Development and Characterization of Novel Genic-SSR Markers in Apple-Juniper Rust Pathogen Gymnosporangium yamadae (Pucciniales: Pucciniaceae) Using Next-Generation Sequencing

Tao, Siqi; Cao, Bin; Tian, Chengming; Liang, Ying‐Mei

doi:10.3390/ijms19041178

Cited by 10 publications

(8 citation statements)

References 38 publications

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“…S1A), indicating conserved sequence characteristics in the transcriptomes. The most frequent unit was ‘AAG’, followed by ‘AG’, ‘AGC’, ‘ACC’, and ‘ACG’, which occur frequently in fungi 26,29 . Similar but different frequencies of coding SSRs represent conserved sequence characteristics in the transcriptomes among the AG-1 subgroups (Fig.…”

Section: Resultsmentioning

confidence: 99%

Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups

Yamamoto

Wang

Lin

et al. 2019

Sci Rep

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Rhizoctonia solani is a fungal species complex that causes necrotrophic crop diseases. It comprises several anastomosis groups, some of which include intra-subgroups, such as AG-1 IA and AG-1 IB, exhibiting varying pathogenicity. Owing to its heterozygous and multinucleate features, genomic analyses of R. solani are still challenging, and understanding of its genetic diversity and genic components is limited. In this study, in order to elucidate the molecular basis of this phytopathogen complex, an integrated transcriptome analysis was undertaken for three subgroups of AG-1, i.e. AG-1 IA, AG-1 IB, and AG-1 IC. Sequence variations suggested substantial evolutionary distances within AG-1. Transcript simple sequence repeats showed comparable characteristics among AG-1, but contained polymorphic sites. Intra-subgroup polymorphisms suggested varying genic heterozygosity within AG-1, suggesting their independent evolutionary trajectory. Sequences of pathogenic factors, phytotoxin biosynthesis pathway enzymes, secreted lignocellulosic enzymes, secreted reactive oxygen species detoxification enzymes, apoplastic/cytoplasmic effector candidates, were conserved among those subgroups. dN/dS ratios of a secretome subset suggested core secreted proteins in AG-1 and distinct evolution of Cys-rich small secreted proteins after differentiation of AG-1 subgroups. Identification of likely pathogenic factors including allergen protein homologues, oxidative phosphorylation and ethylene biosynthesis pathways, and diversification of polysaccharide monooxygenases provides molecular insight into key genomic components that play a role in R. solani pathogenesis.

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Section: Resultsmentioning

confidence: 99%

Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups

Yamamoto

Wang

Lin

et al. 2019

Sci Rep

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“…This has greatly accelerated the development of microsatellites. Currently, RNA‐seq has only been used in the SSR development of G. yamadae among all Gymnosporangium species (Tao et al, 2018). Although G. yamadae and G. asiaticum have similar biological characteristics, their microsatellites are not universal.…”

Section: Discussionmentioning

confidence: 99%

Development of SSR markers from transcriptome data for the pear rust pathogenGymnosporangium asiaticum

Weng

Tao

Liang

2020

Journal of Phytopathology

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The pear‐cypress rust Gymnosporangium asiaticum is one of the most significant causal agents of pear rust in Asian pear, severely affecting the pear industry. Research on the genetic diversity of this widespread pathogen has been hampered due to the absence of molecular markers. In the current study, we developed 16 novel microsatellite markers for G. asiaticum from transcriptome data by combining next‐generation sequencing and PCR screening. These polymorphic markers were tested on 96 individuals from nine provinces in China. The number of alleles for these markers ranged from two to nine, with an average of five at each locus. The polymorphic information content ranged from 0.0411 to 0.7666, with an average of 0.4417. In addition, the observed (HO) and expected (HE) heterozygosities were 0.0312–0.6941 and 0.0417–0.8000, respectively. We also observed low‐to‐moderate levels of genetic differentiation and extremely significant gene flow between the nine provinces. Of these 16 developed simple sequence repeat loci, 11 were transferable to other Gymnosporangium species. These new microsatellite markers can be used in future large‐scale studies of the genetic structure and diversity of G. asiaticum.

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“…The rust fungus, Gymnosporangium yamadae (Miyabe ex G. Yamada, 1904) infects apple trees and shrubs, causing serious diseases [2]. The G. yamadae fungal parasite afflicts coniferous trees, apple trees, and other species in the genus Malus [3]. In an earlier field experiment, we found obvious red patches on rust-infected tissues present on the leaves of Malus 'Profusion'.…”

Section: Introductionmentioning

confidence: 88%

Transcriptome Sequencing and Expression Analysis of Genes Related to Anthocyanin Biosynthesis in Leaves of Malus ‘Profusion’ Infected by Japanese Apple Rust

Liu

Wang

Meng

et al. 2019

Forests

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Anthocyanins play many roles in plants, including providing protection from biotic and abiotic stresses. Japanese apple rust (Gymnosporangium yamadae Miyabe ex G. Yamada) causes serious diseases in plants of the genus Malus and results in reduced fruit production and quality. However, few studies have been done to unravel the molecular mechanisms of anthocyanin formation in rust-infected apple leaves. To identify new regulatory genes in apple leaves that may be involved in regulating rust-induced anthocyanin biosynthesis, we measured anthocyanin content and sequenced the transcriptomes of rust-infected and uninfected tissues of Malus ‘Profusion’ leaves. Significant color changes and anthocyanin enrichment (especially cyanidin-3-galactoside chloride) occurred in infected tissues, whereas no significant color change and a low anthocyanin level were observed in uninfected tissue. We identified 10,045 differentially expressed genes (DEGs) in these two tissue types, including 6021 genes that were upregulated in the infected tissue and 4024 genes that were downregulated. We also identified five structural genes that are putative regulators of anthocyanin biosynthesis. In addition, 56 MYB genes, 36 bHLH genes, and one WD40 gene were identified among the obtained DEGs. According to the phylogeny of the amino acid sequences of transcription factors known to be involved in anthocyanin biosynthesis, one MYB gene (MYB114-like) and two bHLH genes (bHLH33 and bHLHA-like) may relate to anthocyanin biosynthesis in rust-infected apple leaves. These data will provide insights into the molecular mechanisms underlying anthocyanin accumulation upon rust infection.

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Development and Characterization of Novel Genic-SSR Markers in Apple-Juniper Rust Pathogen Gymnosporangium yamadae (Pucciniales: Pucciniaceae) Using Next-Generation Sequencing

Cited by 10 publications

References 38 publications

Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups

Integrative transcriptome analysis discloses the molecular basis of a heterogeneous fungal phytopathogen complex, Rhizoctonia solani AG-1 subgroups

Development of SSR markers from transcriptome data for the pear rust pathogenGymnosporangium asiaticum

Transcriptome Sequencing and Expression Analysis of Genes Related to Anthocyanin Biosynthesis in Leaves of Malus ‘Profusion’ Infected by Japanese Apple Rust

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