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Phylogenetic and structural analysis of the phospholipase A2 gene family in vertebrates.

Huang Q, Wu Y, Qin C, He W, Wei X - Int. J. Mol. Med. (2014)

Bottom Line: In this study, we downloaded 49 genomic data sets of PLA from different species, including the human, house mouse, Norway rat, pig, dog, chicken, cattle, African clawed frog, Sumatran orangutan and the zebrafish species.Phylogenetic relationships were determined using the neighbor-joining (NJ), minimum evolution (ME) and maximum parsimony (MP) methods, as well as the Bayesian information criterion.The results were then presented as phylogenetic trees.

View Article: PubMed Central - PubMed

Affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, P.R. China.

ABSTRACT
The phospholipase A (PLA)2 family is the most complex gene family of phospholipases and plays a crucial role in a number of physiological activities. However, the phylogenetic background of the PLA2 gene family and the amino acid residues of the PLA2G7 gene following positive selection gene remain undetermined. In this study, we downloaded 49 genomic data sets of PLA from different species, including the human, house mouse, Norway rat, pig, dog, chicken, cattle, African clawed frog, Sumatran orangutan and the zebrafish species. Phylogenetic relationships were determined using the neighbor-joining (NJ), minimum evolution (ME) and maximum parsimony (MP) methods, as well as the Bayesian information criterion. The results were then presented as phylogenetic trees. Positive selection sites were detected using site, branch and branch‑site models. These methods led us to the following assumptions: i) closer lineages were observed between PLA2G16 and PLA2G6, PLA2G7 and PLA2G4, PLA2G3 and PLA2G12, as well as among PLA2G10, PLA2G5 and PLA2G15; ii) PLA2G5 appeared to be the origin of the PLA2 family, and PLA2G7 was one of the most evolutionarily distant PLA2 proteins; iii) 16 positive-selection sites were detected and were marked in the PLA2G7 protein sequence as 327D, 257Q, 276G, 34s, 66G, 67C, 319S, 28N, 50S, 54T, 58R, 75T, 88Q, 92R, 179H and 191K.

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Phylogenetic trees of the PLA2 gene in vertebrates. (A) Phylogenetic tree produced using the NJ method; (B) phylogenetic tree produced using the ME method; (C) phylogenetic tree produced using the MP method. Genes with a crimson disc belong to the PLA2G16 group; genes with an orange disc belong to the PLA2G6 group; genes with a grey disc belong to the PLA2G10 group; genes with a dark blue disc belong to the PLA2G10 group; genes with a yellow disc belong to the PLA2G15 group; genes with a red disc belong to the PLA2G7 group; genes with a green disc belong to the PLA2G4 group; genes with a purple disc belong to the PLA2G3 group; genes with a light blue disc belong to the PLA2G12 group. (D) Phylogenetic tree of the PLA2 gene in vertebrates produced using the Bayesian method. Genes with a crimson branch belong to the PLA2G16 group; genes with an orange branch belong to the PLA2G6 group; genes with a grey branch belong to the PLA2G10 group; genes with a dark blue branch belong to the PLA2G10 group; genes with a yellow branch belong to the PLA2G15 group; genes with a red branch belong to the PLA2G7 group; genes with a green branch belong to the PLA2G4 group; genes with a purple branch belong to the PLA2G3 group; genes with a light blue branch belong to the PLA2G12 group; genes in pink belong to mammals; genes in dark yellow belong to birds; genes in dark green belong to amphibians; genes in sky blue belong to fish. NJ, neighbor-joining; ME, minimum evolution; MP, maximum parsimony.
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f2-ijmm-35-03-0587: Phylogenetic trees of the PLA2 gene in vertebrates. (A) Phylogenetic tree produced using the NJ method; (B) phylogenetic tree produced using the ME method; (C) phylogenetic tree produced using the MP method. Genes with a crimson disc belong to the PLA2G16 group; genes with an orange disc belong to the PLA2G6 group; genes with a grey disc belong to the PLA2G10 group; genes with a dark blue disc belong to the PLA2G10 group; genes with a yellow disc belong to the PLA2G15 group; genes with a red disc belong to the PLA2G7 group; genes with a green disc belong to the PLA2G4 group; genes with a purple disc belong to the PLA2G3 group; genes with a light blue disc belong to the PLA2G12 group. (D) Phylogenetic tree of the PLA2 gene in vertebrates produced using the Bayesian method. Genes with a crimson branch belong to the PLA2G16 group; genes with an orange branch belong to the PLA2G6 group; genes with a grey branch belong to the PLA2G10 group; genes with a dark blue branch belong to the PLA2G10 group; genes with a yellow branch belong to the PLA2G15 group; genes with a red branch belong to the PLA2G7 group; genes with a green branch belong to the PLA2G4 group; genes with a purple branch belong to the PLA2G3 group; genes with a light blue branch belong to the PLA2G12 group; genes in pink belong to mammals; genes in dark yellow belong to birds; genes in dark green belong to amphibians; genes in sky blue belong to fish. NJ, neighbor-joining; ME, minimum evolution; MP, maximum parsimony.

