scholarly journals Reference genome assembly for Australian Ascochyta lentis isolate Al4

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Robert C Lee ◽  
Lina Farfan-Caceres ◽  
Johannes W Debler ◽  
Angela H Williams ◽  
Robert A Syme ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Management Practices ◽  
Reference Genome ◽  
Ascochyta Blight ◽  
Australian Isolate ◽  
Reference Genome Assembly ◽  
Fungal Plant Pathogens ◽  
Ascochyta Lentis

Abstract Ascochyta lentis causes ascochyta blight in lentil (Lens culinaris Medik.) and yield loss can be as high as 50%. With careful agronomic management practices, fungicide use, and advances in breeding resistant lentil varieties, disease severity and impact to farmers have been largely controlled. However, evidence from major lentil producing countries, Canada and Australia, suggests that A. lentis isolates can change their virulence profile and level of aggressiveness over time and under different selection pressures. In this paper, we describe the first genome assembly for A. lentis for the Australian isolate Al4, through the integration of data from Illumina and PacBio SMRT sequencing. The Al4 reference genome assembly is almost 42 Mb in size and encodes 11,638 predicted genes. The Al4 genome comprises 21 full-length and gapless chromosomal contigs and two partial chromosome contigs each with one telomere. We predicted 31 secondary metabolite clusters, and 38 putative protein effectors, many of which were classified as having an unknown function. Comparison of A. lentis genome features with the recently published reference assembly for closely related A. rabiei show that genome synteny between these species is highly conserved. However, there are several translocations and inversions of genome sequence. The location of secondary metabolite clusters near transposable element and repeat-rich genomic regions was common for A. lentis as has been reported for other fungal plant pathogens.

scholarly journals A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

2020 ◽  
Vol 33 (7) ◽  
pp. 880-883
Author(s):  
Stefan Kusch ◽  
Heba M. M. Ibrahim ◽  
Catherine Zanchetta ◽  
Celine Lopez-Roques ◽  
Cecile Donnadieu ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Reference Genome ◽  
Close Relative ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Reference Genome Assembly

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.

scholarly journals ONT-based draft genome assembly and annotation of Alternaria atra

2021 ◽  
Author(s):  
Bhawna Bonthala ◽  
Corinn Sophia Small ◽  
Maximilian Anton Lutz ◽  
Alexander Graf ◽  
Stefan Krebs ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Plant Pathogens ◽  
Biocontrol Agent ◽  
Reference Genome ◽  
Gene Prediction ◽  
Draft Genome ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Reference Genome Assembly ◽  
Wide Range

Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.

scholarly journals The Chromosome-Level Reference Genome Assembly for Panax notoginseng and Insights into Ginsenoside Biosynthesis

2020 ◽  
pp. 100113 ◽  
Author(s):  
Zhouqian Jiang ◽  
Lichan Tu ◽  
Weifei Yang ◽  
Yifeng Zhang ◽  
Tianyuan Hu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Panax Notoginseng ◽  
Ginsenoside Biosynthesis ◽  
Reference Genome Assembly ◽  
Chromosome Level

scholarly journals Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14

2020 ◽  
Vol 10 (7) ◽  
pp. 2131-2140
Author(s):  
Ramisah Mohd Shah ◽  
Angela H. Williams ◽  
James K. Hane ◽  
Julie A. Lawrence ◽  
Lina M. Farfan-Caceres ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Dna Sequences ◽  
Genome Assembly ◽  
Ascochyta Blight ◽  
Ascochyta Rabiei ◽  
Causal Organism ◽  
Protein Coding ◽  
Putative Protein ◽  
Genomic Regions ◽  
Genome Assemblies

Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.

scholarly journals A Short-Read Genome Assembly Resource for Leveillula taurica Causing Powdery Mildew Disease of Sweet Pepper (Capsicum annuum)

2020 ◽  
Vol 33 (6) ◽  
pp. 782-786
Author(s):  
Stefan Kusch ◽  
Márk Z. Németh ◽  
Niloofar Vaghefi ◽  
Heba M. M. Ibrahim ◽  
Ralph Panstruga ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Capsicum Annuum ◽  
Genome Assembly ◽  
Reference Genome ◽  
Gc Content ◽  
Sweet Pepper ◽  
Mesophyll Cells ◽  
Short Read ◽  
Leveillula Taurica ◽  
Reference Genome Assembly

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.

scholarly journals Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2

2019 ◽  
Vol 102 (4) ◽  
pp. 3254-3258 ◽  
Author(s):  
T. Johnson ◽  
M. Keehan ◽  
C. Harland ◽  
T. Lopdell ◽  
R.J. Spelman ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Short Communication ◽  
Reference Genome ◽  
Pseudoautosomal Region ◽  
Reference Genome Assembly

scholarly journals Investigating the accuracy of imputed genotypes in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

2020 ◽  
Author(s):  
Isis da Costa Hermisdorff ◽  
Raphael Bermal Costa ◽  
Lucia Galvão de Albuquerque ◽  
Hubert Pausch ◽  
Naveen Kumar Kadri
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Bovine Genome ◽  
Imputation Accuracy ◽  
Quality Score ◽  
Reference Panel ◽  
Marker Density ◽  
Model Based ◽  
Reference Genome Assembly ◽  
Nellore Cattle

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.

Chromosome‐level reference genome assembly and gene editing of the dead‐leaf butterfly Kallima inachus

2020 ◽  
Vol 20 (4) ◽  
pp. 1080-1092 ◽  
Author(s):  
Jie Yang ◽  
Wenting Wan ◽  
Meng Xie ◽  
Junlai Mao ◽  
Zhiwei Dong ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gene Editing ◽  
Reference Genome ◽  
Dead Leaf ◽  
Reference Genome Assembly ◽  
The Dead ◽  
Chromosome Level
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