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

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.

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

BioMed Research International ◽

10.1155/2018/5862437 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 4

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.

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Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Bioscience Reports ◽

10.1042/bsr20192252 ◽

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.

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638. Comparative Genomics of Mycoplasma pneumoniae Isolated From Children with Pneumonia: South Korea, 2010–2016

Open Forum Infectious Diseases ◽

10.1093/ofid/ofz360.706 ◽

2019 ◽

Vol 6 (Supplement_2) ◽

pp. S295-S295

Author(s):

Hoan J Lee ◽

Joon Kee Lee ◽

Yun Young Choi ◽

Ji Young Park ◽

Moon-Woo Seong ◽

...

Keyword(s):

Comparative Genomics ◽

South Korea ◽

Mycoplasma Pneumoniae ◽

Gc Content ◽

Genomic Analysis ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Whole Genome

Abstract Background This study applied high-throughput whole-genome sequencing (WGS) technologies to investigate the comparative genomics of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during two epidemics from 2010 to 2016 in comparison with a global collection of 48 Mycoplasma pneumoniae strains which includes seven countries ranging from 1944 to 2017. Methods A total number of 30 M. pneumoniae strains were selected for whole-genome sequence analysis from two epidemics, 2010–2012 and 2014–2016. Next-generation sequencing (NGS) of all M. pneumoniae strains was performed using the Illumina MiSeq desktop sequencer. Comparative genomic analysis was performed using BLAST Ring Image Generator (BRIG), MAUVE, MAFFT, CLC Phylogeny Module, SnpEff, and Pathosystems Resource Integration Center (PATRIC). Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to>99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea, formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusion The comparative genomics of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high. Disclosures All authors: No reported disclosures.

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Draft Genome Sequence of Ciprofloxacin and Ceftriaxone Resistant Campylobacter jejuni MM26-781 Assigned to Novel ST Isolated From Common Pigeon in Lithuania

Evolutionary Bioinformatics ◽

10.1177/1176934319868469 ◽

2019 ◽

Vol 15 ◽

pp. 117693431986846

Author(s):

Jurgita Aksomaitiene ◽

Sigita Ramonaite ◽

Aleksandr Novoslavskij ◽

Mindaugas Malakauskas ◽

Egle Kudirkiene

Keyword(s):

Antibiotic Resistance ◽

Campylobacter Jejuni ◽

Genome Sequence ◽

Molecular Mechanisms ◽

Draft Genome ◽

Columba Livia ◽

Draft Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Wide Range

Campylobacter jejuni is an important zoonotic pathogen known to be resistant to a wide range of antibiotics worldwide. Campylobacter jejuni may be intrinsically resistant to antibiotics or can acquire antibiotic resistance determinants through gene transfer. However, the knowledge of molecular mechanisms of antimicrobial resistance among Campylobacter isolates from wild birds, especially in Lithuania, is limited. Whole genome sequencing (WGS) is a tool for better understanding the evolutionary and epidemiologic dynamics of C jejuni. This study describes a draft whole genome sequence of C jejuni MM26-781 isolated from a common pigeon ( Columba livia) in Lithuania in 2011 and assigned to ST-6424 (CC179) sequence type. The draft genome sequence contained 1.68 Mb, comprising 1651 coding genes, 40 transfer RNAs, 1 ribosomal RNA, and 69 pseudogenes with an average G + C content of 30.4%. The RAST (Rapid Annotation using Subsystem Technology) pipeline annotated (NCTC11168) a total of 305 subsystems in the genome of C jejuni MM26-781 strain, with most of the genes associated with amino acids and derivatives related to metabolism (18.93%) and protein metabolism (14.43%). The genes and mutations related to antibiotic resistance, including gyrA and gyrB genes associated with quinolone resistance, blaOXA-448 gene (locus tag C9371_07715) associated with resistance to β-lactams, rpoB gene associated with resistance to rifamycin, vgaE gene associated with resistance to streptogramin and efflux system CmeABC ( cmeA, cmeB, cmeC), efflux pump PmrA, and transcriptional regulator CmeR responsible for multidrug resistance in C jejuni MM26-781 chromosome, were identified. Also, the virulence factors, including ciaB, cadF, ceuE, pldA, motB, and bd1A genes, were identified by WGS data analysis.

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Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation

Diversity ◽

10.3390/d10040113 ◽

2018 ◽

Vol 10 (4) ◽

pp. 113 ◽

Cited By ~ 8

Author(s):

Sunitha Joseph ◽

Rebecca O’Connor ◽

Abdullah Al Mutery ◽

Mick Watson ◽

Denis Larkin ◽

...

