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The landscape of nucleotide polymorphism among 13,500 genes of the conifer picea glauca, relationships with functions, and comparison with medicago truncatula.

Pavy N, Deschênes A, Blais S, Lavigne P, Beaulieu J, Isabel N, Mackay J, Bousquet J - Genome Biol Evol (2013)

Bottom Line: Conifer-specific sequences were also generally associated with the highest A/S ratios.These patterns confirm that the breadth of gene expression is a contributing factor to the evolution of nucleotide polymorphism.However, a number of families with high A/S ratios were found specific to P. glauca, suggesting cases of divergent evolution at the functional level.

View Article: PubMed Central - PubMed

Affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada.

ABSTRACT
Gene families differ in composition, expression, and chromosomal organization between conifers and angiosperms, but little is known regarding nucleotide polymorphism. Using various sequencing strategies, an atlas of 212k high-confidence single nucleotide polymorphisms (SNPs) with a validation rate of more than 92% was developed for the conifer white spruce (Picea glauca). Nonsynonymous and synonymous SNPs were annotated over the corresponding 13,498 white spruce genes representative of 2,457 known gene families. Patterns of nucleotide polymorphisms were analyzed by estimating the ratio of nonsynonymous to synonymous numbers of substitutions per site (A/S). A general excess of synonymous SNPs was expected and observed. However, the analysis from several perspectives enabled to identify groups of genes harboring an excess of nonsynonymous SNPs, thus potentially under positive selection. Four known gene families harbored such an excess: dehydrins, ankyrin-repeats, AP2/DREB, and leucine-rich repeat. Conifer-specific sequences were also generally associated with the highest A/S ratios. A/S values were also distributed asymmetrically across genes specifically expressed in megagametophytes, roots, or in both, harboring on average an excess of nonsynonymous SNPs. These patterns confirm that the breadth of gene expression is a contributing factor to the evolution of nucleotide polymorphism. The A/S ratios of Medicago truncatula genes were also analyzed: several gene families shared between P. glauca and M. truncatula data sets had similar excess of synonymous or nonsynonymous SNPs. However, a number of families with high A/S ratios were found specific to P. glauca, suggesting cases of divergent evolution at the functional level.

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Functions of the protein families encompassing 10 members or more in Picea glauca (a) and Medicago truncatula (b) and associated with the lowest (a1; b1) or highest (a2; b2) A/S ratios (gene set enrichment analysis, Fisher’s exact test, two-tailed, P < 0.05).
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evt143-F4: Functions of the protein families encompassing 10 members or more in Picea glauca (a) and Medicago truncatula (b) and associated with the lowest (a1; b1) or highest (a2; b2) A/S ratios (gene set enrichment analysis, Fisher’s exact test, two-tailed, P < 0.05).

Mentions: Next, the patterns of nucleotide polymorphism were analyzed across gene families based on 7,622 genes belonging to 2,457 PFAM families. In total, 102 families were significantly differentially distributed (P < 0.05) toward the highest or lowest A/S ratios (supplementary table S4, Supplementary Material online). We focused our analyses on 48 families represented by 10 gene members or more (supplementary table S4, Supplementary Material online, and figs. 3 and 4). The majority of these families could be grouped into only five types of proteins: enzymes, proteins associated with membranes or cytoskeleton, proteins involved in the degradation or protection of proteins, in protein–protein interactions, and in the regulation of gene expression or in DNA folding (fig. 4). As with the GO term analysis, a majority of the families (96.1%) were characterized by the lowest A/S ratios; however, four families were associated with the highest A/S ratios, that is, the AP2 family, the ankyrin repeat family, the leucine-rich repeat (LRR) family, and the dehydrins (figs. 2 and 3a). The LRRs and dehydrins were among genes with the highest A/S ratios with averages of 0.66 and 1.19, respectively (figs. 2 and 3a). For the AP2 and ankyrin repeat families, the A/S ratios were moderate (0.27 and 0.31, respectively, on average).Fig. 3.—


The landscape of nucleotide polymorphism among 13,500 genes of the conifer picea glauca, relationships with functions, and comparison with medicago truncatula.

