scholarly journals Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger

2021 ◽  
Author(s):  
Valeria Ellena ◽  
Sjoerd J. Seekles ◽  
Arthur F.J. Ram ◽  
Matthias G. Steiger
Keyword(s):  
Aspergillus Niger ◽  
Genome Sequence ◽  
Model Organism ◽  
Nuclear Genome ◽  
Fungal Species ◽  
Cell Factory ◽  
Dna Assembly ◽  
High Quality ◽  
Genetic Organization ◽  
Wide Range

Abstract Background Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Due to its economic importance and its role as model organism to study fungal fermentation, its genome was one of the first Aspergillus genomes to be sequenced in 2007. Nowadays, the genome sequences of at least five other A. niger strains are available. These, however, do not include the neotype strain CBS 554.65. Results In this study, the genome of CBS 554.65 was sequenced with PacBio. A high-quality nuclear genome sequence consisting of 17 contigs with a N50 value of 4.07 Mbp was obtained. The sequencing covered all the 8 centromeric regions of the chromosomes. In addition, a complete circular mitochondrial DNA assembly was obtained. In silico analyses revealed the presence of a MAT1-2-1 gene in this genome, contrary to the so far sequenced A. niger strains, which all contain a MAT1-1-1 gene. An alignment at the MAT locus showed a different position of the MAT1-1-1 gene of ATCC 1015 compared to the MAT1-2-1 gene of CBS 554.65, relative to the surrounding genes. In addition, 24 other sequenced isolates of A. niger showed a 1:1 ratio of MAT1-1 and MAT1-2 loci. While the genetic organization of the MAT1-2 locus of CBS 554.65 is similar to what is found in other aspergilli, the genetic organization of the MAT1-1 locus is flipped in all sequenced strains. Conclusions This study, besides providing a high-quality genome sequence of an important A. niger strain, suggests the occurrence of genetic flipping or switching events at the MAT1-1 locus of A. niger. These results provide new insights in the mating system of A. niger and could contribute to the investigation and potential discovery of sexuality of this so far asexual fungal species.

scholarly journals Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1–2 locus of Aspergillus niger

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Valeria Ellena ◽  
Sjoerd J. Seekles ◽  
Gabriel A. Vignolle ◽  
Arthur F. J. Ram ◽  
Matthias G. Steiger
Keyword(s):  
Aspergillus Niger ◽  
Genome Sequence ◽  
Model Organism ◽  
Nuclear Genome ◽  
Cell Factory ◽  
Dna Assembly ◽  
High Quality ◽  
Wide Range ◽  
Conserved Genes ◽  
A Cell

Abstract Background Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Its genome was one of the first Aspergillus genomes to be sequenced in 2007, due to its economic importance and its role as model organism to study fungal fermentation. Nowadays, the genome sequences of more than 20 A. niger strains are available. These, however, do not include the neotype strain CBS 554.65. Results The genome of CBS 554.65 was sequenced with PacBio. A high-quality nuclear genome sequence consisting of 17 contigs with a N50 value of 4.07 Mbp was obtained. The assembly covered all the 8 centromeric regions of the chromosomes. In addition, a complete circular mitochondrial DNA assembly was obtained. Bioinformatic analyses revealed the presence of a MAT1-2-1 gene in this genome, contrary to the most commonly used A. niger strains, such as ATCC 1015 and CBS 513.88, which contain a MAT1-1-1 gene. A nucleotide alignment showed a different orientation of the MAT1–1 locus of ATCC 1015 compared to the MAT1–2 locus of CBS 554.65, relative to conserved genes flanking the MAT locus. Within 24 newly sequenced isolates of A. niger half of them had a MAT1–1 locus and the other half a MAT1–2 locus. The genomic organization of the MAT1–2 locus in CBS 554.65 is similar to other Aspergillus species. In contrast, the region comprising the MAT1–1 locus is flipped in all sequenced strains of A. niger. Conclusions This study, besides providing a high-quality genome sequence of an important A. niger strain, suggests the occurrence of genetic flipping or switching events at the MAT1–1 locus of A. niger. These results provide new insights in the mating system of A. niger and could contribute to the investigation and potential discovery of sexuality in this species long thought to be asexual.

