scholarly journals Whole genome sequence of an edible and potential medicinal fungus, Cordyceps guangdongensis

2018 ◽  
Author(s):  
Chenghua Zhang ◽  
Wangqiu Deng ◽  
Wenjuan Yan ◽  
Taihui Li
Keyword(s):  
Gene Annotation ◽  
Wild Strain ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Single Spore ◽  
Edible Fungus ◽  
Single Spore Isolate ◽  
Biological Studies ◽  
Pharmaceutical Industries

ABSTRACTCordyceps guangdongensis is an edible fungus which has been approved as a Novel Food by the Chinese Ministry of Public Health in 2013. It also has a broad application prospect in pharmaceutical industries with many medicinal activities. In this study, the whole genome of C. guangdongensis GD15, a single spore isolate from a wild strain, was sequenced and assembled with Illumina and PacBio sequencing technology. The generated genome is 29.05 Mb in size, comprising 9 scaffolds with an average GC content of 57.01%. It is predicted to contain a total of 9150 protein-coding genes. Sequence identification and comparative analysis indicated that the assembled scaffolds contained two complete chromosomes and four single-end chromosomes, showing a high level assembly. Gene annotation revealed a diversity of transporters that could contribute to the genome size and evolution. Besides, approximately 15.49% and 13.70% genes involved in metabolic processes were annotated by KEGG and COG respectively. Genes belonging to CAZymes accounted for a proportion of 2.84% of the total genes. In addition, 435 transcription factors (TFs) were identified, which were involved in various biological processes. Among the identified TFs, the fungal transcription regulatory proteins (18.39%) and fungal-specific TFs (19.77%) represented the two largest classes of TFs. These data provided a much needed genomic resource for studying C. guangdongensis, laying a solid foundation for further genetic and biological studies, especially for elucidating the genome evolution and exploring the regulatory mechanism of fruiting body development.

scholarly journals The Whole-Genome Sequence of the Novel Yeast Species Metschnikowia persimmonesis Isolated from Medicinal Plant Diospyros kaki Thunb

2021 ◽  
Author(s):  
Endang Rahmat ◽  
Inkyu Park ◽  
Youngmin Kang
Keyword(s):  
Gc Content ◽  
Whole Genome Sequence ◽  
Diospyros Kaki ◽  
Whole Genome ◽  
The Novel ◽  
Data Set ◽  
Draft Assembly ◽  
Future Possibility ◽  
Complete Set ◽  
New Yeast

Abstract The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high quality whole-genome assembly of M. persimmonesis produced by PacBio RSII sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7,029 genes and 6,939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

scholarly journals Whole-Genome Sequence of Fish-Pathogenic Enterococcus faecalis Strain BFFF11

2020 ◽  
Vol 9 (7) ◽  
Author(s):  
Tasmina Akter ◽  
M. Mahbubur Rahman ◽  
Alfred Chin Yen Tay ◽  
Rakib Ehsan ◽  
M. Tofazzal Islam
Keyword(s):  
Enterococcus Faecalis ◽  
Genome Sequence ◽  
Gc Content ◽  
Fish Farm ◽  
Pathogenic Bacterium ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

A fish-pathogenic bacterium, Enterococcus faecalis strain BFFF11, was isolated from a tilapia suffering from streptococcosis in a fish farm in the Gazipur district of Bangladesh. The whole genome of this strain, BFFF11, was 3,067,042 bp, with a GC content of 37.4%.

scholarly journals Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum β-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Pushpa Lata ◽  
Subramaniam S. Govindarajan ◽  
Feng Qi ◽  
Jian-Liang Li ◽  
Santosh K. Maurya ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences ◽  
Central Florida ◽  
Magnolia Grandiflora ◽  
Extended Spectrum

ABSTRACT Pantoea americana strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from Magnolia grandiflora in central Florida, USA. Here, we report the de novo whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.

