Displaying publications 1 - 20 of 859 in total

  1. Chan KG, Yin WF, Goh SY
    Genome Announc, 2014;2(3).
    PMID: 24812228 DOI: 10.1128/genomeA.00427-14
    Pandoraea pnomenusa strain 3kgm has been identified as a quorum-sensing strain isolated from soil. Here, we report the complete genome sequence of P. pnomenusa strain 3kgm by using the Pacific Biosciences single-molecule real-time (PacBio RS SMRT) sequencer high-resolution technology.
    Matched MeSH terms: Base Sequence
  2. Liew KJ, Teo SC, Shamsir MS, Goh KM
    Microbiol Resour Announc, 2019 Nov 14;8(46).
    PMID: 31727717 DOI: 10.1128/MRA.01238-19
    Longimonas halophila and Longibacter salinarum are type strains of underexplored genera affiliated with Salisaetaceae Herein, we report the draft genome sequences of two strains of these bacteria, L. halophila KCTC 42399 and L. salinarum KCTC 52045, with the intent of broadening knowledge of this family. Genome annotation and gene mining revealed that both bacteria exhibit amylolytic abilities.
    Matched MeSH terms: Base Sequence
  3. Tan KK, Tiong V, Tan JY, Wong JE, Teoh BT, Abd-Jamil J, et al.
    Trop Biomed, 2021 Sep 01;38(3):283-288.
    PMID: 34362871 DOI: 10.47665/tb.38.3.069
    Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64- Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.
    Matched MeSH terms: Base Sequence
  4. Sam KK, Lau NS, Furusawa G, Amirul AA
    Genome Announc, 2017 Oct 19;5(42).
    PMID: 29051257 DOI: 10.1128/genomeA.01147-17
    Hahella sp. strain CCB-MM4 is a halophilic bacterium isolated from estuarine mangrove sediment. The genome sequence of Hahella sp. CCB-MM4 provides insights into exopolysaccharide biosynthesis and the lifestyle of the bacterium thriving in a saline mangrove environment.
    Matched MeSH terms: Base Sequence
  5. Nijman V
    Folia Primatol., 2020;91(3):228-239.
    PMID: 31578029 DOI: 10.1159/000502093
    Great progress has been made in unravelling the evolutionary history of Asian colobines, largely through the use of dated molecular phylogenies based on multiple markers. The Presbytis langurs are a case in point, with more allopatric species being identified, recognition of Presbytis thomasi from Sumatra rather than P. potenziani from the Mentawai Islands as being the most basal species of the group, and the discovery that P. rubicunda from Borneo is nested among the Sumatran species and only made it to Borneo in the last 1.3 million years. Based on variation in mitochondrial d-loop, it has recently been argued that Malaysia's P. femoralis femoralis is actually P. neglectus neglectus. Unfortunately, despite being available, sequences from the type locality, Singapore, were excluded from the analysis, and none of the newly generated sequences was deposited in GenBank. I manually reconstructed these sequences, which allowed me to present a molecular phylogeny that includes 8 additional sequences from West Malaysia and Singapore. P. neglectus from Malaysia and P. femoralis from Singapore form one monophyletic clade, with minimal divergence. I conclude that recognition of P. neglectus is erroneous and the name is a junior synonym of P. femoralis. Colobine taxonomy and systematics have advanced, and continue to advance, mostly by considering evidence from a wide range of individuals, species and data sets (molecular, behavioural and morphological) rather than focusing on single molecular markers from 1 or 2 species from one small geographic area. For an orderly taxonomic debate where evidence can be evaluated and reinterpreted it is essential that newly generated sequences are deposited in public repositories.
    Matched MeSH terms: Base Sequence*
  6. Tan KH, Sheng KY, Chang CY, Yin WF, Chan KG
    Genome Announc, 2015;3(1).
