Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.

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Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

GigaScience ◽

10.1093/gigascience/giz112 ◽

2019 ◽

Vol 8 (9) ◽

Cited By ~ 11

Author(s):

Yu Xing ◽

Yang Liu ◽

Qing Zhang ◽

Xinghua Nie ◽

Yamin Sun ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Genetic Improvement ◽

De Novo ◽

Draft Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

High Quality ◽

Chinese Chestnut ◽

Castanea Mollissima

AbstractBackgroundThe Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.FindingsWe produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.ConclusionsThe high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

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Whole genome sequence analysis reveals high genetic variation of newly isolated Acidithiobacillus ferrooxidans IO-2C

Scientific Reports ◽

10.1038/s41598-019-49213-x ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Anila Fariq ◽

John C. Blazier ◽

Azra Yasmin ◽

Terry J. Gentry ◽

Youjun Deng

Keyword(s):

Acidithiobacillus Ferrooxidans ◽

Genomic Analysis ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Whole Genome Sequence ◽

Whole Genome ◽

Protein Coding ◽

Acidophilic Bacterium ◽

Iron Sulphate ◽

Acidic Conditions

Abstract Acidithiobacillus ferrooxidans, a chemolithoautotrophic bacterium, is well known for its mineral oxidizing properties. The current study combines experimental and whole genome sequencing approaches to investigate an iron oxidizing, extreme acidophilic bacterium, A. ferrooxidans isolate (IO-2C) from an acid seep area near Carlos, TX, USA. Strain IO-2C was capable of oxidizing iron i.e. iron sulphate and iron ammonium sulphate yielding shwertmannite and jarosite minerals. Further, the bacterium’s genome was sequenced, assembled and annotated to study its general features, structure and functions. To determine genetic heterogeneity, it was compared with the genomes of other published A. ferrooxidans strains. Pan-genome analysis displayed low gene conservation and significant genetic diversity in A. ferrooxidans species comprising of 6926 protein coding sequences with 23.04% (1596) core genes, 46.13% (3195) unique and 30.82% (2135) accessory genes. Variant analysis showed >75,000 variants, 287 of them with a predicted high impact, in A. ferrooxidans IO-2C genome compared to the reference strain, resulting in abandonment of some important functional key genes. The genome contains numerous functional genes for iron and sulphur metabolism, nitrogen fixation, secondary metabolites, degradation of aromatic compounds, and multidrug and heavy metal resistance. This study demonstrated the bio-oxidation of iron by newly isolated A. ferrooxidans IO-2C under acidic conditions, which was further supported by genomic analysis. Genomic analysis of this strain provided valuable information about the complement of genes responsible for the utilization of iron and tolerance of other metals.

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Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate

Genome Announcements ◽

10.1128/genomea.00556-16 ◽

2016 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

María Lázaro-Díez ◽

Santiago Redondo-Salvo ◽

Aroa Arboleya-Agudo ◽

Javier Gonzalo Ocejo-Vinyals ◽

Itziar Chapartegui-González ◽

...

Keyword(s):

Adult Patient ◽

Single Molecule ◽

Genome Assembly ◽

Complete Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

Smrt Sequencing ◽

Protein Coding ◽

Hafnia Alvei ◽

Protein Coding Genes

A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding genes are predicted from this assembly.

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

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400563 ◽

2019 ◽

Vol 9 (10) ◽

pp. 3057-3066 ◽

Cited By ~ 2

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.

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Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1501764112 ◽

2015 ◽

Vol 112 (11) ◽

pp. E1257-E1262 ◽

Cited By ~ 103

Author(s):

Yan-Bo Sun ◽

Zi-Jun Xiong ◽

Xue-Yan Xiang ◽

Shi-Ping Liu ◽

Wei-Wei Zhou ◽

...

