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Contrasting patterns of nucleotide polymorphism suggest different selective regimes within different parts of the PgiC1 gene in Festuca ovina L

Li, Yuan LU ; Hansson, Bengt LU ; Ghatnekar, Lena LU and Prentice, Honor C. LU (2017) In Hereditas 154.
Abstract

BACKGROUND: Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5' and 3' portions of the gene.

METHODS: In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene.

RESULTS: Our study confirms that the two portions of the PgiC1 gene show substantially different levels of DNA polymorphism and also suggests that the peptide encoded by the 3' portion of PgiC1 is... (More)

BACKGROUND: Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5' and 3' portions of the gene.

METHODS: In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene.

RESULTS: Our study confirms that the two portions of the PgiC1 gene show substantially different levels of DNA polymorphism and also suggests that the peptide encoded by the 3' portion of PgiC1 is functionally and structurally more important than that encoded by the 5' portion. Although there was some evidence of purifying selection (dN/dS test) on the 5' portion of the gene, the signature of purifying selection was considerably stronger on the 3' portion of the gene (dN/dS and McDonald-Kreitman tests). Several tests support the action of balancing selection within the 5' portion of the gene. Wall's B and Q tests were significant only for the 5' portion of the gene. There were also marked peaks of nucleotide diversity, Tajima's D and the dN/dS ratio at or around a PgiC1 codon site (within the 5' portion of the gene) that a previous study had suggested was subject to positive diversifying selection.

CONCLUSIONS: Our results suggest that the two portions of the gene have been subject to different selective regimes. Purifying selection appears to have been the main force contributing to the relatively low level of polymorphism within the 3' portion of the sequence. In contrast, it is possible that balancing selection has contributed to the maintenance of the polymorphism within the 5' portion of the gene.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Cytosolic phosphoglucose isomerase, Festuca ovina, Nucleotide polymorphism, PgiC1, Purifying selection
in
Hereditas
volume
154
publisher
Wiley-Blackwell
external identifiers
  • scopus:85027507861
ISSN
1601-5223
DOI
10.1186/s41065-017-0032-6
language
English
LU publication?
yes
id
1349e5b8-50f1-4323-8ba6-264df6766312
date added to LUP
2017-09-14 13:16:25
date last changed
2017-09-15 03:00:02
@article{1349e5b8-50f1-4323-8ba6-264df6766312,
  abstract     = {<p>BACKGROUND: Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5' and 3' portions of the gene.</p><p>METHODS: In the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene.</p><p>RESULTS: Our study confirms that the two portions of the PgiC1 gene show substantially different levels of DNA polymorphism and also suggests that the peptide encoded by the 3' portion of PgiC1 is functionally and structurally more important than that encoded by the 5' portion. Although there was some evidence of purifying selection (dN/dS test) on the 5' portion of the gene, the signature of purifying selection was considerably stronger on the 3' portion of the gene (dN/dS and McDonald-Kreitman tests). Several tests support the action of balancing selection within the 5' portion of the gene. Wall's B and Q tests were significant only for the 5' portion of the gene. There were also marked peaks of nucleotide diversity, Tajima's D and the dN/dS ratio at or around a PgiC1 codon site (within the 5' portion of the gene) that a previous study had suggested was subject to positive diversifying selection.</p><p>CONCLUSIONS: Our results suggest that the two portions of the gene have been subject to different selective regimes. Purifying selection appears to have been the main force contributing to the relatively low level of polymorphism within the 3' portion of the sequence. In contrast, it is possible that balancing selection has contributed to the maintenance of the polymorphism within the 5' portion of the gene.</p>},
  articleno    = {11},
  author       = {Li, Yuan and Hansson, Bengt and Ghatnekar, Lena and Prentice, Honor C.},
  issn         = {1601-5223},
  keyword      = {Cytosolic phosphoglucose isomerase,Festuca ovina,Nucleotide polymorphism,PgiC1,Purifying selection},
  language     = {eng},
  publisher    = {Wiley-Blackwell},
  series       = {Hereditas},
  title        = {Contrasting patterns of nucleotide polymorphism suggest different selective regimes within different parts of the PgiC1 gene in Festuca ovina L},
  url          = {http://dx.doi.org/10.1186/s41065-017-0032-6},
  volume       = {154},
  year         = {2017},
}