    PMID: 25657288 DOI: 10.1128/genomeA.01542-14
    Dickeya sp. strain 2B12 was isolated from a freshwater lake in Malaysia. Here, we report the draft genome sequence of Dickeya sp. 2B12 sequenced by the Illumina MiSeq platform. With the genome sequence available, this genome sequence will be useful for the study of quorum-sensing activity in this isolate.
    Matched MeSH terms: Base Sequence
  7. Ee R, Ambrose M, Lazenby J, Williams P, Chan KG, Roddam L
    Genome Announc, 2015;3(1).
    PMID: 25657265 DOI: 10.1128/genomeA.01389-14
    Pandoraea is an emerging respiratory pathogen capable of causing chronic lung infections in people with cystic fibrosis (CF), but the clinical significance of this infection is ambiguous. We have sequenced and annotated the genomes of two multidrug-resistant Pandoraea pnomenusa isolates recovered 11 months apart from the same CF patient.
    Matched MeSH terms: Base Sequence
  8. Chan KG, Tee KK, Yin WF, Tan JY
    Genome Announc, 2014;2(6).
    PMID: 25502672 DOI: 10.1128/genomeA.01276-14
    Pluralibacter gergoviae FB2, a bacterial strain isolated from packed food, has been found to exhibit quorum-quenching properties. Hence, we report the first, complete genome of P. gergoviae sequenced using the Pacific Biosciences single-molecule, real-time (SMRT) platform.
    Matched MeSH terms: Base Sequence
  9. Chan KG, Chin PS, Tee KK, Chang CY, Yin WF, Sheng KY
    Genome Announc, 2015;3(2).
    PMID: 25745006 DOI: 10.1128/genomeA.00079-15
    Here, we present the draft genome sequence of Aeromonas caviae strain L12, which shows quorum-sensing activity. The availability of this genome sequence is important to the research of the quorum-sensing regulatory system in this isolate.
    Matched MeSH terms: Base Sequence
  10. Chan KG, Tan KH, Yin WF, Tan JY
    Genome Announc, 2014;2(6).
    PMID: 25523782 DOI: 10.1128/genomeA.01339-14
    We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from pickled mackerel sashimi, sequenced by third-generation sequencing technology. To the best of our knowledge, this is the first documentation that reports the complete genome of Cedecea neteri.
    Matched MeSH terms: Base Sequence
  11. Tan WS, Yin WF, Chan KG
    Genome Announc, 2015;3(1).
    PMID: 25555739 DOI: 10.1128/genomeA.01372-14
    Aeromonas hydrophila species can be found in warm climates and can survive in different environments. They possess the ability to communicate within their populations, which is known as quorum sensing. In this work, we present the draft genome sequence of A. hydrophila M013, a bacterium isolated from a Malaysian tropical rainforest waterfall.
    Matched MeSH terms: Base Sequence
  12. Chan KG, Wong CS, Yin WF, Chan XY
    Genome Announc, 2014;2(2).
    PMID: 24744329 DOI: 10.1128/genomeA.00258-14
    Pseudomonas aeruginosa has a broad range of habitation, from aquatic environments to human lungs. The coexistence of quorum-sensing and quorum-quenching activities occurs in P. aeruginosa strain MW3a. In this work, we present the draft genome sequence of P. aeruginosa MW3a, an interesting bacterium isolated from a marine environment.
    Matched MeSH terms: Base Sequence
  13. Ng KT, Lee YM, Al-Darraji HA, Xia X, Takebe Y, Chan KG, et al.
    Genome Announc, 2013 Jan;1(1).
    PMID: 23409272 DOI: 10.1128/genomeA.00168-12
    We report the full genome sequence of hepatitis C virus (HCV) subtype 6n from Kuala Lumpur, Malaysia. Phylogenetic analysis of the isolate 10MYKJ032 suggests that Southeast Asia might be the origin for the HCV subtype 6n and highlights the possible spread of this lineage from Southeast Asia to other regions.
    Matched MeSH terms: Base Sequence
  14. Chan KG, Yunos NY
    Genome Announc, 2016;4(2).