Keyword(s):

De Novo ◽

Structural Evolution ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Whole Genome ◽

Protein Coding ◽

Comparable Rate ◽

Evolutionary Studies ◽

Genomic Studies ◽

The Difference

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

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First Complete Genome Sequence of Marinilactibacillus piezotolerans Strain 15R, a Marine Lactobacillus Isolated from Coal-Bearing Sediment 2.0 Kilometers below the Seafloor, Determined by PacBio Single-Molecule Real-Time Technology

Genome Announcements ◽

10.1128/genomea.01625-16 ◽

2017 ◽

Vol 5 (7) ◽

Cited By ~ 2

Author(s):

Yuli Wei ◽

Junwei Cao ◽

Jiasong Fang ◽

Chiaki Kato ◽

Weicheng Cui

Keyword(s):

Genome Sequence ◽

Single Molecule ◽

Whole Genome Sequence ◽

Northwestern Pacific ◽

Whole Genome ◽

Protein Coding ◽

Coding Sequences ◽

Content Type ◽

Subsurface Sediment ◽

Candidate Protein

ABSTRACT Marinilactibacillus piezotolerans strain 15R is a facultatively anaerobic heterotrophic lactobacillus isolated from deep marine subsurface sediment nearly 2 km below the seafloor in the northwestern Pacific. We report here the first whole-genome sequence of strain 15R. The identified genome sequence has 2,767,908 bp, 35.4% G+C content, and predicted 2,552 candidate protein-coding sequences, with no identified plasmids.

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Whole-Genome Assembly of Klebsiella pneumoniae Coproducing NDM-1 and OXA-232 Carbapenemases Using Single-Molecule, Real-Time Sequencing

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.03180-14 ◽

2014 ◽

Vol 58 (10) ◽

pp. 5947-5953 ◽

Cited By ~ 43

Author(s):

Yohei Doi ◽

Tracy H. Hazen ◽

Matthew Boitano ◽

Yu-Chih Tsai ◽

Tyson A. Clark ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Real Time ◽

Single Molecule ◽

De Novo ◽

Whole Genome Sequence ◽

Mercury Resistance ◽

Whole Genome ◽

Smrt Sequencing ◽

Single Chromosome ◽

Content Type

ABSTRACTThe whole-genome sequence of a carbapenem-resistantKlebsiella pneumoniaestrain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run.K. pneumoniaePittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of theK. pneumoniaereference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids are unique. The plasmid pPKPN1, an IncHI1B-like plasmid, carries theblaNDM-1,armA, andqnrB1genes, along with tellurium and mercury resistance operons.blaNDM-1is carried on a unique structure in which Tn125is further bracketed by IS26downstream of a class 1 integron. The IncFIA-like plasmid pPKPN3 also carries an array of resistance elements, includingblaCTX-M-15and a mercury resistance operon. The ColE-type plasmid pPKPN4 carryingblaOXA-232is identical to a plasmid previously reported from France. SMRT sequencing was useful in resolving the complex bacterial genomic structures in thede novoassemblies.

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Whole-Genome Sequence of Acinetobacter pittii HUMV-6483 Isolated from Human Urine

Genome Announcements ◽

10.1128/genomea.00658-17 ◽

2017 ◽

Vol 5 (29) ◽

Author(s):

Itziar Chapartegui-González ◽

María Lázaro-Díez ◽

Santiago Redondo-Salvo ◽

Laura Alted-Pérez ◽

Javier Gonzalo Ocejo-Vinyals ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Human Urine ◽

Complete Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

Protein Coding ◽

Content Type ◽

Protein Coding Genes ◽

Acinetobacter Pittii

ABSTRACT Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly.

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Whole Genome Sequencing Reveals Identification of New Acinetobacter spp. (maqsudiensis) from Local Meat Samples Collected from Dhaka, Bangladesh

10.20944/preprints201811.0138.v1 ◽

2018 ◽

Author(s):

Muhammad Maqsud Hossain ◽

Abdus Sadique ◽

Aura Rahman ◽

Abdul Khaleque ◽

Abdul Mueed Ibne Momen ◽

...

Keyword(s):

Genome Sequence ◽

Draft Genome ◽

Genomic Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Acinetobacter Species ◽

E Coli ◽

Potential Marker ◽

Meat Samples ◽

Generation Technology

In this study we announce the draft genome sequence of a newly identified Acinetobacter species cross-reacting with E. coli serotype 0157:H7. The advent of Next-Generation technology has paved to way to discover new species which could otherwise be misidentified using conventional cultural and serotyping methods. The whole genome sequence of this isolate will help to identify potential marker/s of intervention and further genomic analysis might also shed light onto the virulence properties of this newly identified Acinetobacter species which has been provided the new name of Acinetobacter maqsudiensis.

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