MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Tamura, Koichiro; Dudley, Joel T.; Nei, Masatoshi; Kumar, Sudhir

doi:10.1093/molbev/msm092

Cited by 26,224 publications

(18,837 citation statements)

References 8 publications

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“…The phylogeny tree was constructed using the neighbourjoining method with MEGA4 version 4.0 [25]. Bootstrap proportions were used to assess the robustness of the tree with 1,000 bootstrap replications.…”

Section: Methodsmentioning

confidence: 99%

Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

Kang

Moon

Kim

et al. 2012

Malar J

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BackgroundPlasmodium vivax Duffy binding protein (PvDBP) plays an essential role in erythrocyte invasion and a potential asexual blood stage vaccine candidate antigen against P. vivax. The polymorphic nature of PvDBP, particularly amino terminal cysteine-rich region (PvDBPII), represents a major impediment to the successful design of a protective vaccine against vivax malaria. In this study, the genetic polymorphism and natural selection at PvDBPII among Myanmar P. vivax isolates were analysed.MethodsFifty-four P. vivax infected blood samples collected from patients in Myanmar were used. The region flanking PvDBPII was amplified by PCR, cloned into Escherichia coli, and sequenced. The polymorphic characters and natural selection of the region were analysed using the DnaSP and MEGA4 programs.ResultsThirty-two point mutations (28 non-synonymous and four synonymous mutations) were identified in PvDBPII among the Myanmar P. vivax isolates. Sequence analyses revealed that 12 different PvDBPII haplotypes were identified in Myanmar P. vivax isolates and that the region has evolved under positive natural selection. High selective pressure preferentially acted on regions identified as B- and T-cell epitopes of PvDBPII. Recombination may also be played a role in the resulting genetic diversity of PvDBPII.ConclusionsPvDBPII of Myanmar P. vivax isolates displays a high level of genetic polymorphism and is under selective pressure. Myanmar P. vivax isolates share distinct types of PvDBPII alleles that are different from those of other geographical areas. These results will be useful for understanding the nature of the P. vivax population in Myanmar and for development of PvDBPII-based vaccine.

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Section: Methodsmentioning

confidence: 99%

Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

Kang

Moon

Kim

et al. 2012

Malar J

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“…Sequencing of the purified PCR product was carried out by Eurofins, MWG-Biotech. Sequences were aligned and the data analyzed using MEGA ® (Molecular Evolutionary Genetic Analysis) v 4.0 software [76] MEGA4.…”

Section: Methodsmentioning

confidence: 99%

Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content

et al. 2010

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BackgroundRecent QTL and gene expression studies have highlighted ankyrins as positional and functional candidate genes for meat quality. Our objective was to characterise the promoter region of the bovine ankyrin 1 gene and to test polymorphisms for association with sensory and technological meat quality measures.ResultsSeven novel promoter SNPs were identified in a 1.11 kb region of the ankyrin 1 promoter in Angus, Charolais and Limousin bulls (n = 15 per breed) as well as 141 crossbred beef animals for which meat quality data was available. Eighteen haplotypes were inferred with significant breed variation in haplotype frequencies. The five most frequent SNPs and the four most frequent haplotypes were subsequently tested for association with sensory and technological measures of meat quality in the crossbred population. SNP1, SNP3 and SNP4 (which were subsequently designated regulatory SNPs) and SNP5 were associated with traits that contribute to sensorial and technological measurements of tenderness and texture; Haplotype 1 and haplotype 4 were oppositely correlated with traits contributing to tenderness (P < 0.05). While no single SNP was associated with intramuscular fat (IMF), a clear association with increased IMF and juiciness was observed for haplotype 2.ConclusionThe conclusion from this study is that alleles defining haplotypes 2 and 4 could usefully contribute to marker SNP panels used to select individuals with improved IMF/juiciness or tenderness in a genome-assisted selection framework.

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“…Neighbor‐joining (NJ) trees for the relationships between the individuals were constructed with mega v4 (Tamura et al . 2007). The average genetic distance between individuals was 0.23 ± 0.03 across all six breeds.…”

Section: Interpopulation Genetic Variabilitymentioning

confidence: 99%

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

et al. 2015

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SummaryThe Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole‐genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor‐joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome‐wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.

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MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Cited by 26,224 publications

References 8 publications

Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

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