    PMID: 26941152 DOI: 10.1128/genomeA.00081-16
    Here, we report the draft genome sequence of Chromobacterium piscinae strain ND17. This bacterium was isolated from a fresh water sample in Malaysia and exhibits quorum-sensing activity. This first draft genome of C. piscinae strain ND17 will pave the way to future studies of the quorum-sensing properties of this isolate.
    Matched MeSH terms: Base Sequence
  15. Chan KG, Yin WF, Tee KK, Chang CY, Priya K
    Genome Announc, 2015;3(3).
    PMID: 26021935 DOI: 10.1128/genomeA.00565-15
    We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former landfill site, sequenced by the Illumina MiSeq platform. This genome sequence will be useful to further understand the quorum-sensing system of this isolate.
    Matched MeSH terms: Base Sequence
  16. Chan KG, Chen JW, Chang CY, Yin WF, Chan XY
    Genome Announc, 2015;3(2).
    PMID: 25814592 DOI: 10.1128/genomeA.00095-15
    In this work, we describe the genome of Lysinibacillus sp. strain A1, which was isolated from tropical soil. Analysis of its genome sequence shows the presence of a gene encoding for a putative peptidase responsible for nitrogen compounds.
    Matched MeSH terms: Base Sequence
  17. Subramaniam R, Siddiquee S, Aguol KA, Hoque MZ, Kumar SV
    Data Brief, 2019 Apr;23:103796.
    PMID: 31372442 DOI: 10.1016/j.dib.2019.103796
    Members of the genus Tinctoporellus, which belong to the wood-degrading basidiomycetes, possess the ability to synthesize an array of industrially potent enzymes and metabolites. Here, we present the draft genome sequence of the species Tinctoporellus epimiltinus strain RS1, which is the first to represent its genus. The genome was sequenced using Illumina's 2 × 150 bp paired-end Nextera protocol. The draft genome assembly was 46.2 Mb in size consisting of 13,791 protein coding genes. Identification of carbohydrate active enzymes and laccases from the data may be useful in order to harness the metabolic potentials of the fungi. The data can be accessed at ENA under the accession number FTLJ00000000.
    Matched MeSH terms: Base Sequence
  18. Teoh CP, Lavin P, Najimudin N, Lee PC, Iancu L, Purcarea C, et al.
    Microbiol Resour Announc, 2021 Feb 25;10(8).
    PMID: 33632855 DOI: 10.1128/MRA.00063-21
    Here, we report the draft genome sequence of Flavobacterium sp. strain PL002, isolated from Antarctic Porphyra algae. The 4,299,965-bp genome sequence is assembled into 170 contigs, has 32.92% GC content, and 3,734 predicted genes.
    Matched MeSH terms: Base Sequence
  19. Lavin P, Henríquez-Castillo C, Yong ST, Valenzuela-Heredia D, Oses R, Frez K, et al.
    Microbiol Resour Announc, 2021 Feb 04;10(5).
    PMID: 33541887 DOI: 10.1128/MRA.01453-20
    The draft genome sequence of Streptomyces fildesensis strain INACH3013, a psychrotrophic bacterium isolated from Northwest Antarctic soil, was reported. The genome sequence totaling 9,306,785 bp resulted from 122 contigs characterized by a GC content of 70.55%.
    Matched MeSH terms: Base Sequence
  20. Gan HM, Lee MVJ, Savka MA
    Microbiol Resour Announc, 2018 Sep;7(9).
    PMID: 30533933 DOI: 10.1128/MRA.01045-18
    Using Illumina and Nanopore reads, we assembled a high-quality draft genome sequence of Allorhizobium vitis K309T (= ATCC 49767T, = NCPPB 3554T), a phytopathogenic strain isolated from a grapevine in Australia. The hybrid approach generated 50% fewer contigs and a 3-fold increase in the N50 value compared with the previous Illumina-only assembly.
    Matched MeSH terms: Base Sequence
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