scholarly journals The chromosome-level reference genome assembly for Dendrobium officinale and its utility of functional genomics research and molecular breeding study

2021 ◽  
Author(s):  
Zhitao Niu ◽  
Fei Zhu ◽  
Yajuan Fan ◽  
Chao Li ◽  
Benhou Zhang ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Genome Assembly ◽  
Molecular Breeding ◽  
Reference Genome ◽  
Dendrobium Officinale ◽  
Reference Genome Assembly ◽  
Genomics Research ◽  
Chromosome Level

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

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

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 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.

scholarly journals Chromosome-Level Aspergillus flavus Strain CA14 Genome Assembly

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Mark A. Weaver ◽  
Brian M. Mack ◽  
Matthew K. Gilbert
Keyword(s):  
Secondary Metabolism ◽  
Aspergillus Flavus ◽  
Genome Assembly ◽  
Full Length ◽  
Content Type ◽  
Genomics Research ◽  
Chromosome Level

ABSTRACT We report here a chromosome-level genome assembly of the aflatoxigenic fungus Aspergillus flavus strain CA14. This strain is the basis for numerous studies in fungal physiology and secondary metabolism. This full-length assembly will aid in subsequent genomics research.

Sign in / Sign up

Export Citation Format

Share Document