scholarly journals Chromosome-Level Genome Sequence of Aspergillus chevalieri M1, Isolated from Katsuobushi

2021 ◽  
Vol 10 (37) ◽  
Author(s):  
Chihiro Kadooka ◽  
Kazuki Mori ◽  
Kayu Okutsu ◽  
Yumiko Yoshizaki ◽  
Kazunori Takamine ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Significant Role ◽  
Filamentous Fungus ◽  
Sequence Data ◽  
Genomic Research ◽  
Content Type ◽  
Ripening Process ◽  
Chromosome Level

In this study, we report the chromosome-level genome sequence of the osmophilic filamentous fungus Aspergillus chevalieri M1, which was isolated from a dried bonito, katsuobushi. This fungus plays a significant role in the fermentation and ripening process. Thus, elucidating the sequence data for this fungus will aid in subsequent genomic research on the fungi involved in katsuobushi production.

scholarly journals Genome Sequence of Pseudomonas sp. Strain AN3A02, Isolated from Rhizosphere of Deschampsia antarctica Desv., with Antagonism against Botrytis cinerea

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Matías Poblete-Morales ◽  
Claudia Rabert ◽  
Andrés F. Olea ◽  
Héctor Carrasco ◽  
Raúl Calderón ◽  
...  
Keyword(s):  
Botrytis Cinerea ◽  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Deschampsia Antarctica ◽  
Dual Culture ◽  
Content Type ◽  
A Genome ◽  
Antarctic Continent

ABSTRACT Here, we announce the draft genome sequence of Pseudomonas sp. strain AN3A02, isolated from the rhizosphere of one of the only two species of vascular plants existing in the Antarctic continent, Deschampsia antarctica Desv. This isolate, which inhibited the mycelial growth of Botrytis cinerea in dual culture, has a genome sequence of 6,778,644 bp, with a G+C content of 60.4%. These draft genome sequence data provide insight into the genetics underpinning the antifungal activity of this strain.

scholarly journals Draft Genome Sequence of Filamentous Fungus Phialemoniopsis curvata, Isolated from Diesel Fuel

2019 ◽  
Vol 8 (30) ◽  
Author(s):  
Vanessa A. Varaljay ◽  
Wanda J. Lyon ◽  
Audra L. Crouch ◽  
Carrie A. Drake ◽  
Jeffrey M. Hollomon ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Genome Size ◽  
Genome Sequence ◽  
Diesel Fuel ◽  
Filamentous Fungus ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Beta Oxidation ◽  
Content Type

Phialemoniopsis curvata D216 is a filamentous fungus isolated from contaminated diesel fuel. The genome size is 40.3 Mbp with a G+C content of 54.81%. Its genome encodes enzymes and pathways likely involved in the degradation of and survival in fuel, including lipases, fatty acid transporters, and beta oxidation.

scholarly journals Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

2014 ◽  
Vol 53 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Miquette Hall ◽  
Marie A. Chattaway ◽  
Sandra Reuter ◽  
Cyril Savin ◽  
Eckhard Strauch ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Multilocus Sequence Typing ◽  
Sequence Data ◽  
Species Level ◽  
Reference Laboratory ◽  
Whole Genome ◽  
Pathogenic Species ◽  
Data Set ◽  
Content Type ◽  
Genome Sequence Data

The genusYersiniais a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identifyYersiniastrains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic speciesYersinia enterocoliticato whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification ofYersiniaisolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available forY. enterocolitica.

scholarly journals Genome Sequence Data of Lactobacillus ruminis ICIS-540, Isolated from the Intestine of a Healthy Woman

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Elena V. Ivanova ◽  
Anastasia V. Bekpergenova ◽  
Natalia B. Perunova ◽  
Sergey V. Andryuschenko ◽  
Taisia A. Bondarenko ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Sequence Data ◽  
Draft Genome ◽  
Healthy Woman ◽  
Human Colon ◽  
Draft Genome Sequence ◽  
Coding Sequences ◽  
Content Type ◽  
Lactobacillus Ruminis

ABSTRACT Data on the draft genome sequence of Lactobacillus ruminis ICIS-540 are presented in this report. This Lactobacillus strain was isolated from the human colon as a prospective probiotic candidate. The genome size was 2,397,517 bp (G+C content, 42.7%). Annotation revealed 2,847 coding sequences, including 2,573 proteins.

scholarly journals Chromosome-Level Genome Sequence of Leishmania (Leishmania) tropica Strain CDC216-162, Isolated from an Afghanistan Clinical Case

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
Yvette Unoarumhi ◽  
Dhwani Batra ◽  
Mili Sheth ◽  
Vidhya Narayanan ◽  
Wuling Lin ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Clinical Case ◽  
Illumina Miseq ◽  
Considerable Improvement ◽  
Genomic Sequencing ◽  
Leishmania Tropica ◽  
Genome Sequences ◽  
Content Type ◽  
Chromosome Level

