scholarly journals Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

2019 ◽  
Vol 9 (10) ◽  
pp. 3057-3066 ◽  
Author(s):  
Eoin O’Connor ◽  
Jamie McGowan ◽  
Charley G. P. McCarthy ◽  
Aniça Amini ◽  
Helen Grogan ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Agaricus Bisporus ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Protein Coding ◽  
Single Strain ◽  
Protein Coding Genes ◽  
Starting Point

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as ‘Heirloom’. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60–70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

Comparison of three species of Elizabethkingia genus by whole-genome sequence analysis

2021 ◽  
Vol 368 (5) ◽  
Author(s):  
Chen Yang ◽  
Zhe Liu ◽  
Shuai Yu ◽  
Kun Ye ◽  
Xin Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Analysis ◽  
Information Storage ◽  
Whole Genome Sequence ◽  
Neonatal Meningitis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Significant Finding ◽  
Beta Lactams ◽  
Clusters Of Orthologous Groups

Abstract Elizabethkingia are found to cause severe neonatal meningitis, nosocomial pneumonia, endocarditis and bacteremia. However, there are few studies on Elizabethkingia genus by comparative genomic analysis. In this study, three species of Elizabethkingia were found: E. meningoseptica, E. anophelis and E. miricola. Resistance genes and associated proteins of seven classes of antibiotics including beta-lactams, aminoglycosides, macrolides, tetracyclines, quinolones, sulfonamides and glycopeptides, as well as multidrug resistance efflux pumps were identified from 20 clinical isolates of Elizabethkingia by whole-genome sequence. Genotype and phenotype displayed a good consistency in beta-lactams, aminoglycosides and glycopeptides, while contradictions exhibited in tetracyclines, quinolones and sulfonamides. Virulence factors and associated genes such as hsp60 (htpB), exopolysaccharide (EPS) (galE/pgi), Mg2+ transport (mgtB/mgtE) and catalase (katA/katG) existed in all clinical and reference strains. The functional analysis of the clusters of orthologous groups indicated that ‘metabolism’ occupied the largest part in core genome, ‘information storage and processing’ was the largest group in both accessory genome and unique genome. Abundant mobile elements were identified in E. meningoseptica and E. anophelis. The most significant finding in our study was that a single clone of E. anophelis had been circulating within diversities of departments in a clinical setting for nearly 18 months.

scholarly journals Whole-Genome Sequence ofCorynebacterium auriscanisStrain CIP 106629 Isolated from a Dog with Bilateral Otitis from the United Kingdom

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Sandeep Tiwari ◽  
Syed Babar Jamal ◽  
Leticia Castro Oliveira ◽  
Dominique Clermont ◽  
Chantal Bizet ◽  
...  
Keyword(s):  
United Kingdom ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The United Kingdom ◽  
Circular Genome

In this work, we describe a set of features ofCorynebacterium auriscanisCIP 106629 and details of the draft genome sequence and annotation. The genome comprises a 2.5-Mbp-long single circular genome with 1,797 protein-coding genes, 5 rRNA, 50 tRNA, and 403 pseudogenes, with a G+C content of 58.50%.

scholarly journals Complete Genome Sequence of Staphylococcus epidermidis 1457

2017 ◽  
Vol 5 (22) ◽  
Author(s):  
Madeline R. Galac ◽  
Jason Stam ◽  
Rosslyn Maybank ◽  
Mary Hinkle ◽  
Dietrich Mack ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Staphylococcus Epidermidis ◽  
Complete Genome Sequence ◽  
Genetic Manipulation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Protein Coding ◽  
Content Type ◽  
Related Research ◽  
Protein Coding Genes

ABSTRACT Staphylococcus epidermidis 1457 is a frequently utilized strain that is amenable to genetic manipulation and has been widely used for biofilm-related research. We report here the whole-genome sequence of this strain, which encodes 2,277 protein-coding genes and 81 RNAs within its 2.4-Mb genome and plasmid.

scholarly journals Whole-Genome Sequence of Rummeliibacillus stabekisii Strain PP9 Isolated from Antarctic Soil

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Fábio Faria da Mota ◽  
Renata Estebanez Vollú ◽  
Diogo Jurelevicius ◽  
Lucy Seldin
Keyword(s):  
Soil Sample ◽  
Genome Sequence ◽  
Noncoding Rnas ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Whole Genome ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Protein Coding Genes

The whole genome of Rummeliibacillus stabekisii PP9, isolated from a soil sample from Antarctica, consists of a circular chromosome of 3,412,092 bp and a circular plasmid of 8,647 bp, with 3,244 protein-coding genes, 12 copies of the 16S-23S-5S rRNA operon, 101 tRNA genes, and 6 noncoding RNAs (ncRNAs).

scholarly journals Improved Draft Genome Sequence of Microcystis aeruginosa NIES-298, a Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan

2018 ◽  
Vol 6 (5) ◽  
Author(s):  
Haruyo Yamaguchi ◽  
Shigekatsu Suzuki ◽  
Masanobu Kawachi
Keyword(s):  
Microcystis Aeruginosa ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Lake Kasumigaura ◽  
Protein Coding ◽  
Protein Coding Genes

ABSTRACT Microcystis aeruginosa is a globally well-known bloom-forming cyanobacterium. An improved draft whole-genome sequence of M. aeruginosa NIES-298, which is a microcystin-producing strain isolated from Lake Kasumigaura, Japan, is published here. The genome comprises approximately 5.0 Mbp, with an average G+C content of 42.6% and 4,537 predicted protein-coding genes.

scholarly journals Whole-Genome Sequence of Streptococcus parauberis Strain SP-llh, Isolated from Cows with Mastitis in Western China

2017 ◽  
Vol 5 (2) ◽  
Author(s):  
Longhai Liu ◽  
Feng Yang ◽  
Xinpu Li ◽  
Jinyin Luo ◽  
Zhe Zhang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Western China ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Streptococcus Parauberis ◽  
Large Contigs

ABSTRACT Streptococcus parauberis strain SP-llh was isolated from cows with mastitis in western China in 2015. The 2,522,235-bp genome sequence consists of 46 large contigs in 14 scaffolds and contains 2,620 predicted protein-coding genes, with a G+C content of 35.3%.

scholarly journals Whole-Genome Sequence of Mycobacterium bovis W-1171, Isolated from the Laryngopharyngeal Lymph Node of a Wild Boar in South Korea

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Narae Kim ◽  
Yunho Jang ◽  
So-young Park ◽  
Woong-seog Song ◽  
Jong-Taek Kim ◽  
...  
Keyword(s):  
Lymph Node ◽  
South Korea ◽  
Wild Boar ◽  
Mycobacterium Bovis ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Free Ranging

Mycobacterium bovis W-1171 was isolated from a wild boar living in a free-ranging field in Gyeonggido, South Korea. The whole-genome sequence of this strain was determined in 50 contigs, which was 4,304,865 bp with a 65.57% G+C content. In total 3,945 protein-coding genes were predicted from this assembly.

scholarly journals Whole-Genome Sequence of Haloimpatiens lingqiaonensis Strain P8956

2019 ◽  
Vol 8 (43) ◽  
Author(s):  
Hussein Anani ◽  
Didier Raoult ◽  
Pierre-Edouard Fournier
Keyword(s):  
Genome Sequence ◽  
Bacterial Isolate ◽  
Paper Mill ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Paper Mill Wastewater ◽  
Rna Genes

In 2016, Haloimpatiens lingqiaonensis was described as a bacterial isolate from paper mill wastewater. Previously, no whole-genome sequence was available for this microorganism. Whole-genome sequencing of strain P8956 yielded a 3,295,388-bp genome with a 30.7% G+C content, 2,917 protein-coding genes, and 95 predicted RNA genes.

scholarly journals The complete genome sequence of a bile-isolated Stenotrophomonas maltophilia ZT1

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Min Zhang ◽  
Lixiang Li ◽  
Hongwei Pan ◽  
Tao Zhou
Keyword(s):  
Genome Sequence ◽  
Stenotrophomonas Maltophilia ◽  
Gc Content ◽  
Genomic Analysis ◽  
Whole Genome Sequence ◽  
Functional Verification ◽  
Comparative Genomic ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Human Bile

Abstract Background Stenotrophomonas maltophilia is one of the most frequently isolated opportunistic pathogens that can cause infections in humans. Many researches concerned the mechanism of antibiotic resistance displayed by S. maltophilia, however, the mechanism of its pathogenesis and its adaptation to special niches, such as bile, remain unclear. Results In this study, the S. maltophilia strain ZT1 was isolated from human bile. Its genome was sequenced and a circular chromosome of 4,391,471 bp was obtained with a GC content of 66.51%. There were 3962 protein-coding sequences, 7 rRNAs and 74 tRNAs in the chromosome. Compared with Virulence Factor Database, we identified more than 500 candidate virulence genes including genes encoding fimbrial assembly protein, enterobactin synthesis pathway proteins, efflux pumps, and the DNA and/or proteins secretion system in the genome of strain ZT1. Additionally, there were at least 22 genes related to bile adaption, including emrAB, acrRAB, galU, rfbC, tolC and mdtABC. Conclusions This is the first study to reveal the whole genome sequence of the ZT1 strain of S. maltophilia isolated from human bile. We identified hundreds virulence factors and 22 bile adaptation-related genes in the genome of the S. maltophilia strain ZT1. Further comparative genomic analysis and functional verification would aid in understanding the pathogenesis and bile adaptation of S. maltophilia.

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