Whole Genome Sequencing and Annotation of Naematelia aurantialba (Basidiomycota, Edible-Medicinal Fungi)

Naematelia aurantialba is a rare edible fungus with both nutritional and medicinal values and especially rich in bioactive polysaccharides. However, due to the lack of genomic information, researches on the mining of active compounds, artificial breeding and cultivation, genetics, and molecular biology are limited. To facilitate the medicinal and food applications of N. aurantialba, we sequenced and analyzed the whole genome of N. aurantialba for the first time. The 21-Mb genome contained 15 contigs, and a total of 5860 protein-coding genes were predicted. The genome sequence shows that 296 genes are related to polysaccharide synthesis, including 15 genes related to nucleoside-activated sugar synthesis and 11 genes related to glucan synthesis. The genome also contains genes and gene clusters for the synthesis of other active substances, including terpenoids, unsaturated fatty acids, and bioactive proteins. In addition, it was also found that N. aurantialba was more closely related to Naematelia encephala than to Tremella fuciformis. In short, this study provides a reference for molecular cognition of N. aurantialba and related researches.

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Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

Phytopathology ◽

10.1094/phyto-08-21-0353-a ◽

2021 ◽

Author(s):

James Tambong ◽

Renlin Xu ◽

Diane Cuppels ◽

Julie T Chapados ◽

suzanne Gerdis ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Draft Genome ◽

Genome Mining ◽

Gene Clusters ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Protein Coding ◽

Genome Data ◽

Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

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Identification ofKlebsiellacapsule synthesis loci from whole genome data

10.1101/071415 ◽

2016 ◽

Cited By ~ 3

Author(s):

Kelly L. Wyres ◽

Ryan R. Wick ◽

Claire Gorrie ◽

Adam Jenney ◽

Rainer Follador ◽

...

Keyword(s):

Dna Sequences ◽

Sequence Data ◽

Gene Clusters ◽

Whole Genome Sequence ◽

Multi Drug Resistance ◽

Reference Database ◽

Whole Genome ◽

Genome Sequences ◽

Protein Coding ◽

Genome Data

AbstractBackgroundKlebsiella pneumoniaeand close relatives are a growing cause of healthcare-associated infections for which increasing rates of multi-drug resistance are a major concern. TheKlebsiellapolysaccharide capsule is a major virulence determinant and epidemiological marker. However, little is known about capsule epidemiology since serological typing is not widely accessible, and many isolates are serologically non-typeable. Molecular methods for capsular typing are needed, but existing methods lack sensitivity and specificity and fail to take advantage of the information available in whole-genome sequence data, which is increasingly being generated for surveillance and investigation ofKlebsiella.MethodsWe investigated the diversity of capsule synthesis loci (K loci) among a large, diverse collection of 2503 genome sequences ofK. pneumoniaeand closely related species. We incorporated analyses of both full-length K locus DNA sequences and clustered protein coding sequences to identify, annotate and compare K locus structures, and we propose a novel method for identifying K loci based on full locus information extracted from whole genome sequences.ResultsA total of 134 distinct K loci were identified, including 31 novel types. Comparative analysis of K locus gene content detected 508 unique protein coding gene clusters that appear to reassort via homologous recombination, generating novel K locus types. Extensive nucleotide diversity was detected among thewziandwzcgenes, both within and between K loci, indicating that current typing schemes based on these genes are inadequate. As a solution, we introduceKaptive, a novel software tool that automates the process of identifying K loci from large sets ofKlebsiellagenomes based on full locus information.ConclusionsThis work highlights the extensive diversity ofKlebsiellaK loci and the proteins that they encode. We propose a standardised K locus nomenclature forKlebsiella, present a curated reference database of all known K loci, and introduce a tool for identifying K loci from genome data (https://github.com/katholt/Kaptive). These developments constitute important new resources for theKlebsiellacommunity for use in genomic surveillance and epidemiology.

