Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens<i>Phakopsora pachyrhizi</i>and<i>P. meibomiae</i>

Stone, Christine L.; Buitrago, Martha Lucia Posada; Boore, Jeffrey L.; Frederick, Reid D.

doi:10.3852/09-198

Cited by 26 publications

(26 citation statements)

References 44 publications

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“…As shown in Figure 5, Hvcontig_161 (71,379 bp, %GC = 33%) and Hvcontig_171 (45,581 bp, %GC = 35%) cover over 70% of the mitochondrial genome of PGT. We also found that 7 contigs of the HvCat assembly entirely covered the mitochondrial genomes of PGT (79,748 bp) and the soybean rust Phakopsora pachyrhizi (31,825 bp; Stone et al, 2010) (results not shown). From this analysis we estimate that the Hva mitochondrial genome it is at least of the size of the PGT mitochondrial genome.…”

Section: Resultsmentioning

confidence: 63%

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Cristancho¹,

Botero-Rozo

Giraldo³

et al. 2014

Front. Plant Sci.

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Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.

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Section: Resultsmentioning

confidence: 63%

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Cristancho¹,

Botero-Rozo

Giraldo³

et al. 2014

Front. Plant Sci.

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“…Particularly, the small scaffold 484 presented a strikingly high sequencing depth. Two genes encoding an ATP synthase F0 subunit and a NADH dehydrogenase subunit presenting strong similarity with resident genes of the soybean rust Phakopsora pachyrhizi mitochondrial genome (Stone et al, 2010) are present on this scaffold. Thus, our analysis identifies a new mitochondrial scaffold that will help in refining the genome assembly.…”

Section: Discussionmentioning

confidence: 99%

Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors

Persoons

Morin²,

Delaruelle³

et al. 2014

Front. Plant Sci.

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Melampsora larici-populina is a fungal pathogen responsible for foliar rust disease on poplar trees, which causes damage to forest plantations worldwide, particularly in Northern Europe. The reference genome of the isolate 98AG31 was previously sequenced using a whole genome shotgun strategy, revealing a large genome of 101 megabases containing 16,399 predicted genes, which included secreted protein genes representing poplar rust candidate effectors. In the present study, the genomes of 15 isolates collected over the past 20 years throughout the French territory, representing distinct virulence profiles, were characterized by massively parallel sequencing to assess genetic variation in the poplar rust fungus. Comparison to the reference genome revealed striking structural variations. Analysis of coverage and sequencing depth identified large missing regions between isolates related to the mating type loci. More than 611,824 single-nucleotide polymorphism (SNP) positions were uncovered overall, indicating a remarkable level of polymorphism. Based on the accumulation of non-synonymous substitutions in coding sequences and the relative frequencies of synonymous and non-synonymous polymorphisms (i.e., PN/PS), we identify candidate genes that may be involved in fungal pathogenesis. Correlation between non-synonymous SNPs in genes encoding secreted proteins (SPs) and pathotypes of the studied isolates revealed candidate genes potentially related to virulences 1, 6, and 8 of the poplar rust fungus.

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“…The intergenic regions amount to 30 % and 27 % in Peltigera membranacea and Peltigera malacea respectively and are rich in simple direct, inverted and tandem repeats which can mediate genome evolution, e.g. by errors in recombination producing duplications, inversions and deletions (Alexander et al 2010;Stone et al 2010).…”

Section: Non-coding Regions: Repeats and Tarsmentioning

confidence: 99%

Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny

et al. 2012

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Analysis of the complete mitochondrial genome sequences of the soybean rust pathogensPhakopsora pachyrhiziandP. meibomiae

Cited by 26 publications

References 44 publications

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors

Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny

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