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Comparative and evolutionary analysis of major peanut allergen gene families.

Ratnaparkhe MB, Lee TH, Tan X, Wang X, Li J, Kim C, Rainville LK, Lemke C, Compton RO, Robertson J, Gallo M, Bertioli DJ, Paterson AH - Genome Biol Evol (2014)

Bottom Line: These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events.Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes.Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia Directorate of Soybean Research, Indian Council of Agriculture Research (ICAR), Indore, (M.P.), India.

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Alignment of Arah3 BACs (AHF44O16, AHF259D10) with inferred syntenic regions from soybean (GM), pigeonpea (CC), Medicago (MT), Phaseolus vulgaris (Pv), chickpea (Ca), poplar (PT), Arabidopsis (AT), Vitis (VV), and tomato (SL). Genes are shown with directional blocks, with specific colors displaying their sources. Numbers 1–31 indicate gene order corresponding to the genes present on peanut BAC AHF44O16. Gene synteny is shown with lines, and the color scheme displays different homologous relationships. Comparative gene synteny indicates that the position of the Arah3 gene is not well conserved in syntenic regions and Arah3 orthologs are not seen in close proximity to the low copy genes in other plants, as observed in Arah1. Orthologs of Arah3 were identified only in soybean, Vitis, and Arabidopsis. Red box indicates allergen-encoding genes.
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evu189-F9: Alignment of Arah3 BACs (AHF44O16, AHF259D10) with inferred syntenic regions from soybean (GM), pigeonpea (CC), Medicago (MT), Phaseolus vulgaris (Pv), chickpea (Ca), poplar (PT), Arabidopsis (AT), Vitis (VV), and tomato (SL). Genes are shown with directional blocks, with specific colors displaying their sources. Numbers 1–31 indicate gene order corresponding to the genes present on peanut BAC AHF44O16. Gene synteny is shown with lines, and the color scheme displays different homologous relationships. Comparative gene synteny indicates that the position of the Arah3 gene is not well conserved in syntenic regions and Arah3 orthologs are not seen in close proximity to the low copy genes in other plants, as observed in Arah1. Orthologs of Arah3 were identified only in soybean, Vitis, and Arabidopsis. Red box indicates allergen-encoding genes.

Mentions: Arah1 orthologs are highly conserved in eudicots including soybean, pigeonpea, Medicago, Lotus, poplar, Vitis, Arabidopsis, and tomato. The physical location of Arah1 is also conserved as nearby genes (Gene No. 7, 9, 10, and 14) are located in close proximity to Arah1 homologs in pigeonpea, soybean, chickpea, common bean, Lotus, Arabidopsis, Vitis, and tomato (fig. 8). In soybean, homologs of Arah1 are found on chromosomes 10 and 20, but absent from corresponding homoeologous chromosomes 1 and 2. In contrast to Arah1 orthologs, the positions of the Arah3 genes are not well conserved in syntenic regions and Arah3 orthologs are not seen in close proximity to low copy genes in other plants (fig. 9). Orthologs of Arah3 were identified only in soybean, Arabidopsis, and Vitis, being absent from the syntenic regions in other species studied. There also appears to have been gene loss of Arah3 homologs in soybean and other species, or at least a failure to expand. The soybean genes most similar to Arah3 are located on chromosome 3 and approximately 7.7 Mb from the aligned regions. Chromosome rearrangements in this region might be responsible for the different positions of Arah3-related genes.Fig. 9.—


Comparative and evolutionary analysis of major peanut allergen gene families.

Ratnaparkhe MB, Lee TH, Tan X, Wang X, Li J, Kim C, Rainville LK, Lemke C, Compton RO, Robertson J, Gallo M, Bertioli DJ, Paterson AH - Genome Biol Evol (2014)

Alignment of Arah3 BACs (AHF44O16, AHF259D10) with inferred syntenic regions from soybean (GM), pigeonpea (CC), Medicago (MT), Phaseolus vulgaris (Pv), chickpea (Ca), poplar (PT), Arabidopsis (AT), Vitis (VV), and tomato (SL). Genes are shown with directional blocks, with specific colors displaying their sources. Numbers 1–31 indicate gene order corresponding to the genes present on peanut BAC AHF44O16. Gene synteny is shown with lines, and the color scheme displays different homologous relationships. Comparative gene synteny indicates that the position of the Arah3 gene is not well conserved in syntenic regions and Arah3 orthologs are not seen in close proximity to the low copy genes in other plants, as observed in Arah1. Orthologs of Arah3 were identified only in soybean, Vitis, and Arabidopsis. Red box indicates allergen-encoding genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4202325&req=5

evu189-F9: Alignment of Arah3 BACs (AHF44O16, AHF259D10) with inferred syntenic regions from soybean (GM), pigeonpea (CC), Medicago (MT), Phaseolus vulgaris (Pv), chickpea (Ca), poplar (PT), Arabidopsis (AT), Vitis (VV), and tomato (SL). Genes are shown with directional blocks, with specific colors displaying their sources. Numbers 1–31 indicate gene order corresponding to the genes present on peanut BAC AHF44O16. Gene synteny is shown with lines, and the color scheme displays different homologous relationships. Comparative gene synteny indicates that the position of the Arah3 gene is not well conserved in syntenic regions and Arah3 orthologs are not seen in close proximity to the low copy genes in other plants, as observed in Arah1. Orthologs of Arah3 were identified only in soybean, Vitis, and Arabidopsis. Red box indicates allergen-encoding genes.
Mentions: Arah1 orthologs are highly conserved in eudicots including soybean, pigeonpea, Medicago, Lotus, poplar, Vitis, Arabidopsis, and tomato. The physical location of Arah1 is also conserved as nearby genes (Gene No. 7, 9, 10, and 14) are located in close proximity to Arah1 homologs in pigeonpea, soybean, chickpea, common bean, Lotus, Arabidopsis, Vitis, and tomato (fig. 8). In soybean, homologs of Arah1 are found on chromosomes 10 and 20, but absent from corresponding homoeologous chromosomes 1 and 2. In contrast to Arah1 orthologs, the positions of the Arah3 genes are not well conserved in syntenic regions and Arah3 orthologs are not seen in close proximity to low copy genes in other plants (fig. 9). Orthologs of Arah3 were identified only in soybean, Arabidopsis, and Vitis, being absent from the syntenic regions in other species studied. There also appears to have been gene loss of Arah3 homologs in soybean and other species, or at least a failure to expand. The soybean genes most similar to Arah3 are located on chromosome 3 and approximately 7.7 Mb from the aligned regions. Chromosome rearrangements in this region might be responsible for the different positions of Arah3-related genes.Fig. 9.—

Bottom Line: These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events.Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes.Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia Directorate of Soybean Research, Indian Council of Agriculture Research (ICAR), Indore, (M.P.), India.

Show MeSH
Related in: MedlinePlus