scholarly journals Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal Tolerance

2021 ◽  
Vol 12 ◽  
Author(s):  
Bin-Bin Chi ◽  
Ya-Nan Lu ◽  
Ping-Chuan Yin ◽  
Hong-Yan Liu ◽  
Hui-Ying Chen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Metal Tolerance ◽  
Gc Content ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Gene Arrangement ◽  
Comparative Genomic ◽  
Evolutionary Divergence ◽  
Penicillium Janthinellum ◽  
Chromium Resistance

Heavy metal pollution is a global knotty problem and fungi hold promising potential for the remediation of wastewater containing heavy metals. Here, a new highly chromium-tolerance species, Penicillium janthinellum P1, is investigated. The genome of P1 was sequenced and assembled into 30 Mb genome size containing 10,955 predicted protein-coding genes with a GC content of 46.16% through an integrated method of Illumina short-read sequencing and single-molecule real-time Pacific Biosciences sequencing platforms. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of Penicillium janthinellum P1 and Penicillium oxalicum 114-2 was estimated to be 74 MYA. 33 secondary metabolism gene clusters were identified via antiSMASH software, mainly including non-ribosomal peptide synthase genes and T1 polyketide synthase genes. 525 genes were annotated to encode enzymes that act on carbohydrates, involving 101 glucose-degrading enzymes and 24 polysaccharide synthase. By whole-genome sequence analysis, large numbers of metal resistance genes were found in strain P1. Especially ABC transporter and Superoxide dismutase ensure that the P1 fungus can survive in a chromium-polluted environment. ChrA and ChrR were also identified as key genes for chromium resistance. Analysis of their genetic loci revealed that the specific coding-gene arrangement may account for the fungus’s chromium resistance. Genetic information and comparative analysis of Penicillium janthinellum are valuable for further understanding the mechanism of high resistance to heavy metal chromium, and gene loci analysis provides a new perspective for identifying chromium-resistant strains.

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.

Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium

2020 ◽  
Author(s):  
Jiaokun Li ◽  
Tianyuan Gu ◽  
Weimin Zeng ◽  
Runlan Yu ◽  
Yuandong Liu ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Resistance Genes ◽  
Complete Genome ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Comparative Genomic ◽  
Bacillus Sp ◽  
Bacillus Genus

Abstract Background: Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. Results: Here, we identified a 5,579,638 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As(III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Further, a series of genes associated with Sb(III) and other heavy metal(loid)s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), we found that Bacillus sp. S3 was a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed that evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal(loid)s resistance genes emphasized its indispensable roles in the harsh eco-environment of Bacillus genus. The real-time Quantitative PCR (RT-qPCR) results of Sb(III)-related genes indicated that the Sb(III) resistance was constantly increased under the Sb(III) stress. Conclusions: The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationship between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.

scholarly journals Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis

2009 ◽  
Vol 191 (14) ◽  
pp. 4492-4501 ◽  
Author(s):  
Keh-Ming Wu ◽  
Ling-Hui Li ◽  
Jing-Jou Yan ◽  
Nina Tsao ◽  
Tsai-Lien Liao ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Liver Abscess ◽  
Nosocomial Infections ◽  
Capsular Polysaccharide ◽  
Gene Clusters ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Major Health Problem

ABSTRACT Nosocomial infections caused by antibiotic-resistant Klebsiella pneumoniae are emerging as a major health problem worldwide, while community-acquired K. pneumoniae infections present with a range of diverse clinical pictures in different geographic areas. In particular, an invasive form of K. pneumoniae that causes liver abscesses was first observed in Asia and then was found worldwide. We are interested in how differences in gene content of the same species result in different diseases. Thus, we sequenced the whole genome of K. pneumoniae NTUH-K2044, which was isolated from a patient with liver abscess and meningitis, and analyzed differences compared to strain MGH 78578, which was isolated from a patient with pneumonia. Six major types of differences were found in gene clusters that included an integrative and conjugative element, clusters involved in citrate fermentation, lipopolysaccharide synthesis, and capsular polysaccharide synthesis, phage-related insertions, and a cluster containing fimbria-related genes. We also conducted comparative genomic hybridization with 15 K. pneumoniae isolates obtained from community-acquired or nosocomial infections using tiling probes for the NTUH-K2044 genome. Hierarchical clustering revealed three major groups of genomic insertion-deletion patterns that correlate with the strains' clinical features, antimicrobial susceptibilities, and virulence phenotypes with mice. Here we report the whole-genome sequence of K. pneumoniae NTUH-K2044 and describe evidence showing significant genomic diversity and sequence acquisition among K. pneumoniae pathogenic strains. Our findings support the hypothesis that these factors are responsible for the changes that have occurred in the disease profile over time.

scholarly journals Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China

2021 ◽  
Vol 10 (1) ◽  
pp. 66
Author(s):  
Zhaoying Su ◽  
Shaojing Wang ◽  
Shicheng Yang ◽  
Yujun Yin ◽  
Yunke Cao ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Salt Tolerance ◽  
Petroleum Hydrocarbon ◽  
Produced Water ◽  
Metal Tolerance ◽  
Heavy Metal Tolerance ◽  
Gene Clusters ◽  
Alkane Degradation ◽  
Degrading Bacteria ◽  
Depth Analysis

The genome of Exiguobacterium aurantiacum SW-20 (E. aurantiacum SW-20), a salt-tolerant microorganism with petroleum hydrocarbon-degrading ability isolated from the Changqing Oilfield, was sequenced and analyzed. Genomic data mining even comparative transcriptomics revealed that some genes existed in SW-20 might be related to the salt tolerance. Besides, genes related to petroleum hydrocarbon degradation discovered in genomic clusters were also found in the genome, indicating that these genes have a certain potential in the bioremediation of petroleum pollutants. Multiple natural product biosynthesis gene clusters were detected, which was critical for survival in the extreme conditions. Transcriptomic studies revealed that some genes were significantly up-regulated as salinity increased, implying that these genes might be related to the salt tolerance of SW-20 when living in a high salt environment. In our study, gene clusters including salt tolerance, heavy metal tolerance and alkane degradation were all compared. When the same functional gene clusters from different strains, it was discovered that the gene composition differed. Comparative genomics and in-depth analysis provided insights into the physiological features and adaptation strategies of E. aurantiacum SW-20 in the oilfield environment. Our research increased the understanding of niches adaption of SW-20 at genomic level.

