A Markovian analysis of bacterial genome sequence constraints

ABSTRACT Gordonia sp. strain X0973 is a Gram-positive, weakly acid-fast, aerobic actinomycete obtained from a human abscess with Gordonia araii NBRC 100433T as its closest phylogenetic neighbor. Here, we report using Illumina MiSeq and PacBio reads to assemble the complete and circular genome sequence of 3.75 Mbp with 3,601 predicted coding sequences.

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Optical mapping as a routine tool for bacterial genome sequence finishing

BMC Genomics ◽

10.1186/1471-2164-8-321 ◽

2007 ◽

Vol 8 (1) ◽

pp. 321 ◽

Cited By ~ 85

Author(s):

Phil Latreille ◽

Stacie Norton ◽

Barry S Goldman ◽

John Henkhaus ◽

Nancy Miller ◽

...

Keyword(s):

Genome Sequence ◽

Optical Mapping ◽

Bacterial Genome ◽

Bacterial Genome Sequence

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What does a bacterial genome sequence represent? Mis-assignment of MAFF 303099 to the genospecies Mesorhizobium loti

Microbiology ◽

10.1099/00221287-148-11-3330 ◽

2002 ◽

Vol 148 (11) ◽

pp. 3330-3331 ◽

Cited By ~ 34

Author(s):

Sarah L. Turner ◽

Xue-Xian Zhang ◽

Fu-Di Li ◽

J. Peter W. Young

Keyword(s):

Genome Sequence ◽

Bacterial Genome ◽

Mesorhizobium Loti ◽

Bacterial Genome Sequence

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Bacterial genome sequence bagged

Science ◽

10.1126/science.7624767 ◽

1995 ◽

Vol 269 (5223) ◽

pp. 468-470 ◽

Cited By ~ 23

Author(s):

R Nowak

Keyword(s):

Genome Sequence ◽

Bacterial Genome ◽

Bacterial Genome Sequence

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Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins

Frontiers in Microbiology ◽

10.3389/fmicb.2021.698322 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiao Fei ◽

Qiuchun Li ◽

John Elmerdahl Olsen ◽

Xinan Jiao

Keyword(s):

Genome Sequence ◽

Protein Function ◽

Pathogenic Bacteria ◽

Bacterial Genome ◽

Sequencing Data ◽

Protein Coding ◽

Virulence Proteins ◽

Bacterial Genome Sequence ◽

Associated Proteins

With the rapid advancement of sequencing technology, handling of large sequencing data to analyze for protein coding capacity and functionality of predicted proteins has become an urgent demand. There is a lack of simple and effective tools to functionally annotate large number of unknown proteins in a personalized and customized workflow. To address this, we developed Duo, which batch-analyze functional similarities of predicted proteins. Duo can screen query proteins with specific characteristics based on highly flexible and customizable reference inputs from the user. In the current study, Duo was applied to screen for virulence associated proteins in the genome-sequence of Salmonella Typhimurium. Based on the analysis, recommendation for choice of Seed_database in order to get a reasonable number of predicted proteins for further analysis, and recommendation for preparing a Reference_proteins set for Duo was given. Delta-bitscore analysis was shown to be useful tool to focus the follow-up on predicted proteins. A successful screen for virulence proteins in the bacterial genome-sequence was further performed in a selection of 32 pathogenic bacteria, documenting the ability of Duo to work on a broad collection of bacteria. We anticipate that Duo will be a useful auxiliary tool for personalized and customized protein function research in the future.

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Minimum taxonomic criteria for bacterial genome sequence depositions and announcements

Journal of Microbiological Methods ◽

10.1016/j.mimet.2012.02.008 ◽

2012 ◽

Vol 89 (1) ◽

pp. 18-21 ◽

Cited By ~ 8

Author(s):

Matthew J. Bull ◽

Julian R. Marchesi ◽

Peter Vandamme ◽

Sue Plummer ◽

Eshwar Mahenthiralingam

Keyword(s):

Genome Sequence ◽

Bacterial Genome ◽

Bacterial Genome Sequence

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Genome announcement of Steinernema khuongi and its associated symbiont from Florida

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab053 ◽

2021 ◽

Vol 11 (4) ◽

Author(s):

Anil Baniya ◽

Peter DiGennaro

Keyword(s):

Biological Control ◽

Comparative Genomics ◽

Genome Sequence ◽

Bacterial Genome ◽

Draft Genome ◽

Control Measures ◽

Symbiotic Bacteria ◽

Total Length ◽

Central Ridge ◽

Promising Source

Abstract Citrus root weevil (Diaprepes abbreviates) causes significant yield loss in citrus, especially in Florida. A promising source of control for this pest is biological control agents, namely, native entomopathogenic nematodes (EPNs) within the genus Steinernema. Two species of endemic EPN in Florida are S. diaparepesi, abundant within the central ridge, and S. khuongi, dominating the flatwood regions of the state. These citrus-growing regions differ significantly in their soil habitats, which impacts the potential success of biological control measures. Although the genome sequence of S. diaprepesi is currently available, the genome sequence of S. khuongi and identity of the symbiotic bacteria is still unknown. Understanding the genomic differences between these two nematodes and their favored habitats can inform successful biological control practices. Here, MiSeq libraries were used to simultaneously sequence and assemble the draft genome of S. khuongi and its associated symbionts. The final draft genome for S. khuongi has 8,794 contigs with a total length of ∼82 Mb, a largest contig of 428,226 bp, and N50 of 46 kb; its BUSCO scores indicate that it is > 86% complete. An associated bacterial genome was assembled with a total length of ∼3.5 Mb, a largest contig at 116,532 bp, and N50 of 17,487 bp. The bacterial genome encoded 3,721 genes, similar to other Xenorhabdus genomes. Comparative genomics identified the symbiotic bacteria of S. khuongi as Xenorhabdus poinarii. These new draft genomes of a host and symbiont can be used as a valuable tool for comparative genomics with other EPNs and its symbionts to understand host range and habitat suitability.

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