MEGA biocentric software for sequence and phylogenetic analysis: a review

Sohpal, Vipan Kumar; Dey, Apurba; Singh, Amarpal

doi:10.1504/ijbra.2010.034072

Cited by 61 publications

(39 citation statements)

References 26 publications

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“…A neighbor-joining distance tree was constructed using the translated amino acid sequence of genes annotated as DNA polymerases to compare them to those of other known bacteriophages 44 - 47 . A DNA polymerase gene is present in all phages included in EcoShield™ and it serves as a useful marker for comparison to other phages 48 .…”

Section: Methodsmentioning

confidence: 99%

Bacteriophage cocktail significantly reduces Escherichia coli O157

et al. 2012

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Foods contaminated with Escherichia coli O157:H7 cause more than 63,000 foodborne illnesses in the United States every year, resulting in a significant economic impact on medical costs and product liabilities. Efforts to reduce contamination with E. coli O157:H7 have largely focused on washing, application of various antibacterial chemicals, and gamma-irradiation, each of which has practical and environmental drawbacks. A relatively recent, environmentally-friendly approach proposed for eliminating or significantly reducing E. coli O157:H7 contamination of foods is the use of lytic bacteriophages as biocontrol agents. We found that EcoShield™, a commercially available preparation composed of three lytic bacteriophages specific for E. coli O157:H7, significantly (p < 0.05) reduced the levels of the bacterium in experimentally contaminated beef by ≥ 94% and in lettuce by 87% after a five minute contact time. The reduced levels of bacteria were maintained for at least one week at refrigerated temperatures. However, the one-time application of EcoShield™ did not protect the foods from recontamination with E. coli O157:H7. Our results demonstrate that EcoShield™ is effective in significantly reducing contamination of beef and lettuce with E. coli O157:H7, but does not protect against potential later contamination due to, for example, unsanitary handling of the foods post processing.

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Section: Methodsmentioning

confidence: 99%

Bacteriophage cocktail significantly reduces Escherichia coli O157

et al. 2012

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“…The 16S rRNA gene sequences were then all aligned in the Clustal W implementation of Bioedit (Ibis Bioscience). MEGA program was subsequently used to produce unrooted neighbour-joining phylogenetic trees (Kimura-2 correction; bootstrap values for 500 replicates) [31]. All the sequences described in this study have been submitted to the EMBL database under the accession numbers HE648175 to HE648215.…”

Section: Methodsmentioning

confidence: 99%

Effect of Elodea nuttallii Roots on Bacterial Communities and MMHg Proportion in a Hg Polluted Sediment

et al. 2012

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The objective of this study was to assess the effect of a rooted macrophyte Elodea nuttallii on rhizosphere bacterial communities in Hg contaminated sediments. Specimens of E. nuttallii were exposed to sediments from the Hg contaminated Babeni reservoir (Olt River, Romania) in our microcosm. Plants were allowed to grow for two months until they occupied the entirety of the sediments. Total Hg and MMHg were analysed in sediments where an increased MMHg percentage of the total Hg in pore water of rhizosphere sediments was found. E. nuttallii roots also significantly changed the bacterial community structure in rhizosphere sediments compared to bulk sediments. Deltaproteobacteria dominated the rhizosphere bacterial community where members of Geobacteraceae within the Desulfuromonadales and Desulfobacteraceae were identified. Two bacterial operational taxonomic units (OTUs) which were phylogenetically related to sulfate-reducing bacteria (SRB) became abundant in the rhizosphere. We suggest that these phylotypes could be potentially methylating bacteria and might be responsible for the higher MMHg percentage of the total Hg in rhizosphere sediments. However, SRB were not significantly favoured in rhizosphere sediments as shown by qPCR. Our findings support the hypothesis that rooted macrophytes created a microenvironment favorable for Hg methylation. The presence of E. nuttallii in Hg contaminated sediments should therefore not be overlooked.

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“…The nucleotide and amino acid sequences from individual genes were aligned using clustalW and MUSCLE with manual modifications, respectively [47,48]. Non-homologous regions in each alignment were removed.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Dynamics of chloroplast genomes in green plants

Liu

et al. 2015

Genomics

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Chloroplasts are essential organelles, in which genes have widely been used in the phylogenetic analysis of green plants. Here, we took advantage of the breadth of plastid genomes (cpDNAs) sequenced species to investigate their dynamic changes. Our study showed that gene rearrangements occurred more frequently in the cpDNAs of green algae than in land plants. Phylogenetic trees were generated using 55 conserved protein-coding genes including 33 genes for photosynthesis, 16 ribosomal protein genes and 6 other genes, which supported the monophyletic evolution of vascular plants, land plants, seed plants, and angiosperms. Moreover, we could show that seed plants were more closely related to bryophytes rather than pteridophytes. Furthermore, the substitution rate for cpDNA genes was calculated to be 3.3×10(-10), which was almost 10 times lower than genes of nuclear genomes, probably because of the plastid homologous recombination machinery.

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MEGA biocentric software for sequence and phylogenetic analysis: a review

Cited by 61 publications

References 26 publications

Bacteriophage cocktail significantly reduces Escherichia coli O157

Bacteriophage cocktail significantly reduces Escherichia coli O157

Effect of Elodea nuttallii Roots on Bacterial Communities and MMHg Proportion in a Hg Polluted Sediment

Dynamics of chloroplast genomes in green plants

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