Mentions: A total of 49 sequences from 10 species were used to reconstruct a phylogenetic tree for the PLA2 gene family using the NJ, ME, MP methods, as well as the Bayesian information criterion with bootstrap value detection. The details of the included data are presented in Table I. A total of 25 nodes (56.81% in total) showed bootstrap values ≥95% and 34 nodes (77.27% in total) had bootstrap values ≥80% in the Bayes building tree (Fig. 2D). In each subgroup, mammal data, including data from the Sumatran orangutan, pig, Norway rat, human, house mouse, dog and cattle were gathered. The data from the African clawed frog, chicken and zebrafish were much more original than those from mammals, indicating that the taxonomy of host organisms reflects the phylogenetic background of the PLA2 gene family. The vertebrate PLA2 gene family was sorted into nine lineages according to the type of reaction for catalyzing phospholipids. PLA2G7 seems to be the most distant lineage in this gene family, indicating a large number of structural changes accumulating on them. Furthermore, all the groups were divided into two major clades; clade 1 included PLA2G16, PLA2G6, PLA2G10, PLA2G5 and PLA2G15, whereas clade 2 included PLA2G7, PLA2G4, PLA2G3 and PLA2G12. Closer lineages were observed between PLA2G16 and PLA2G6, PLA2G7 and PLA2G4, PLA2G3 and PLA2G12, well as among PLA2G10, PLA2G5 and PLA2G15. Moreover, the phylogenetic relationships obtained by the NJ, ME and MP methods were different (Fig. 2A–C).


Phylogenetic and structural analysis of the phospholipase A2 gene family in vertebrates.

Huang Q, Wu Y, Qin C, He W, Wei X - Int. J. Mol. Med. (2014)

Phylogenetic trees of the PLA2 gene in vertebrates. (A) Phylogenetic tree produced using the NJ method; (B) phylogenetic tree produced using the ME method; (C) phylogenetic tree produced using the MP method. Genes with a crimson disc belong to the PLA2G16 group; genes with an orange disc belong to the PLA2G6 group; genes with a grey disc belong to the PLA2G10 group; genes with a dark blue disc belong to the PLA2G10 group; genes with a yellow disc belong to the PLA2G15 group; genes with a red disc belong to the PLA2G7 group; genes with a green disc belong to the PLA2G4 group; genes with a purple disc belong to the PLA2G3 group; genes with a light blue disc belong to the PLA2G12 group. (D) Phylogenetic tree of the PLA2 gene in vertebrates produced using the Bayesian method. Genes with a crimson branch belong to the PLA2G16 group; genes with an orange branch belong to the PLA2G6 group; genes with a grey branch belong to the PLA2G10 group; genes with a dark blue branch belong to the PLA2G10 group; genes with a yellow branch belong to the PLA2G15 group; genes with a red branch belong to the PLA2G7 group; genes with a green branch belong to the PLA2G4 group; genes with a purple branch belong to the PLA2G3 group; genes with a light blue branch belong to the PLA2G12 group; genes in pink belong to mammals; genes in dark yellow belong to birds; genes in dark green belong to amphibians; genes in sky blue belong to fish. NJ, neighbor-joining; ME, minimum evolution; MP, maximum parsimony.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4314415&req=5