ABSTRACT PacBio and Illumina MiSeq platforms were used for genomic sequencing of a Leishmania (Leishmania) tropica strain isolated from a patient infected in Pakistan. PacBio assemblies were generated using Flye v2.4 and polished with MiSeq data. The results represent a considerable improvement of the currently available genome sequences in the GenBank database.

scholarly journals Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Jonathan Koong ◽  
Claire Johnson ◽  
Rayane Rafei ◽  
Monzer Hamze ◽  
Garry S. A. Myers ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Genome Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Opportunistic Pathogen ◽  
Outer Core ◽  
Content Type ◽  
Geographical Regions ◽  
Long Read ◽  
Complex Evolutionary History

Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.

scholarly journals Genome Sequence of the Emerging Mycotoxin-Producing Filamentous Fungus Fusarium tricinctum Strain INRA104

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Nadia Ponts ◽  
Florence Richard-Forget ◽  
Honghai Zhang ◽  
Gérard Barroso ◽  
Chen Zhao
Keyword(s):  
Mitochondrial Genome ◽  
Genome Size ◽  
Genome Sequence ◽  
Filamentous Fungus ◽  
Gc Content ◽  
Phytopathogenic Fungus ◽  
Content Type ◽  
Fusarium Tricinctum

The genome of the phytopathogenic fungus Fusarium tricinctum strain INRA104 was sequenced at a fold-coverage of more than 500×. This led to 23 scaffolds, including one scaffold for the mitochondrial genome, for a total genome size of 42.8 Mb, with an average GC content of 45% and 13,387 predicted genes.

scholarly journals Draft Genome Sequence of Byssochlamys sp. Isolate BYSS01, a Filamentous Fungus Adapted to the Fuel Environment

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Osman Radwan ◽  
Thusitha S. Gunasekera ◽  
Oscar N. Ruiz
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Filamentous Fungus ◽  
Aromatic Compounds ◽  
Draft Genome ◽  
Jet Fuel ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Branched Alkanes

ABSTRACT Byssochlamys sp. isolate BYSS01 (anamorph, Paecilomyces sp.), which was isolated from jet fuel, is highly adapted to grow in hydrocarbons, having predicted genes involved in degradation of n -alkanes, branched alkanes, and aromatic compounds. The draft genome size is estimated at 29 Mb, containing 8,509 proteins.

scholarly journals Fungal Genomic Resources for Strain Identification and Diversity Analysis of 1900 Fungal Species

2021 ◽  
Vol 7 (4) ◽  
pp. 288
Author(s):  
Mir Asif Iquebal ◽  
Sarika Jaiswal ◽  
Vineet Kumar Mishra ◽  
Rahul Singh Jasrotia ◽  
Ulavappa B. Angadi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
In Silico ◽  
Sequence Data ◽  
Fungal Species ◽  
Genomic Research ◽  
Whole Genome Sequence ◽  
Strain Identification ◽  
Diversity Analysis ◽  
Whole Genome

Identification and diversity analysis of fungi is greatly challenging. Though internal transcribed spacer (ITS), region-based DNA fingerprinting works as a “gold standard” for most of the fungal species group, it cannot differentiate between all the groups and cryptic species. Therefore, it is of paramount importance to find an alternative approach for strain differentiation. Availability of whole genome sequence data of nearly 2000 fungal species are a promising solution to such requirement. We present whole genome sequence-based world’s largest microsatellite database, FungSatDB having >19M loci obtained from >1900 fungal species/strains using >4000 assemblies across globe. Genotyping efficacy of FungSatDB has been evaluated by both in-silico and in-vitro PCR. By in silico PCR, 66 strains of 8 countries representing four continents were successfully differentiated. Genotyping efficacy was also evaluated by in vitro PCR in four fungal species. This approach overcomes limitation of ITS in species, strain signature, and diversity analysis. It can accelerate fungal genomic research endeavors in agriculture, industrial, and environmental management.

scholarly journals Revised Transcriptome-Based Gene Annotation for Aspergillus flavus Strain NRRL 3357

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
E. Anne Hatmaker ◽  
Xiaofan Zhou ◽  
Matthew E. Mead ◽  
Heungyun Moon ◽  
Jae-Hyuk Yu ◽  
...  
Keyword(s):  
Aspergillus Flavus ◽  
Filamentous Fungus ◽  
Sequence Data ◽  
Gene Annotation ◽  
Stress Conditions ◽  
Content Type ◽  
Transcript Sequence ◽  
Long Read

ABSTRACT Aspergillus flavus is an agriculturally and medically important filamentous fungus that produces mycotoxins, including aflatoxins, which are potent carcinogens. Here, we generated short- and long-read transcript sequence data from the growth of A. flavus strain NRRL 3357 under both typical and stress conditions to produce a new annotation of its genome.

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