scholarly journals A Hybrid Genome Assembly Resource for Podosphaera xanthii, the Main Causal Agent of Powdery Mildew Disease in Cucurbits

Author(s):  
Álvaro Polonio ◽  
Luis Díaz-Martínez ◽  
Dolores Fernández-Ortuño ◽  
Antonio de Vicente ◽  
Diego F. Romero ◽  
...  

Podosphaera xanthii is the main causal agent of powdery mildew in cucurbits and, arguably, the most important fungal pathogen of cucurbit crops. Here, we present the first reference genome assembly for P. xanthii. We performed a hybrid genome assembly, using reads from Illumina NextSeq550 and PacBio Sequel S3. The short and long reads were assembled into 1,727 scaffolds with a N50 size of 163,173 bp, resulting in a 142 Mb genome size. The combination of homology-based and ab initio predictions allowed predicting 14,911 complete genes. Repetitive sequences comprised 76.2 % of the genome. Our P. xanthii genome assembly improves considerably the molecular resources for research on P. xanthii−cucurbit interactions and provides new opportunities for further genomics, transcriptomics and evolutionary studies in powdery mildew fungi.

2020 ◽  
Vol 33 (6) ◽  
pp. 782-786
Author(s):  
Stefan Kusch ◽  
Márk Z. Németh ◽  
Niloofar Vaghefi ◽  
Heba M. M. Ibrahim ◽  
Ralph Panstruga ◽  
...  

Powdery mildew of sweet pepper (Capsicum annuum) is an economically important disease. It is caused by Leveillula taurica, an obligate biotrophic ascomycete with a partly endophytic mycelium and haustoria, i.e., feeding structures formed in the mesophyll cells of infected host plant tissues. The molecular basis of its pathogenesis is largely unknown because genomic resources only exist for epiphytically growing powdery mildew fungi with haustoria formed exclusively in epidermal cells of their plant hosts. Here, we present the first reference genome assembly for an isolate of L. taurica isolated from sweet pepper in Hungary. The short read–based assembly consists of 23,599 contigs with a total length of 187.2 Mbp; the scaffold N50 is 13,899 kbp and N90 is 3,522 kbp; and the average GC content is 39.2%. We detected at least 92,881 transposable elements covering 55.5 Mbp (30.4%). BRAKER predicted 19,751 protein-coding gene models in this assembly. Our reference genome assembly of L. taurica is the first resource to study the molecular pathogenesis and evolution of a powdery mildew fungus with a partly endophytic lifestyle.


2020 ◽  
Vol 33 (7) ◽  
pp. 880-883
Author(s):  
Stefan Kusch ◽  
Heba M. M. Ibrahim ◽  
Catherine Zanchetta ◽  
Celine Lopez-Roques ◽  
Cecile Donnadieu ◽  
...  

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.


2019 ◽  
Vol 102 (4) ◽  
pp. 3254-3258 ◽  
Author(s):  
T. Johnson ◽  
M. Keehan ◽  
C. Harland ◽  
T. Lopdell ◽  
R.J. Spelman ◽  
...  

Plant Disease ◽  
2011 ◽  
Vol 95 (9) ◽  
pp. 1188-1188 ◽  
Author(s):  
J.-G. Tsay ◽  
R.-S. Chen ◽  
H.-L. Wang ◽  
W.-L. Wang ◽  
B.-C. Weng

Powdery mildew can be found in most papaya (Carica papaya L.) fields during the winter and spring seasons in Taiwan. It usually causes severe yellowing of the leaf lamina and petiole and serious defoliation. Three types of powdery mildew fungi were isolated from papaya leaves in Chiayi City (23.28°N, 120.28°E) at the beginning of 2008. Conidia of the first one were single, globose, hyaline, and 24 to 36 × 14 to 18 μm (average 30.2 × 15.6 μm) without fibrosin bodies and with straight or occasionally flexuous conidiophores at the base. The second one had short pseudo-chains of two to four conidia which were ellipsoidal to ovoid, hyaline, and 24 to 40 × 12 to 16 μm (average 29.7 × 13.4 μm) without fibrosin bodies. The third type had chains of ellipsoidal conidia that were hyaline, 24 to 28 × 12 to 16 μm (average 26.3 × 14.4 μm) and contained fibrosin bodies. To confirm the identity of the three fungi, the internal transcribed spacer (ITS) region of rDNA was amplified using the primer pairs G1 (5′-TCC GTA GGT GAA CCT GCG GAA GGA T-3′)/Ed2 (5′-CGC GTA GAG CCC ACG TCG GA-3′), G1 (5′-TCC GTA GGT GAA CCT GCG GAA GGA T-3′)/On2 (5′-TGT GAT CCA TGT GAC TGG AA-3′), and S1 (5′-GGA TCA TTA CTG AGC GCG AGG CCC CG-3′)/S2 (5′-CGC CGC CCT GGC GCG AGA TAC A-3′). The alignment of obtained sequences (GenBank Accession Nos. GU358452, 507 bp; GU358451, 580 bp; and GU358450, 455 bp) showed a sequence identity of 100, 99, and 99% with the ITS sequences of Erysiphe diffusa, Oidium neolycopersici, and Podosphaera xanthii (GenBank Accession Nos. FJ378880, EU909694, and GQ927254), respectively. On the basis of morphological characteristics and ITS sequence similarities, these fungi were identified as E. diffusa (Cooke & Peck) U. Braun & S. Takam., O. neolycopersici L. Kiss, and P. xanthii (Castagne) U. Braun & S. Takam., respectively (1,3). Single colonies on papaya leaves infected with powdery mildew were identified in the laboratory and maintained on papaya leaves as inoculum. Pathogenicity was confirmed through inoculations by gently pressing a single colony of each fungus onto leaves of healthy papaya seedlings (cv. Horng-Fe). Five seedlings were inoculated for each fungus and then covered with plastic bags for 2 days. Five noninoculated seedlings served as control. After inoculation, treated plants were maintained separately from the control in different rooms of a greenhouse at 25°C under natural daylight conditions. Seven days after inoculation, typical symptoms of powdery mildew were observed on inoculated plants, but not on noninoculated plants. The same species from diseased lesions following artificial inoculation with each fungus were identified with light microscopy. Papaya was previously described as a host to O. caricae Noack in many tropical and subtropical areas of the world including Taiwan (2). However E. cruciferarum, Golovinomyces cichoracearum, Oidiopsis sicula, O. caricae, O. caricae-papayae, O. caricicola, O. indicum, O. papayae, Ovulariopsis papayae, P. caricae-papayae, P. macularis, P. xanthii, and Streptopodium caricae were reported to infect papaya (4). To our knowledge, this is the first report of papaya powdery mildew caused by E. diffusa and O. neolycopersici in the world and the first report of the three fungi found on papaya in Taiwan. References: (1) U. Braun and S. Takamatsu. Schlechtendalia 4:1, 2000. (2) H. S. Chien and H. L. Wang. J. Agric. Res. China 33:320, 1984. (3) L. Kiss et al. Mycol. Res. 105:684, 2001. (4) J. R. Liberato et al. Mycol. Res. 108:1185, 2004.