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Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara

BMC Genomics ◽

10.1186/s12864-021-07866-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Chahira Zerouki ◽

Farid Bensalah ◽

Suvi Kuittinen ◽

Ari Pappinen ◽

Ossi Turunen

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uv Light ◽

Sand Dunes ◽

Gene Clusters ◽

Extreme Environment ◽

Climatic Conditions ◽

Whole Genome ◽

Protein Coding ◽

Algerian Sahara

Abstract Background Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening for antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study desert Streptomyces microbiology and ecology from a genomic perspective. Results Strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequencing as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed using Pacific Biosciences Sequel II technology (PacBio), which showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified protein coding genes was 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17. Although the strains have different phenotypes and are from different regions, they showed very high similarities at the DNA level. The two strains are more similar to each other than either is to the closest database strain. The search for potential secondary metabolites was performed using antiSMASH and predicted 29 biosynthetic gene clusters (BGCs). Several BGCs and proteins were related to the biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. Conclusion The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information provides tools to study ecological adaptation in a desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first to be sequenced for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to more profoundly explore the desert microbiome.

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Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Genomics ◽

10.1016/j.ygeno.2020.05.004 ◽

2020 ◽

Vol 112 (5) ◽

pp. 2915-2921 ◽

Cited By ~ 2

Author(s):

Thiago Mafra Batista ◽

Heron Oliveira Hilario ◽

Gabriel Antônio Mendes de Brito ◽

Rennan Garcias Moreira ◽

Carolina Furtado ◽

...

Keyword(s):

Secondary Metabolites ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Binding Protein ◽

Protein A ◽

Gene Clusters ◽

Whole Genome ◽

Ice Binding ◽

Ice Binding Protein

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Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium

International Journal of Genomics ◽

10.1155/2018/3505428 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Hongyan Zhao ◽

Kejian Tian ◽

Qing Qiu ◽

Yu Wang ◽

Hongyan Zhang ◽

...

Keyword(s):

Sole Source ◽

Rhodococcus Opacus ◽

Whole Genome ◽

Metabolic Potential ◽

Protein Coding ◽

Degrading Enzymes ◽

Degrading Bacterium ◽

Rhodococcus Jostii Rha1 ◽

Multiple Strains ◽

Rhodococcus Sp

We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4 Mbp with G + C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.

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Whole-Genome Sequencing Reveals a New Genospecies ofMethylobacteriumsp. GXS13, Isolated fromVitis viniferaL. Xylem Sap

Genome Announcements ◽

10.1128/genomea.01695-15 ◽

2016 ◽

Vol 4 (1) ◽

Cited By ~ 1

Author(s):

Wan Xin Lai ◽

Han Ming Gan ◽

André O. Hudson ◽

Michael A. Savka

Keyword(s):

Xylem Sap ◽

Gene Clusters ◽

Homoserine Lactone ◽

Whole Genome Sequence ◽

Whole Genome ◽

Acyl Homoserine Lactone ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Cell Wall Modification ◽

Cytokinin Synthesis

The whole-genome sequence of a new genospecies ofMethylobacteriumsp., named GXS13 and isolated from grapevine xylem sap, is reported and demonstrates potential for methylotrophy, cytokinin synthesis, and cell wall modification. In addition, biosynthetic gene clusters were identified for cupriachelin, carotenoid, and acyl-homoserine lactone using the antiSMASH server.

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A toolkit enabling efficient, scalable and reproducible gene tagging in trypanosomatids

Open Biology ◽

10.1098/rsob.140197 ◽

2015 ◽

Vol 5 (1) ◽

pp. 140197 ◽

Cited By ~ 97

Author(s):

Samuel Dean ◽

Jack Sunter ◽

Richard J. Wheeler ◽

Ian Hodkinson ◽

Eva Gluenz ◽

...

Keyword(s):

Trypanosoma Brucei ◽

Large Datasets ◽

Gene Tagging ◽

Deletion Mutants ◽

Whole Genome ◽

Leishmania Mexicana ◽

Protein Coding ◽

Achievable Goal ◽

Endogenous Loci ◽

Pcr Conditions

One of the first steps in understanding a protein's function is to determine its localization; however, the methods for localizing proteins in some systems have not kept pace with the developments in other fields, creating a bottleneck in the analysis of the large datasets that are generated in the post-genomic era. To address this, we developed tools for tagging proteins in trypanosomatids. We made a plasmid that, when coupled with long primer PCR, can be used to produce transgenes at their endogenous loci encoding proteins tagged at either terminus or within the protein coding sequence. This system can also be used to generate deletion mutants to investigate the function of different protein domains. We show that the length of homology required for successful integration precluded long primer PCR tagging in Leishmania mexicana . Hence, we developed plasmids and a fusion PCR approach to create gene tagging amplicons with sufficiently long homologous regions for targeted integration, suitable for use in trypanosomatids with less efficient homologous recombination than Trypanosoma brucei . Importantly, we have automated the primer design, developed universal PCR conditions and optimized the workflow to make this system reliable, efficient and scalable such that whole genome tagging is now an achievable goal.