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

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.

scholarly journals Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium

2019 ◽  
Author(s):  
Jiaokun Li ◽  
Tianyuan Gu ◽  
Weimin Zeng ◽  
Runlan Yu ◽  
Yuandong Liu ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Resistance Genes ◽  
Complete Genome ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Evolutionary Relationships ◽  
Comparative Genomic ◽  
Bacillus Sp ◽  
Origin And Evolution ◽  
Bacillus Genus

Abstract Background: Antimonite [Sb(III)]-oxidizing bacterium have great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 isolated from antimony-contaminated soil showed high Sb(III) resistance and Sb(III) oxidation efficiency. However, very little genomic information and evolutionary relationships that bacterial oxidation of Sb(III) is available. Results: Here, we identified a 5579638 bp chromosome with 40.30% GC content and a 241339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contains key aioB gene potentially encoding As(III)/Sb(III) oxidase, is not shared with other Bacillus strains. Further, a series of genes associated with Sb(III) and other heavy metal(loid) were also ascertained, reflecting adaptive advantage for growth in the harsh eco-environment. It is noteworthy that Bacillus sp. S3 is a novel species within the Bacillus genus as indicated by phylogenetic relationship and the average nucleotide identities (ANI) analysis. The presence of genomic plasticity demonstrated a high number of mobile genetic elements (MGEs) that were mainly distributed on chromosomes within the Bacillus genus. The core genome contained 554 core genes and many unique genes were dissected in analyzed genomes, indicating a conserved core but adaptive pan repertoire. Whole genomic alignment indicates that frequently genomic reshuffling and rearrangements, genetic gain and loss, and other recombination events occurred during the evolutionary history of Bacillus genus. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed that evolutionary relationships and events of horizontal gene transfer (HGT) among the Bacillus genus. The assessment of functionality of heavy metal(loid) resistance genes emphasized its indispensable roles in the harsh eco-environment of Bacillus genus. The real-time Quantitative PCR(RT-qPCR) results of Sb(III)-related genes indicated that the Sb(III) resistance was constantly increased under the Sb(III) stress. Conclusions: The insights provided in this study shed light on the molecular details of Bacillus sp. S3 coping with Sb(III), which extended our understanding on the evolutionary relationship between Bacillus sp. S3 and other closely related species and will enrich the Sb(III) resistance genetic data sources.

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.

scholarly journals Genome Resource for Pseudomonas sp. Strain L22-9: A Potential Novel Species with Antifungal Activity

2020 ◽  
pp. PHYTO-06-20-024
Author(s):  
Jingling Liang ◽  
Sai Wang ◽  
Ayizekeranmu Yiming ◽  
Luoyi Fu ◽  
Wenhan Nie ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
Novel Species ◽  
Gc Content ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Pseudomonas Sp ◽  
Fungal Phytopathogens ◽  
Antimicrobial Metabolites

Pseudomonas is a complex genus with increasing numbers of new species. Recently, we isolated Pseudomonas sp. strain L22-9, which showed antifungal activity against several fungal phytopathogens. Here, we report the whole genome sequence of strain L22-9. Genomic analysis revealed that strain L22-9 contains one circular DNA chromosome of 6,730,360 bp length with 60.9% GC content. Bioinformatics analysis identified gene clusters in the genome that synthesize antimicrobial metabolites such as 2,4-diacetylphloroglucinol synthesis and hydrogen cyanide synthase. Further analysis suggests that strain L22-9 is a novel species of the genus Pseudomonas. This genome would be a valuable resource for future research in phytopathology.

scholarly journals The whole-genome sequence analysis of Morchella sextelata

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mei-Han ◽  
Qingshan-Wang ◽  
Baiyintala ◽  
Wuhanqimuge
Keyword(s):  
De Novo ◽  
Gc Content ◽  
Gene Clusters ◽  
Essential Amino Acids ◽  
Biologically Active ◽  
Whole Genome Sequence ◽  
Daily Consumption ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Morphological Studies

Abstract Morchella are macrofungi and are also called morels, as they exhibit a morel-like upper cap structure. Morels contain abundant essential amino acids, vitamins and biologically active compounds, which provide substantial health benefits. Approximately 80 species of Morchella have been reported, and even more species have been isolated. However, the lack of wild Morchella resources and the difficulties associated with culturing Morchella have caused a shortage in the morels available for daily consumption. Additionally, in-depth genomic and morphological studies are still needed. In this study, to provide genomic data for further investigations of culturing techniques and the biological functions of Morchella sextelata (M. sextelata), de novo genome sequencing was carried out on the Illumina HiSeq. 4000 platform using both the Illumina 150 and PacBio systems. The final estimated genome size of M. sextelata was 52.93 Mb, containing 59 contigs and a GC content of 47.37%. A total of 9,550 protein-coding genes were annotated. In addition, the repeat sequences, gene components and gene functions were analyzed using various databases. Furthermore, the secondary metabolite gene clusters and the predicted structures of their products were analyzed. Finally, a genomic comparison of different species of Morchella was performed.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

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