Author(s):  
Marion Claudia Müller ◽  
Lukas Kunz ◽  
Johannes Peter Graf ◽  
Seraina Schudel ◽  
Beat Keller

The emergence of new fungal pathogens through hybridization represents a serious challenge for agriculture. Hybridization between the wheat mildew (Blumeria graminis f.sp. tritici) and rye mildew (B.g. f.sp. secalis) pathogens have led to the emergence of a new mildew form (B.g. f.sp. triticale) growing on triticale, a man-made amphiploid crop derived from crossing rye and wheat which was originally resistant to the powdery mildew disease. The identification of the genetic basis of host-adaptation in triticale mildew has been hampered by the lack of a reference genome. Here we report the 141.4 Mb reference assembly of triticale mildew isolate THUN-12 derived from long-read sequencing and genetic map-based scaffolding. All eleven triticale mildew chromosomes were assembled from telomere-to-telomere and revealed that 19.7% of the hybrid genome was inherited from the rye mildew parental lineage. We identified lineage-specific regions in the hybrid, inherited from the rye or wheat mildew parental lineages, that harbour numerous bona fide candidate effectors. We propose that the combination of lineage-specific effectors in the hybrid genome is crucial for host-adaptation, allowing the fungus to simultaneously circumvent the immune systems contributed by wheat and rye in the triticale crop. In line with this we demonstrate the functional transfer of the SvrPm3 effector from wheat to triticale mildew, a virulence effector that specifically suppresses resistance of the wheat Pm3 allelic series. This transfer is the likely underlying cause for the observed poor effectiveness of several Pm3 alleles against triticale mildew and exemplifies the negative implications of pathogen hybridizations on resistance breeding.


2020 ◽  
Author(s):  
Isis da Costa Hermisdorff ◽  
Raphael Bermal Costa ◽  
Lucia Galvão de Albuquerque ◽  
Hubert Pausch ◽  
Naveen Kumar Kadri

AbstractBackgroundImputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of variants on the reference genome assembly. Using high-density genotypes of 3938 Nellore cattle from Brazil, we investigated the accuracy of imputation from 50K to 777K SNP density, using map positions determined according to the bovine genome assemblies UMD3.1 and ARS-UCD1.2. We assessed the effect of reference and target panel sizes on the pre-phasing-based imputation quality using ten-fold cross-validation. Further, we compared the reliability of the model-based imputation quality score (Rsq) from Minimac3 to empirical imputation accuracy.ResultsThe overall accuracy of imputation measured as the squared correlation between true and imputed allele dosages (R2dose) was virtually identical using either the UMD3.1 or ARS-UCD1.2 genome assembly. When the size of the reference panel increased from 250 to 2000, R2dose increased from 0.845 to 0.917, and the number of polymorphic markers in the imputed data set increased from 586,701 to 618,660. Advantages in both accuracy and marker density were also observed when larger target panels were imputed, likely resulting from more accurate haplotype inference. Imputation accuracy and the marker density in the imputed data increased from 0.903 to 0.913 and from 593,239 to 595,570 when haplotypes were inferred in 500 and 2900 target animals, respectively. The model-based imputation quality scores from Minimac3 (Rsq) were highly correlated to but systematically higher than empirically estimated accuracies. The correlation between these metrics increased with the size of the reference panel and MAF of imputed variants.ConclusionsAccurate imputation of BovineHD BeadChip markers is possible in Nellore cattle using the new bovine reference genome assembly ARS-UCD1.2. The use of large reference and target panels improves the accuracy of the imputed genotypes and provides genotypes for more markers segregating at low frequency for downstream genomic analyses. The model-based imputation quality score from Minimac3 (Rsq) can be used to detect poorly imputed variants but its reliability depends on the size of the reference panel used and MAF of the imputed variants.


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