-naphthoate (DHNA) pathways responsible for MNQ biosynthesis and their expression profiles in I. balsamina will facilitate adoption of genetic/metabolic engineering or synthetic biology approaches to further increase production for pre-commercialization. In this study, HPLC analysis showed that MNQ was present in significantly higher quantities in the capsule pericarps throughout three developmental stages (early-, mature- and postbreaker stages) whilst its immediate precursor, 2-hydroxy-1,4-naphthoquinone (lawsone) was mainly detected in mature leaves. Transcriptomes of I. balsamina derived from leaf, flower, and three capsule developmental stages were generated, totalling 59.643 Gb of raw reads that were assembled into 94,659 unigenes (595,828 transcripts). A total of 73.96% of unigenes were functionally annotated against seven public databases and 50,786 differentially expressed genes (DEGs) were identified. Expression profiles of 20 selected genes from four major secondary metabolism pathways were studied and validated using qRT-PCR method. Majority of the DHNA pathway genes were found to be significantly upregulated in early stage capsule compared to flower and leaf, suggesting tissue-specific synthesis of MNQ. Correlation analysis identified 11 candidate unigenes related to three enzymes (NADH-quinone oxidoreductase, UDP-glycosyltransferases and S-adenosylmethionine-dependent O-methyltransferase) important in the final steps of MNQ biosynthesis based on genes expression profiles consistent with MNQ content. This study provides the first molecular insight into the dynamics of MNQ biosynthesis and accumulation across different tissues of I. balsamina and serves as a valuable resource to facilitate further manipulation to increase production of MNQ.

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Section: Discussionsupporting

confidence: 85%

Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L.

Foong

Chai

et al. 2020

Sci Rep

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“…Polymorphic SSR marker candidates were discovered 43 and will hopefully serve as an exciting new source as the ongoing molecular studies of this pathogen 44 continues. While there is much to learn about the genetics of P. obducens, recent research available 45 regarding I. walleriana was published identifying disease resistance genes as well as SSRs and SNPs 46 sites which may aid in breeding impatiens for resistance to IDM (Bhattarai et al 2018). There is 47 strong consumer demand for IDM-resistant I. walleriana cultivars.…”

Section: Introduction 30mentioning

confidence: 99%

Transcriptional profiling of Impatiens walleriana genes through different stages of downy mildew infection reveals novel genes involved in disease susceptibility

Suarez

2019

Preprint

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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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“…The recent advances in RNA sequencing have enabled unprecedented depth and accuracy for transcriptome analyses. Using this powerful approach, differential gene expression associated with resistant and susceptible crop genotypes has been examined in various pathosystems to understand the molecular basis of plant defense responses 19,[44][45][46][47]48 . In this study, we applied this tool along with the newly available spinach and P. effusa genome resources, to analyze gene expression during incompatible and compatible spinach-P. effusa interactions.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew

Kandel

Hulse‐Kemp

Stoffel

et al. 2020

Sci Rep

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Downy mildew of spinach is caused by the obligate oomycete pathogen, Peronospora effusa. the disease causes significant economic losses, especially in the organic sector of the industry where the use of synthetic fungicides is not permitted for disease control. New pathotypes of this pathogen are increasingly reported which are capable of breaking resistance. In this study, we took advantage of new spinach genome resources to conduct RNA-seq analyses of transcriptomic changes in leaf tissue of resistant and susceptible spinach cultivars Solomon and Viroflay, respectively, at an early stage of pathogen establishment (48 hours post inoculation, hpi) to a late stage of symptom expression and pathogen sporulation (168 hpi). Fold change differences in gene expression were recorded between the two cultivars to identify candidate genes for resistance. In Solomon, the hypersensitive inducible genes such as pathogenesis-related gene PR-1, glutathione-S-transferase, phospholipid hydroperoxide glutathione peroxidase and peroxidase were significantly up-regulated uniquely at 48 hpi and genes involved in zinc finger CCCH protein, glycosyltransferase, 1-aminocyclopropane-1-carboxylate oxidase homologs, receptor-like protein kinases were expressed at 48 hpi through 168 hpi. The types of genes significantly up-regulated in Solomon in response to the pathogen suggests that salicylic acid and ethylene signaling pathways mediate resistance. Furthermore, many genes involved in the flavonoid and phenylpropanoid pathways were highly expressed in Viroflay compared to Solomon at 168 hpi. As anticipated, an abundance of significantly down-regulated genes was apparent at 168 hpi, reflecting symptom development and sporulation in cultivar Viroflay, but not at 48 hpi. In the pathogen, genes encoding RxLR-type effectors were expressed during early colonization of cultivar Viroflay while crinkler-type effector genes were expressed at the late stage of the colonization. Our results provide insights on gene expression in resistant and susceptible spinach-P. effusa interactions, which can guide future studies to assess candidate genes necessary for downy mildew resistance in spinach.The demand for prepackaged ready to eat salad mixes has resulted in increased production of leafy greens in recent years. Currently, spinach is cultivated in more than 60 countries globally, with over 53 million tons of total production annually 1 . In the US, nearly four hundred thousand tons of spinach are produced every year 1 . There has also been a rapid increase in the demand for spinach in the US, beginning in the 1990s 2,3 . The Salinas Valley of California is sometimes referred to as 'Salad Bowl of America' since this region produces the majority of leafy greens grown in the US as well as nearly half of the total spinach in California 4,5 .Downy mildew disease of spinach is caused by the obligate oomycete pathogen Peronospora effusa (Phylum Oomycota, Kingdom Stramenopila) 6 . Downy mildew on spinach can sometimes cause 100% yield loss in organic production s...

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Comparative Analysis of Impatiens Leaf Transcriptomes Reveal Candidate Genes for Resistance to Downy Mildew Caused by Plasmopara obducens

Cited by 14 publications

References 53 publications

Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L.

Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L.

Transcriptional profiling of Impatiens walleriana genes through different stages of downy mildew infection reveals novel genes involved in disease susceptibility

Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew

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