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

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652324 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fenghua Tian ◽

Changtian Li ◽

Yu Li

Keyword(s):

Single Molecule ◽

De Novo ◽

Genomic Analysis ◽

Single Copy ◽

Whole Genome Sequence ◽

Type I ◽

Whole Genome ◽

Uridine Diphosphate ◽

Protein Coding ◽

Medicinal Value

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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Quorum sensing and genomic studies of a marine bacterium Vibrio variabilis strain T01

10.7287/peerj.preprints.1029v1 ◽

2015 ◽

Author(s):

Kok-Gan Chan ◽

Nur Izzati Mohamad

Keyword(s):

Quorum Sensing ◽

Coastal Waters ◽

Marine Bacterium ◽

Cell Communication ◽

Whole Genome ◽

Whole Genome Analysis ◽

Protein Coding ◽

Signalling Molecule ◽

Genomic Studies ◽

Rna Genes

Vibrio variabilis strain T01 was isolated from the coastal waters in Hulu Selangor, Malaysia and its genome sequenced. This curved gram-negative bacterium shows cell-to-cell communication properties. The characteristics of the sequenced genome and its annotation processes are described here. The finished assembled whole genome of T01T exhibits genome size of 4,529,728 bp in 83 contigs with 46.22% G+C content, 4053 protein coding genes and 94 RNA genes. The whole genome analysis revealed the presence of quorum sensing signalling molecule synthase gene (luxM) which is crucial to understand the quorum sensing dependent phenotypes in this isolate.

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Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

10.1101/2020.02.02.930693 ◽

2020 ◽

Cited By ~ 2

Author(s):

Conghui Liu ◽

Yuwei Ren ◽

Zaiyuan Li ◽

Qi Hu ◽

Lijuan Yin ◽

...

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Terrestrial Ecosystems ◽

Gene Families ◽

Gene Clusters ◽

Immune Defense ◽

Whole Genome ◽

Genomic Plasticity ◽

Ecological Adaptability ◽

Chromosome Level

AbstractWhole-genome duplication (WGD) has been observed across a wide variety of eukaryotic groups, contributing to evolutionary diversity and environmental adaptability. Mollusks are the second largest group of animals, and are among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition, and no comprehensive research on WGD has been reported in this group. To explore WGD and the A-T transition in Mollusca, we assembled a chromosome-level reference genome for the giant African snail Achatina immaculata, a global invasive species, and compared the genomes of two giant African snails (A. immaculata and Achatina fulica) to the other available mollusk genomes. The chromosome-level macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested the occurrence of a WGD event shared by A. immaculata and A. fulica. The estimated timing of this WGD event (∼70 MYA) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD reported herein may have been a common event shared by all Sigmurethra-Orthurethra species and could have conferred ecological adaptability and genomic plasticity allowing the survival of the K-T extinction. Based on macrosynteny, we deduced an ancestral karyotype containing 8 conserved clusters for the Gastropoda-Bivalvia lineage. To reveal the mechanism of WGD in shaping adaptability to terrestrial ecosystems, we investigated gene families related to the respiration, aestivation and immune defense of giant African snails. Several mucus-related gene families expanded early in the Stylommatophora lineage, functioning in water retention, immune defense and wound healing. The hemocyanins, PCK and FBP families were doubled and retained after WGD, enhancing the capacity for gas exchange and glucose homeostasis in aestivation. After the WGD, zinc metalloproteinase genes were highly tandemly duplicated to protect tissue against ROS damage. This evidence collectively suggests that although the WGD may not have been the direct driver of the A-T transition, it provided an important legacy for the terrestrial adaptation of the giant African snail.

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