Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici

Orquera-Tornakian, Gabriela K.; Garrido, Patricia; Kronmiller, Brent; Hunger, R. M.; Tyler, Brett M.; Garzón, Carla D.; Marek, Stephen M.

doi:10.1016/j.mimet.2017.04.011

Cited by 6 publications

(4 citation statements)

References 58 publications

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“…Switchgrass rust caused by P. novopanici is a significant disease of switchgrass ( Panicum virgatum L.), an important biofuel and forage crop in the United States of America [ 18 ]. Few of the early literature [ 6 , 8 , 18 , 20 , 21 , 22 ] cataloged switchgrass rust pathogen P. novopanici as P. emaculata but a recent sequence comparison [ 18 ] of our fungal isolates with P. novopanici sequences confirmed our isolates as P. novopanici [ 18 , 21 , 22 ]. We recently reported the draft genome sequence of P. novopanici by assembling PacBio and Illumina reads into total length of 99.9 Mb [ 18 ].…”

Section: Introductionmentioning

confidence: 73%

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses

Nandety

Gill

Krom

et al. 2022

Plants

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Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.

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Section: Introductionmentioning

confidence: 73%

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses

Nandety

Gill

Krom

et al. 2022

Plants

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“…The di-nucleotide types have generally been observed to have the highest frequency in many other rusts [ 30 , 31 , 32 , 33 , 34 , 35 ]. Compared with amplification in other fungi [ 22 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ], the PCR amplification efficiency of the primers used here seems relatively low. Gymnosporangium species are demicyclic and we could not collect massive spores by inoculation experiments.…”

Section: Discussionmentioning

confidence: 89%

“…Microsatellites proved to be informative markers that can reveal heterozygotic or heterokaryotic genotypes in diploid or dikaryotic organisms [ 21 , 25 , 35 ]. Moreover, microsatellites are easy-to-use tools for population genetic and ecological studies as well as epidemiological and forensic research [ 27 , 29 ]. The characterization of SSRs requires the identification of genomic fragments containing repetitive sequence motifs [ 26 ].…”

Section: Discussionmentioning

confidence: 99%

“…tritici , P. graminis f. sp. tritici , P. coronata , P. novopanici , P. triticina and coffee rust Hemileia vastatrix [ 22 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 ]. However, no microsatellite primers specific to G. yamadae have been developed to date, so microsatellites for the studies of G. yamadae are urgently required.…”

Section: Introductionmentioning

confidence: 99%

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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

Tao

Cao

Tian

et al. 2018

IJMS

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The Apple-Juniper rust, Gymnosporangium yamadae, is an economically important pathogen of apples and junipers in Asia. The absence of markers has hampered the study of the genetic diversity of this widespread pathogen. In our study, we developed twenty-two novel microsatellite markers for G. yamadae from randomly sequenced regions of the transcriptome, using next-generation sequencing methods. These polymorphic markers were also tested on 96 G. yamadae individuals from two geographical populations. The allele numbers ranged from 2 to 9 with an average value of 6 per locus. The polymorphism information content (PIC) values ranged from 0.099 to 0.782 with an average value of 0.48. Furthermore, the observed (HO) and expected (HE) heterozygosity ranged from 0.000 to 0.683 and 0.04 to 0.820, respectively. These novel developed microsatellites provide abundant molecular markers for investigating the genetic structure and genetic diversity of G. yamadae, which will help us to better understand disease epidemics and the origin and migration routes of the Apple-Juniper rust pathogen. Further studies will also be completed to dissect how human activities influence the formation of current population structures. Furthermore, these SSR (simple sequence repeat) markers can also be used as tools to identify virulence by mapping the whole genomes of different virulent populations. These markers will, thus, assist the development of effective risk-assessment models and management systems for the Apple-Juniper rust pathogen.

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New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States

et al. 2018

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Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici

Cited by 6 publications

References 58 publications

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses

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

New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States

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