f2-ijmm-35-03-0587: Phylogenetic trees of the PLA2 gene in vertebrates. (A) Phylogenetic tree produced using the NJ method; (B) phylogenetic tree produced using the ME method; (C) phylogenetic tree produced using the MP method. Genes with a crimson disc belong to the PLA2G16 group; genes with an orange disc belong to the PLA2G6 group; genes with a grey disc belong to the PLA2G10 group; genes with a dark blue disc belong to the PLA2G10 group; genes with a yellow disc belong to the PLA2G15 group; genes with a red disc belong to the PLA2G7 group; genes with a green disc belong to the PLA2G4 group; genes with a purple disc belong to the PLA2G3 group; genes with a light blue disc belong to the PLA2G12 group. (D) Phylogenetic tree of the PLA2 gene in vertebrates produced using the Bayesian method. Genes with a crimson branch belong to the PLA2G16 group; genes with an orange branch belong to the PLA2G6 group; genes with a grey branch belong to the PLA2G10 group; genes with a dark blue branch belong to the PLA2G10 group; genes with a yellow branch belong to the PLA2G15 group; genes with a red branch belong to the PLA2G7 group; genes with a green branch belong to the PLA2G4 group; genes with a purple branch belong to the PLA2G3 group; genes with a light blue branch belong to the PLA2G12 group; genes in pink belong to mammals; genes in dark yellow belong to birds; genes in dark green belong to amphibians; genes in sky blue belong to fish. NJ, neighbor-joining; ME, minimum evolution; MP, maximum parsimony.
Mentions: A total of 49 sequences from 10 species were used to reconstruct a phylogenetic tree for the PLA2 gene family using the NJ, ME, MP methods, as well as the Bayesian information criterion with bootstrap value detection. The details of the included data are presented in Table I. A total of 25 nodes (56.81% in total) showed bootstrap values ≥95% and 34 nodes (77.27% in total) had bootstrap values ≥80% in the Bayes building tree (Fig. 2D). In each subgroup, mammal data, including data from the Sumatran orangutan, pig, Norway rat, human, house mouse, dog and cattle were gathered. The data from the African clawed frog, chicken and zebrafish were much more original than those from mammals, indicating that the taxonomy of host organisms reflects the phylogenetic background of the PLA2 gene family. The vertebrate PLA2 gene family was sorted into nine lineages according to the type of reaction for catalyzing phospholipids. PLA2G7 seems to be the most distant lineage in this gene family, indicating a large number of structural changes accumulating on them. Furthermore, all the groups were divided into two major clades; clade 1 included PLA2G16, PLA2G6, PLA2G10, PLA2G5 and PLA2G15, whereas clade 2 included PLA2G7, PLA2G4, PLA2G3 and PLA2G12. Closer lineages were observed between PLA2G16 and PLA2G6, PLA2G7 and PLA2G4, PLA2G3 and PLA2G12, well as among PLA2G10, PLA2G5 and PLA2G15. Moreover, the phylogenetic relationships obtained by the NJ, ME and MP methods were different (Fig. 2A–C).

Bottom Line: In this study, we downloaded 49 genomic data sets of PLA from different species, including the human, house mouse, Norway rat, pig, dog, chicken, cattle, African clawed frog, Sumatran orangutan and the zebrafish species.Phylogenetic relationships were determined using the neighbor-joining (NJ), minimum evolution (ME) and maximum parsimony (MP) methods, as well as the Bayesian information criterion.The results were then presented as phylogenetic trees.

View Article: PubMed Central - PubMed

Affiliation: Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, P.R. China.

ABSTRACT
The phospholipase A (PLA)2 family is the most complex gene family of phospholipases and plays a crucial role in a number of physiological activities. However, the phylogenetic background of the PLA2 gene family and the amino acid residues of the PLA2G7 gene following positive selection gene remain undetermined. In this study, we downloaded 49 genomic data sets of PLA from different species, including the human, house mouse, Norway rat, pig, dog, chicken, cattle, African clawed frog, Sumatran orangutan and the zebrafish species. Phylogenetic relationships were determined using the neighbor-joining (NJ), minimum evolution (ME) and maximum parsimony (MP) methods, as well as the Bayesian information criterion. The results were then presented as phylogenetic trees. Positive selection sites were detected using site, branch and branch‑site models. These methods led us to the following assumptions: i) closer lineages were observed between PLA2G16 and PLA2G6, PLA2G7 and PLA2G4, PLA2G3 and PLA2G12, as well as among PLA2G10, PLA2G5 and PLA2G15; ii) PLA2G5 appeared to be the origin of the PLA2 family, and PLA2G7 was one of the most evolutionarily distant PLA2 proteins; iii) 16 positive-selection sites were detected and were marked in the PLA2G7 protein sequence as 327D, 257Q, 276G, 34s, 66G, 67C, 319S, 28N, 50S, 54T, 58R, 75T, 88Q, 92R, 179H and 191K.

Show MeSH