scholarly journals Complete Genome Sequence of the Biocontrol Agent Bacillus velezensis UFLA258 and Its Comparison with Related Species: Diversity within the Commons

2019 ◽  
Vol 11 (10) ◽  
pp. 2818-2823 ◽  
Author(s):  
Fabíola de Jesus Silva ◽  
Larissa Carvalho Ferreira ◽  
Vicente Paulo Campos ◽  
Valter Cruz-Magalhães ◽  
Aline Ferreira Barros ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Hybridization ◽  
Related Species ◽  
Nucleotide Identity ◽  
Full Genome Sequence ◽  
Average Nucleotide Identity ◽  
Bacillus Velezensis ◽  
Circular Chromosome ◽  
Closely Related Species ◽  
Genes Encoding

Abstract In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database were performed. The genome of B. velezensis UFLA258 consisted of a single circular chromosome of 3.95 Mb in length, with a mean GC content of 46.69%. It contained 3,949 genes encoding proteins and 27 RNA genes. Analyses based on Average Nucleotide Identity and Digital DNA–DNA Hybridization and a phylogeny with complete sequences of the rpoB gene confirmed that 19 strains deposited in the database as Bacillus amyloliquefaciens were in fact B. velezensis. In total, 115 genomes were analyzed and taxonomically classified as follows: 105 were B. velezensis, 9 were B. amyloliquefaciens, and 1 was Bacillus siamensis. Although these species are phylogenetically close, the combined analyses of several genomic characteristics, such as the presence of biosynthetic genes encoding secondary metabolites, CRISPr/Cas arrays, Average Nucleotide Identity and Digital DNA–DNA Hybridization, and other information on the strains, including isolation source, allowed their unequivocal classification. This genomic analysis expands our knowledge about the closely related species, B. velezensis, B. amyloliquefaciens, and B. siamensis, with emphasis on their taxonomical status.

scholarly journals Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10343
Author(s):  
Pattsarun Cheawchanlertfa ◽  
Sawannee Sutheeworapong ◽  
Piroon Jenjaroenpun ◽  
Thidathip Wongsurawat ◽  
Intawat Nookaew ◽  
...  
Keyword(s):  
Related Species ◽  
Anaerobic Bacterium ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Circular Chromosome ◽  
Closely Related Species ◽  
Degrading Enzymes ◽  
Cassava Pulp ◽  
Pectinolytic Enzymes ◽  
Genes Encoding

Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas

2020 ◽  
Author(s):  
Antonio Roberto Gomes de Farias ◽  
Wilson José da Silva Junior ◽  
José Bandeira do Nascimento Junior ◽  
Valdir de Queiroz Balbino ◽  
Ana Maria Benko-Iseppon ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Dna Hybridization ◽  
In Silico ◽  
Whole Genome Sequence ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Xanthomonas Citri ◽  
Genome Sequences ◽  
Xanthomonas Species

Abstract Background Xanthomonas citri pv. viticola is one of the most critical grapevine diseases in the Northeast of Brazil, presenting a high risk to Brazilian and worldwide areas of grape production. The X.citri pv. viticola epithet was recently proposed to be changed from X. campestris pv. v iticola based on multilocus sequence analysis and whole-genome sequences. Besides, genomics has revolutionized the field of bacteriology, by associating genome sequencing with comparative analysis such as in silico analysis such as DNA-DNA hybridization, average nucleotide identity, distance between genomes, pan-genomic approach, and phylogenomic, providing valuable insights and knowledge about virulence factors and contributing to increase the understanding and clarifying the taxonomic relationship of Xanthomonas and others prokaryotic species.Results We used the whole-genome sequence of three Brazilian strains and the pathotype to characterize X.citri pv. viticola accessions plus 124 whole-genome sequences of Xanthomonas species available in NCBI, comprising 13 species and 15 pathovars. The whole-genome sequence structure of X. citri pv. viticola was shown presents a high level of conservation concerning other X. citri species. Pan-genomic approaches, average nucleotide identity analysis, and in silico DNA-DNA hybridization were carried out, allowing X.citri pv. viticola characterization and inferences on the phylogenetic relationships within Xanthomonas . The analysis of the sequence of the 128 genomes clustered the Xanthomonas strains in eight main groups according to the recently proposed classification in all approaches used. Also, the analysis revealed that X. hortorum and X. gardneri should be classified as a single species, and the strain 17 of X. campestris and XC01 of X. citri pv. mangiferaeindicae widely described in the literature are misclassified.Conclusions We performed the genomic characterization of three representative Brazilian strains of Xcv . The genomic approaches based in the pan-genome, average nucleotide identity, and in silico DNA-DNA hybridization support the proposed taxonomic position of X.citri pv. viticola and of the recently proposed Xanthomonas species and pathovars. In addition, we detected species delimitation of the misclassified Xanthomonas strains with extensive studies reported in the literature.