scholarly journals Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Amjad B. Khalil ◽  
Neelamegam Sivakumar ◽  
Muhammad Arslan ◽  
Hamna Saleem ◽  
Sami Qarawi
Keyword(s):  
Saudi Arabia ◽  
Hot Spring ◽  
Gc Content ◽  
Morphological Characterization ◽  
Thermophilic Bacterium ◽  
Whole Genome Sequence ◽  
Strictly Aerobic ◽  
Whole Genome ◽  
Aerobic Bacterium ◽  
Wide Range

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

scholarly journals Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

2020 ◽  
Author(s):  
Xueping LI ◽  
Jianhong Li ◽  
Yonghong Qi ◽  
Yonggang Liu ◽  
Minquan Li
Keyword(s):  
Molecular Mechanisms ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Effective Control ◽  
Sequence Length ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Fusarium Equiseti ◽  
Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

scholarly journals Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Sheng-yong Xu ◽  
Na Song ◽  
Shi-jun Xiao ◽  
Tian-xiang Gao
Keyword(s):  
Microsatellite Markers ◽  
Gc Content ◽  
The Philippines ◽  
Whole Genome Sequence ◽  
Northwestern Pacific ◽  
Whole Genome ◽  
Survey Analysis ◽  
Genome Survey ◽  
Sebastiscus Marmoratus ◽  
Wide Range

Abstract The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

scholarly journals Whole-Genome Sequencing of a Year-Round Fruiting Jackfruit Variety Reveals Very High Single Nucleotide Polymorphisms in Inter-Genic Regions

2021 ◽  
Author(s):  
Tofazzal Islam ◽  
Nadia Afroz ◽  
ChuShin Koh ◽  
M. Nazmul Haque ◽  
Md. Jillur Rahman ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
De Novo ◽  
Agricultural Research ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tropical Fruit

Abstract Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing the single copy orthologues (SCOs) in three closely and one distantly related species of BARI Kanthal-3, 706 SCOs were found to be shared across the genomes of the five species. The phylogenetic analysis of the shared SCOs showed that A. heterophyllus is the closest species to BARI Kantal-3. The estimated genome size of BARI Kanthal-3 was 1.04 giga base pairs (Gbp) with a heterozygosity rate of 1.62%. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 includes 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are located in inter-genic regions. Conclusion The whole-genome sequence of A. heterophyllus cv. BARI Kanthal-3 reveals extremely high single nucleotide polymorphisms in inter-genic regions. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting and the markers development for molecular breeding of this highly nutritious fruit crop.

scholarly journals Sequencing, De Novo Assembly, and Annotation of the Complete Genome of a New Thraustochytrid Species, Strain CCAP_4062/3

2018 ◽  
Vol 6 (11) ◽  
Author(s):  
Khawla Seddiki ◽  
François Godart ◽  
Riccardo Aiese Cigliano ◽  
Walter Sanseverino ◽  
Mohamed Barakat ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
De Novo Assembly ◽  
Complete Genome ◽  
De Novo ◽  
Gc Content ◽  
Marine Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences

ABSTRACT Thraustochytrids are ecologically and biotechnologically relevant marine species. We report here the de novo assembly and annotation of the whole-genome sequence of a new thraustochytrid strain, CCAP_4062/3. The genome size was estimated at 38.7 Mb with 11,853 predicted coding sequences, and the GC content was scored at 57%.

scholarly journals Draft Genome Sequence of Aspergillus oryzae BP2-1, Isolated from Traditional Malted Rice in South Korea

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Jongbum Jeon ◽  
Jung A Kim ◽  
Sook-Young Park ◽  
Gye-Won Kim ◽  
Cheon-Seok Park ◽  
...  
Keyword(s):  
South Korea ◽  
Aspergillus Oryzae ◽  
Genome Sequence ◽  
Draft Genome ◽  
Starter Culture ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

The fungus Aspergillus oryzae strain BP2-1 was isolated from the traditional malted starter culture nuruk. We report here the draft whole-genome sequence of A. oryzae BP2-1, which is comprised of 14 scaffolds with a total length of 39,455,382 bp and a GC content of 47.13%.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

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