scholarly journals Genome Assembly and Annotation of Botryosphaeria dothidea sdau11-99, a Latent Pathogen of Apple Fruit Ring Rot in China

Plant Disease ◽  
2020 ◽  
Author(s):  
Chengming Yu ◽  
Yufei Diao ◽  
Quan Lu ◽  
Jiaping Zhao ◽  
Shengnan Cui ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Fungal Pathogen ◽  
Woody Plants ◽  
Reference Genome ◽  
Apple Fruit ◽  
Botryosphaeria Dothidea ◽  
High Quality ◽  
Ring Rot ◽  
Wide Range

Botryosphaeria dothidea is a latent and important fungal pathogen on a wide range of woody plants. Fruit ring rot caused by B. dothidea is a major disease in China on apple. This study establishes a high quality, nearly complete and well annotated genome sequence of B. dothidea strain sdau11-99. The findings of this research provide a reference genome resource for further research on the apple fruit ring rot pathogen on apple and other hosts.

scholarly journals High-quality draft genome sequence of a biofilm forming lignocellulolytic Aspergillus niger strain ATCC 10864

2017 ◽  
Vol 12 (1) ◽  
Author(s):  
Sujay Paul ◽  
Yvette Ludeña ◽  
Gretty K. Villena ◽  
Fengan Yu ◽  
David H. Sherman ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Strain Atcc ◽  
High Quality

scholarly journals Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Xiao-Bao Ding ◽  
Jie Jin ◽  
Yu-Tian Tao ◽  
Wen-Ping Guo ◽  
Li Ruan ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Protein Interactions ◽  
Model Organism ◽  
Functional Gene ◽  
Gene Interactions ◽  
Web Tool ◽  
High Quality ◽  
Functional Interpretation ◽  
Gene Set ◽  
Wide Range

Abstract Drosophila melanogaster is a well-established model organism that is widely used in genetic studies. This species enjoys the availability of a wide range of research tools, well-annotated reference databases and highly similar gene circuitry to other insects. To facilitate molecular mechanism studies in Drosophila, we present the Predicted Drosophila Interactome Resource (PDIR), a database of high-quality predicted functional gene interactions. These interactions were inferred from evidence in 10 public databases providing information for functional gene interactions from diverse perspectives. The current version of PDIR includes 102 835 putative functional associations with balanced sensitivity and specificity, which are expected to cover 22.56% of all Drosophila protein interactions. This set of functional interactions is a good reference for hypothesis formulation in molecular mechanism studies. At the same time, these interactions also serve as a high-quality reference interactome for gene set linkage analysis (GSLA), which is a web tool for the interpretation of the potential functional impacts of a set of changed genes observed in transcriptomics analyses. In a case study, we show that the PDIR/GSLA system was able to produce a more comprehensive and concise interpretation of the collective functional impact of multiple simultaneously changed genes compared with the widely used gene set annotation tools, including PANTHER and David. PDIR and its associated GSLA service can be accessed at http://drosophila.biomedtzc.cn.

scholarly journals Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae

2017 ◽  
Vol 7 (7) ◽  
pp. 2219-2226 ◽  
Author(s):  
Kinnari Matheson ◽  
Lance Parsons ◽  
Alison Gammie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Sequence ◽  
Model Organism ◽  
Laboratory Strain ◽  
Gene Families ◽  
Whole Genome Sequence ◽  
High Quality ◽  
Accurate Identification ◽  
Phenotypic Properties ◽  
Yeast Saccharomyces Cerevisiae

