MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro

doi:10.1093/molbev/msw054

Cited by 38,266 publications

(26,175 citation statements)

References 11 publications

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“…Sequence Alignment and Model Test : Sequences were aligned by ClustalW implemented in MEGA 7 53. The best substitution model was selected by jModelTest according to the Bayesian information criterion (BIC) score.…”

Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)‐like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single‐stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

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Section: Methodsmentioning

confidence: 99%

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

et al. 2018

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“…The bacterial core genome and the number of SNP differences were calculated between isolates of the same MLST type using Harvest suite 1.0 (Treangen et al ., 2014) and mega 7.0 (Kumar et al ., 2016). Phylogenetic trees were constructed using a pairwise distance matrix and the neighbour‐joining algorithm ( mega 7.0, 1000 bootstraps) based on the number of calculated SNP differences between the isolates.…”

Section: Methodsmentioning

confidence: 99%

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

Projahn

Daehre

Semmler

et al. 2018

Microbial Biotechnology

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SummaryHigh prevalence numbers of extended‐spectrum beta‐lactamase‐ (ESBL‐)/plasmid‐mediated AmpC beta‐lactamase‐ (pAmpC‐) producing Escherichia coli in broiler chicken and their distribution along the broiler production chain is an ongoing problem in food production. We, therefore, investigated resistant isolates along the broiler production chain to determine whether there is a constantly occurring direct vertical transmission of the ESBL‐/pAmpC‐producing E. coli from the parent flocks to their offspring or not. We, furthermore, analysed the isolates concerning the occurrence of virulence factors and their ability to form biofilms to estimate their potential to effectively colonize broiler chickens and/or persist and survive in the environment of the broiler production facilities. Using whole genome sequencing, we could show that ESBL‐/pAmpC‐producing E. coli were likely transferred in a step‐wise process along the broiler production chain but not directly from the parent flock to the fattening flock with every single batch of offspring chickens. Additionally, resistant E. coli strains showing an extraintestinal pathogenic genotype as well as high numbers of virulence‐associated genes including the production of curli fibres and cellulose have high capabilities to persist and spread in the broiler production chain.

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“…Protein sequences were aligned using MUSCLE in MEGA 7 (Kumar et al., 2016) followed by manual curation to remove sequences that lack conserved residues and motifs. Protein alignments were imported into IQ‐TREE (v1.4.2) (Nguyen, Schmidt, von Haeseler, & Minh, 2014) to determine best‐fit of protein model evolution.…”

Section: Methodsmentioning

confidence: 99%

“…These codon sequences for the respective Fad and Elovl gene families were aligned using MUSCLE within MEGA 7 (Kumar et al., 2016). Codon alignments were imported into IQ‐TREE (v1.4.2) (Nguyen et al., 2014) to determine best‐fit substitution model (GTR+I+G4), and phylogenetic trees were generated from alignments using 1,000 ultrafast bootstrap iterations.…”

Section: Methodsmentioning

confidence: 99%

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

Surm

Toledo

Prentis

et al. 2018

Ecology and Evolution

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The biosynthesis of long‐chain polyunsaturated fatty acids (LC‐PUFAs, ≥ C20) is reliant on the action of desaturase and elongase enzymes, which are encoded by the fatty acyl desaturase (Fad) and elongation of very long‐chain fatty acid (Elovl) gene families, respectively. In Metazoa, research investigating the distribution and evolution of these gene families has been restricted largely to Bilateria. Here, we provide insights into the phylogenetic and molecular evolutionary histories of the Fad and Elovl gene families in Cnidaria, the sister phylum to Bilateria. Four model cnidarian genomes and six actiniarian transcriptomes were interrogated. Analysis of the fatty acid composition of a candidate cnidarian species, Actinia tenebrosa, was performed to determine the baseline profile of this species. Phylogenetic analysis revealed lineage‐specific gene duplication in actiniarians for both the Fad and Elovl gene families. Two distinct cnidarian Fad clades clustered with functionally characterized Δ5 and Δ6 proteins from fungal and plant species, respectively. Alternatively, only a single cnidarian Elovl clade clustered with functionally characterized Elovl proteins (Elovl4), while two additional clades were identified, one actiniarian‐specific (Novel ElovlA) and the another cnidarian‐specific (Novel ElovlB). In actiniarians, selection analyses revealed pervasive purifying selection acting on both gene families. However, codons in the Elovl gene family show patterns of nucleotide variation consistent with the action of episodic diversifying selection following gene duplication events. Significantly, these codons may encode amino acid residues that are functionally important for Elovl proteins to target and elongate different precursor fatty acids. In A. tenebrosa, the fatty acid analysis revealed an absence of LC‐PUFAs > C20 molecules and implies that the Elovl enzymes are not actively contributing to the elongation of these LC‐PUFAs. Overall, this study has revealed that actiniarians possess Fad and Elovl genes required for the biosynthesis of some LC‐PUFAs, and that these genes appear to be distinct from bilaterians.

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MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Cited by 38,266 publications

References 11 publications

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

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