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

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.

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

10.21203/rs.3.rs-256129/v1 ◽

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.

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

Plant Disease ◽

10.1094/pdis-06-20-1182-a ◽

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.

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

Standards in Genomic Sciences ◽

10.1186/s40793-017-0254-2 ◽

2017 ◽

Vol 12 (1) ◽

Cited By ~ 4

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

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

Database ◽

10.1093/database/baaa005 ◽

2020 ◽

Vol 2020 ◽

Cited By ~ 2

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.

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

G3 Genes|Genome|Genetics ◽

10.1534/g3.117.040022 ◽

2017 ◽

Vol 7 (7) ◽

pp. 2219-2226 ◽

Cited By ~ 19

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.

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

Microbiology Resource Announcements ◽

10.1128/mra.00295-21 ◽

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.

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Predicting complex phenotype–genotype interactions to enable yeast engineering: Saccharomyces cerevisiae as a model organism and a cell factory

Biotechnology Journal ◽

10.1002/biot.201300138 ◽

2013 ◽

Vol 8 (9) ◽

pp. 1017-1034 ◽

Cited By ~ 13

Author(s):

Duygu Dikicioglu ◽

Pınar Pir ◽

Stephen G. Oliver

Keyword(s):

Saccharomyces Cerevisiae ◽

Model Organism ◽

Cell Factory ◽

Complex Phenotype ◽

A Cell

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Draft Genome Sequence of the Yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460

Eukaryotic Cell ◽

10.1128/ec.00114-12 ◽

2012 ◽

Vol 11 (6) ◽

pp. 827-827 ◽

Cited By ~ 12

Author(s):

Xiaoying Liu ◽

Rolf Sommer Kaas ◽

Peter Ruhdal Jensen ◽

Mhairi Workman

Keyword(s):

Genome Size ◽

Genome Sequence ◽

Draft Genome ◽

Open Reading Frames ◽

Draft Genome Sequence ◽

Cell Factory ◽

Pachysolen Tannophilus ◽

Content Type ◽

A Cell ◽

Reading Frames

ABSTRACT A draft genome sequence of the yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460 is presented. The organism has the potential to be developed as a cell factory for biorefineries due to its ability to utilize waste feedstocks. The sequenced genome size was 12,238,196 bp, consisting of 34 scaffolds. A total of 4,463 genes from 5,346 predicted open reading frames were annotated with function.

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