Pavy N, Deschênes A, Blais S, Lavigne P, Beaulieu J, Isabel N, Mackay J, Bousquet J - Genome Biol Evol (2013)

Functions of the protein families encompassing 10 members or more in Picea glauca (a) and Medicago truncatula (b) and associated with the lowest (a1; b1) or highest (a2; b2) A/S ratios (gene set enrichment analysis, Fisher’s exact test, two-tailed, P < 0.05).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814201&req=5

evt143-F4: Functions of the protein families encompassing 10 members or more in Picea glauca (a) and Medicago truncatula (b) and associated with the lowest (a1; b1) or highest (a2; b2) A/S ratios (gene set enrichment analysis, Fisher’s exact test, two-tailed, P < 0.05).
Mentions: Next, the patterns of nucleotide polymorphism were analyzed across gene families based on 7,622 genes belonging to 2,457 PFAM families. In total, 102 families were significantly differentially distributed (P < 0.05) toward the highest or lowest A/S ratios (supplementary table S4, Supplementary Material online). We focused our analyses on 48 families represented by 10 gene members or more (supplementary table S4, Supplementary Material online, and figs. 3 and 4). The majority of these families could be grouped into only five types of proteins: enzymes, proteins associated with membranes or cytoskeleton, proteins involved in the degradation or protection of proteins, in protein–protein interactions, and in the regulation of gene expression or in DNA folding (fig. 4). As with the GO term analysis, a majority of the families (96.1%) were characterized by the lowest A/S ratios; however, four families were associated with the highest A/S ratios, that is, the AP2 family, the ankyrin repeat family, the leucine-rich repeat (LRR) family, and the dehydrins (figs. 2 and 3a). The LRRs and dehydrins were among genes with the highest A/S ratios with averages of 0.66 and 1.19, respectively (figs. 2 and 3a). For the AP2 and ankyrin repeat families, the A/S ratios were moderate (0.27 and 0.31, respectively, on average).Fig. 3.—

Bottom Line: Conifer-specific sequences were also generally associated with the highest A/S ratios.These patterns confirm that the breadth of gene expression is a contributing factor to the evolution of nucleotide polymorphism.However, a number of families with high A/S ratios were found specific to P. glauca, suggesting cases of divergent evolution at the functional level.

View Article: PubMed Central - PubMed

Affiliation: Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Canada.

ABSTRACT
Gene families differ in composition, expression, and chromosomal organization between conifers and angiosperms, but little is known regarding nucleotide polymorphism. Using various sequencing strategies, an atlas of 212k high-confidence single nucleotide polymorphisms (SNPs) with a validation rate of more than 92% was developed for the conifer white spruce (Picea glauca). Nonsynonymous and synonymous SNPs were annotated over the corresponding 13,498 white spruce genes representative of 2,457 known gene families. Patterns of nucleotide polymorphisms were analyzed by estimating the ratio of nonsynonymous to synonymous numbers of substitutions per site (A/S). A general excess of synonymous SNPs was expected and observed. However, the analysis from several perspectives enabled to identify groups of genes harboring an excess of nonsynonymous SNPs, thus potentially under positive selection. Four known gene families harbored such an excess: dehydrins, ankyrin-repeats, AP2/DREB, and leucine-rich repeat. Conifer-specific sequences were also generally associated with the highest A/S ratios. A/S values were also distributed asymmetrically across genes specifically expressed in megagametophytes, roots, or in both, harboring on average an excess of nonsynonymous SNPs. These patterns confirm that the breadth of gene expression is a contributing factor to the evolution of nucleotide polymorphism. The A/S ratios of Medicago truncatula genes were also analyzed: several gene families shared between P. glauca and M. truncatula data sets had similar excess of synonymous or nonsynonymous SNPs. However, a number of families with high A/S ratios were found specific to P. glauca, suggesting cases of divergent evolution at the functional level.

Show MeSH
Related in: MedlinePlus