Keyword(s):

Comparative Genomics ◽

Chicken Genome ◽

Read Depth ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Peregrine Falcon ◽

Whole Genome ◽

Level Sequence ◽

Wide Range ◽

Chromosome Level

Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.

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Whole-Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion

Genome Announcements ◽

10.1128/genomea.00886-17 ◽

2017 ◽

Vol 5 (35) ◽

Cited By ~ 4

Author(s):

Chun-Hao Jiang ◽

Yun Chen ◽

Fang Yan ◽

Zhi-Hang Fan ◽

Jian-Hua Guo

Keyword(s):

Bacillus Cereus ◽

Genome Sequence ◽

Molecular Mechanisms ◽

Growth Promotion ◽

Draft Genome ◽

Gc Content ◽

Whole Genome Sequence ◽

Whole Genome ◽

Content Type ◽

Soilborne Disease

ABSTRACT Bacillus cereus AR156 was originally isolated from the forest soil of Zhenjiang, a city in China. To shed new light on the molecular mechanisms underlying the biological control of soilborne pathogens, the whole genome of this strain was sequenced. Here, we report the draft genome sequence of this strain, consisting of a single circularized contig measuring 5.66 Mb, with an average GC content of 35.5% and 5,367 open reading frames.

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Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data

Genes ◽

10.3390/genes12111830 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1830

Author(s):

Victor B. Pedrosa ◽

Flavio S. Schenkel ◽

Shi-Yi Chen ◽

Hinayah R. Oliveira ◽

Theresa M. Casey ◽

...

Keyword(s):

Milk Production ◽

Genome Sequence ◽

North American ◽

Milk Fat ◽

Molecular Mechanisms ◽

Sequence Data ◽

Whole Genome Sequence ◽

Holstein Cattle ◽

Whole Genome ◽

Production Traits

Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.

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

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab246 ◽

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.

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PSXIV-24 Real-time, on-site whole genome sequencing with oxford nanopore technologies’ MinION

Journal of Animal Science ◽

10.1093/jas/skab235.470 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 257-258

Author(s):

Hanna Ostrovski ◽

Rodrigo Pelicioni Savegnago ◽

Wen Huang ◽

Cedric Gondro

Keyword(s):

Real Time ◽

Ease Of Use ◽

Whole Genome Sequence ◽

Genomic Sequencing ◽

Whole Genome ◽

Illumina Hiseq ◽

Base Calling ◽

Oxford Nanopore ◽

Oxford Nanopore Technologies

Abstract Most quantitative geneticists are traditionally trained for data analysis in genetic evaluation and genomic prediction, but rarely have extensive knowledge of molecular genetics or experience in experimental labs. Recent products, such as those launched by Oxford Nanopore Technologies (ONT), give those quantitative geneticists a comprehensible and hands-on toolkit to explore DNA sequencing. The ‘MinION’, a small DNA sequencer, is of interest for quantitative geneticists due to both the minimal learning curve and the non-proprietary USB connectivity. This device is small enough to be portable, allowing for potential real-time, on-farm sequencing. The objective of this project is to compare the whole genome sequence (WGS) output of the MinION sequencer to that of the Illumina HiSeq 4000. Blood was collected from a 6-month-old Akaushi calf born on a Michigan State University farm. DNA was extracted from the sample using the QIAamp DNA Blood Kit from Qiagen, and library DNA ligation preparation (SQK-LSK109) from ONT was used. After base-calling with guppy software (provided by ONT), the data were preprocessed and experimental runs with the MinION were compared using quality control. Finally, the data were aligned with guppy software, and was compared to the aligned WGS obtained with Illumina HiSeq. Quality results from each MinION indicate that, despite the low amount of sequence collected in each run (~225,303 reads per run), the quality of bases sequenced was high (Q≥7). The aligned data from the Illumina sequencer provided 40x coverage of the genome, with a total of 739,339,742 reads. Although the amount of data obtained with MinION is much smaller than that of Illumina HiSeq, the high quality of MinION’s data combined with its ease of use give an opportunity of genomic sequencing for users who are either inexperienced or do not have access to large genomic sequencing devices.

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

Microbiology Resource Announcements ◽

10.1128/mra.01447-19 ◽

2020 ◽

Vol 9 (7) ◽

Cited By ~ 1

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%.

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