scholarly journals Complete Genome Sequence of the Halophilic Methylotrophic Methanogen Archaeon Methanohalophilus portucalensis Strain FDF-1 T

2018 ◽  
Vol 6 (3) ◽  
Author(s):  
Stéphane L’Haridon ◽  
Erwan Corre ◽  
Yue Guan ◽  
Manikandan Vinu ◽  
Violetta La Cono ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Dna Hybridization ◽  
Complete Genome ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Methanohalophilus Mahii

ABSTRACT We report here the complete genome sequence (2.08 Mb) of Methanohalophilus portucalensis strain FDF-1 T , a halophilic methylotrophic methanogen isolated from the sediment of a saltern in Figeria da Foz, Portugal. The average nucleotide identity and DNA-DNA hybridization analyses show that Methanohalophilus mahii , M. halophilus , and M. portucalensis are three different species within the Methanosarcinaceae family.

scholarly journals Draft Genome Sequence of Mediterraneibacter sp. nov. Strain gm002, Isolated from Human Feces

2019 ◽  
Vol 8 (31) ◽  
Author(s):  
Chien-Hsun Huang ◽  
Jong-Shian Liou ◽  
Chun-Lin Wang ◽  
Lina Huang
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Dna Hybridization ◽  
Novel Species ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Human Feces

Here, we report a draft genome sequence of Mediterraneibacter sp. strain gm002, isolated from human feces in Taiwan. This strain represents a novel species according to whole-genome-based comparisons using the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) thresholds. The genome assembly comprised 3,568,768 bp, with a 38.7% G+C content.

Differentiation of closely related species by DNA hybridization

Meat Science ◽  
1991 ◽  
Vol 30 (4) ◽  
pp. 359-366 ◽  
Author(s):  
Kirsten F. Ebbehøj ◽  
Preben D. Thomsen
Keyword(s):  
Dna Hybridization ◽  
Related Species ◽  
Closely Related Species

scholarly journals Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments

2019 ◽  
Vol 8 (18) ◽  
Author(s):  
Gordon Webster ◽  
Alex J. Mullins ◽  
Andrew J. Watkins ◽  
Edward Cunningham-Oakes ◽  
Andrew J. Weightman ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Dna Hybridization ◽  
In Silico ◽  
Methanogenic Archaea ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.

scholarly journals Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 113 ◽  
Author(s):  
Pavel Kroupin ◽  
Victoria Kuznetsova ◽  
Dmitry Romanov ◽  
Alina Kocheshkova ◽  
Gennady Karlov ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Related Species ◽  
Evolutionary Divergence ◽  
Whole Genome ◽  
Target Genome ◽  
Target Species ◽  
Closely Related Species ◽  
Chromosome Markers

Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.

scholarly journals Complete Genome Sequence of Actinomyces hongkongensis HKU8T Isolated from Human Blood

2017 ◽  
Vol 5 (14) ◽  
Author(s):  
Yan-xia Gao ◽  
Yu-yan Zhou ◽  
Ying Xie ◽  
Man Wang ◽  
Shu-juan Wang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Human Blood ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Human Diseases ◽  
Circular Chromosome ◽  
Content Type ◽  
Genes Encoding

ABSTRACT Members of the genus Actinomyces are strongly associated with human diseases. We present here the complete genome sequence of Actinomyces hongkongensis HKU8T, which consists of one circular chromosome. The strain characteristically contains various genes encoding for enzymes involved in arylamidase utilization.

scholarly journals Complete Genome Sequence of the Bacterial Component of Mysorin Biopreparation

2021 ◽  
Vol 10 (11) ◽  
Author(s):  
Alexey M. Afonin ◽  
Emma S. Gribchenko ◽  
Gulnar A. Akhtemova ◽  
Yuri V. Laktionov ◽  
Andrej P. Kozhemyakov ◽  
...  
Keyword(s):  
Plant Growth ◽  
Genome Sequence ◽  
Soil Microorganisms ◽  
Full Genome Sequence ◽  
Plant Growth Promoting Bacteria ◽  
Full Genome ◽  
Circular Chromosome ◽  
Content Type ◽  
Plant Growth Promoting ◽  
Growth Promoting

ABSTRACT Plants can form various beneficial associations with soil microorganisms, such as associations with plant growth-promoting bacteria (PGPB). In this work, we report the full-genome sequence of the component of Mysorin biopreparation, identified as Microbacterium hominis, consisting of a single 3.5-Mbp circular chromosome.

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