Abstract The yeast Saccharomyces cerevisiae has emerged as a superior model organism. Selection of distinct laboratory strains of S. cerevisiae with unique phenotypic properties, such as superior mating or sporulation efficiencies, has facilitated advancements in research. W303 is one such laboratory strain that is closely related to the first completely sequenced yeast strain, S288C. In this work, we provide a high-quality, annotated genome sequence for W303 for utilization in comparative analyses and genome-wide studies. Approximately 9500 variations exist between S288C and W303, affecting the protein sequences of ∼700 genes. A listing of the polymorphisms and divergent genes is provided for researchers interested in identifying the genetic basis for phenotypic differences between W303 and S288C. Several divergent functional gene families were identified, including flocculation and sporulation genes, likely representing selection for desirable laboratory phenotypes. Interestingly, remnants of ancestor wine strains were found on several chromosomes. Finally, as a test of the utility of the high-quality reference genome, variant mapping revealed more accurate identification of accumulated mutations in passaged mismatch repair-defective strains.

scholarly journals High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534

2021 ◽  
Vol 10 (21) ◽  
Author(s):  
Jason E. Stajich ◽  
Andrea L. Vu ◽  
Howard S. Judelson ◽  
Gregory M. Vogel ◽  
Michael A. Gore ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Transcriptome Sequencing ◽  
Reference Genome ◽  
Phytophthora Capsici ◽  
Rna Seq ◽  
High Quality ◽  
Content Type ◽  
Wide Range ◽  
Illumina Data

The oomycete Phytophthora capsici is a destructive pathogen of a wide range of vegetable hosts, especially peppers and cucurbits. A 94.17-Mb genome assembly was constructed using PacBio and Illumina data and annotated with support from transcriptome sequencing (RNA-Seq) reads.

scholarly journals How to develop objective-driven comprehensive science outreach initiatives aiming at multiple audiences

2015 ◽  
Author(s):  
Sanjai Patel ◽  
Andreas Prokop
Keyword(s):  
Extracurricular Activities ◽  
Public Awareness ◽  
Model Organism ◽  
Added Value ◽  
High Quality ◽  
Science Outreach ◽  
Time Saving ◽  
The Public ◽  
Wide Range ◽  
Multiple Audiences

Science outreach has become increasingly important for researchers and needs to be of ever improving quality, although the time available aside our science, teaching and administration activities is steadily decreasing. To square this circle, effective strategies are required. Here we argue that this can be achieved by setting simple but ambitious overarching objectives for comprehensive outreach initiatives which target multiple audiences, supported by cumulative build-up of shared high-quality resources, as well as the exchange and collaboration amongst scientists with a common outreach aim. To exemplify this strategy, we explain the low-budget, yet high-quality outreach initiative of the Manchester Fly Facility which aims to promote public awareness of the importance of the model organism Drosophila for biomedical research. (1) This initiative targets the general public at science fairs, through public videos, or through extracurricular activities in schools as well as the development of curriculum-relevant sample lessons for teachers - all supported by a dedicated website. (2) The initiative targets university students: by adapting the public outreach resources for their teaching, and through newly developed advanced training strategies that amalgamate the outreach objectives. (3) It targets fellow scientists through blogs, conference presentations and a second website that provides a one-stop-shop for resources, arguments and strategies. As will be explained, this multi-pronged approach is time-saving in the long run and it is powerful because it reaches a wide range of audiences, helps to gain momentum, to build resource, and to gradually improve quality through cross-fertilisation between different activities, and through exchange within the science community. This helps to build communities, and high-quality outreach will have further important added value: arguments that impress the public, tend to be most effective also with reviewers and grant panel members, and often help to readjust aspects of your own scientific work.

scholarly journals A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Fei Chen ◽  
Liyao Su ◽  
Shuaiya Hu ◽  
Jia-Yu Xue ◽  
Hui Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Floral Development ◽  
Peptide Transporter ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Rosa Rugosa ◽  
High Quality ◽  
Wide Range ◽  
High Quality Genome

AbstractRosa rugosa, commonly known as rugged rose, is a perennial ornamental shrub. It produces beautiful flowers with a mild fragrance and colorful seed pods. Unlike many other cultivated roses, R. rugosa adapts to a wide range of habitat types and harsh environmental conditions such as salinity, alkaline, shade, drought, high humidity, and frigid temperatures. Here, we produced and analyzed a high-quality genome sequence for R. rugosa to understand its ecology, floral characteristics and evolution. PacBio HiFi reads were initially used to construct the draft genome of R. rugosa, and then Hi-C sequencing was applied to assemble the contigs into 7 chromosomes. We obtained a 382.6 Mb genome encoding 39,704 protein-coding genes. The genome of R. rugosa appears to be conserved with no additional whole-genome duplication after the gamma whole-genome triplication (WGT), which occurred ~100 million years ago in the ancestor of core eudicots. Based on a comparative analysis of the high-quality genome assembly of R. rugosa and other high-quality Rosaceae genomes, we found a unique large inverted segment in the Chinese rose R. chinensis and a retroposition in strawberry caused by post-WGT events. We also found that floral development- and stress response signaling-related gene modules were retained after the WGT. Two MADS-box genes involved in floral development and the stress-related transcription factors DREB2A-INTERACTING PROTEIN 2 (DRIP2) and PEPTIDE TRANSPORTER 3 (PTR3) were found to be positively selected in evolution, which may have contributed to the unique ability of this plant to adapt to harsh environments. In summary, the high-quality genome sequence of R. rugosa provides a map for genetic studies and molecular breeding of this plant and enables comparative genomic studies of Rosa in the near future.

AMPCOLOY 570

Alloy Digest ◽  
1980 ◽  
Vol 29 (3) ◽  
Keyword(s):  
Corrosion Resistance ◽  
Cast Iron ◽  
Iron Alloy ◽  
Heat Treating ◽  
Nickel Aluminum ◽  
High Quality ◽  
Glass Making ◽  
Temperature Performance ◽  
Wide Range ◽  
Cobalt Iron

Abstract AMPCOLOY 570 is a cast copper-nickel-aluminum-cobalt-iron alloy specially developed for applications involving severe stresses and high temperatures, such as glass-making molds and plate-glass rolls. It is significantly superior to cast iron which has been commonly used for glass-making molds. Good foundry techniques will yield high-quality castings of Ampcoloy 570 in a wide range of section sizes. This datasheet provides information on composition, physical properties, hardness, elasticity, and tensile properties. It also includes information on high temperature performance and corrosion resistance as well as casting, heat treating, machining, and joining. Filing Code: Cu-392. Producer or source: Ampco Metal Inc..

scholarly journals Applicability of Honey on Silkworms (Bombyx mori) and Quality Improvement of Its Biomaterials

2021 ◽  
Vol 11 (10) ◽  
pp. 4613
Author(s):  
Gabriela-Maria Baci ◽  
Alexandra-Antonia Cucu ◽  
Adela Ramona Moise ◽  
Daniel Severus Dezmirean
Keyword(s):  
Quality Improvement ◽  
Bombyx Mori ◽  
Human Health ◽  
Recombinant Proteins ◽  
Therapeutic Agent ◽  
Life Sciences ◽  
Model Organism ◽  
Medical Field ◽  
Wide Range ◽  
Ancient Times

Since ancient times, honey has been considered one of the most illustrious and esteemed natural products. Honey plays two key roles; specifically, it is an appreciated nutritional product, and also exhibits a wide range of beneficial properties for human health as a therapeutic agent. Furthermore, it has been shown that honey has valuable effects on the biological and physiological features of mulberry silkworms (Bombyx mori). Bombyx mori exhibits importance not only for the economy, but it also serves as an important biotechnological bioreactor for the production of recombinant proteins that have a great impact in the medical field and beyond. It also represents an important model organism for life sciences. In view of the fact that silk fibroin serves as a natural biopolymer that displays high biocompatibility with human organisms and due to honey’s various and remarkable properties for human health, the two elements are currently used together in order to develop ideal biomaterials for a wide range of purposes. In this review, by discussing the applicability of honey on Bombyx mori and beyond, the importance of honey for life sciences and related fields is spotlighted.

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