Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome
Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each micros...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
PRAMOD, SREEPRIYA [verfasserIn] PERKINS, ANDY D. [verfasserIn] WELCH, MARK E. [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2014 |
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| Schlagwörter: |
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| Übergeordnetes Werk: |
Enthalten in: Journal of Genetics - Springer India, 1955, 93(2014), 2 vom: Aug., Seite 431-442 |
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| Übergeordnetes Werk: |
volume:93 ; year:2014 ; number:2 ; month:08 ; pages:431-442 |
| Links: |
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| DOI / URN: |
10.1007/s12041-014-0402-z |
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| Katalog-ID: |
SPR024320498 |
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| 520 | |a Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. | ||
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10.1007/s12041-014-0402-z doi (DE-627)SPR024320498 (SPR)s12041-014-0402-z-e DE-627 ger DE-627 rakwb eng PRAMOD, SREEPRIYA verfasserin aut Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. microsatellite (dpeaa)DE-He213 evolution (dpeaa)DE-He213 transcriptome (dpeaa)DE-He213 selection (dpeaa)DE-He213 untranslated regions (dpeaa)DE-He213 . (dpeaa)DE-He213 PERKINS, ANDY D. verfasserin aut WELCH, MARK E. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 93(2014), 2 vom: Aug., Seite 431-442 (DE-627)SPR024069582 nnns volume:93 year:2014 number:2 month:08 pages:431-442 https://dx.doi.org/10.1007/s12041-014-0402-z lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 93 2014 2 08 431-442 |
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10.1007/s12041-014-0402-z doi (DE-627)SPR024320498 (SPR)s12041-014-0402-z-e DE-627 ger DE-627 rakwb eng PRAMOD, SREEPRIYA verfasserin aut Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. microsatellite (dpeaa)DE-He213 evolution (dpeaa)DE-He213 transcriptome (dpeaa)DE-He213 selection (dpeaa)DE-He213 untranslated regions (dpeaa)DE-He213 . (dpeaa)DE-He213 PERKINS, ANDY D. verfasserin aut WELCH, MARK E. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 93(2014), 2 vom: Aug., Seite 431-442 (DE-627)SPR024069582 nnns volume:93 year:2014 number:2 month:08 pages:431-442 https://dx.doi.org/10.1007/s12041-014-0402-z lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 93 2014 2 08 431-442 |
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10.1007/s12041-014-0402-z doi (DE-627)SPR024320498 (SPR)s12041-014-0402-z-e DE-627 ger DE-627 rakwb eng PRAMOD, SREEPRIYA verfasserin aut Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. microsatellite (dpeaa)DE-He213 evolution (dpeaa)DE-He213 transcriptome (dpeaa)DE-He213 selection (dpeaa)DE-He213 untranslated regions (dpeaa)DE-He213 . (dpeaa)DE-He213 PERKINS, ANDY D. verfasserin aut WELCH, MARK E. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 93(2014), 2 vom: Aug., Seite 431-442 (DE-627)SPR024069582 nnns volume:93 year:2014 number:2 month:08 pages:431-442 https://dx.doi.org/10.1007/s12041-014-0402-z lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 93 2014 2 08 431-442 |
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10.1007/s12041-014-0402-z doi (DE-627)SPR024320498 (SPR)s12041-014-0402-z-e DE-627 ger DE-627 rakwb eng PRAMOD, SREEPRIYA verfasserin aut Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. microsatellite (dpeaa)DE-He213 evolution (dpeaa)DE-He213 transcriptome (dpeaa)DE-He213 selection (dpeaa)DE-He213 untranslated regions (dpeaa)DE-He213 . (dpeaa)DE-He213 PERKINS, ANDY D. verfasserin aut WELCH, MARK E. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 93(2014), 2 vom: Aug., Seite 431-442 (DE-627)SPR024069582 nnns volume:93 year:2014 number:2 month:08 pages:431-442 https://dx.doi.org/10.1007/s12041-014-0402-z lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 93 2014 2 08 431-442 |
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10.1007/s12041-014-0402-z doi (DE-627)SPR024320498 (SPR)s12041-014-0402-z-e DE-627 ger DE-627 rakwb eng PRAMOD, SREEPRIYA verfasserin aut Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome 2014 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. microsatellite (dpeaa)DE-He213 evolution (dpeaa)DE-He213 transcriptome (dpeaa)DE-He213 selection (dpeaa)DE-He213 untranslated regions (dpeaa)DE-He213 . (dpeaa)DE-He213 PERKINS, ANDY D. verfasserin aut WELCH, MARK E. verfasserin aut Enthalten in Journal of Genetics Springer India, 1955 93(2014), 2 vom: Aug., Seite 431-442 (DE-627)SPR024069582 nnns volume:93 year:2014 number:2 month:08 pages:431-442 https://dx.doi.org/10.1007/s12041-014-0402-z lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_11 GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_30 GBV_ILN_31 GBV_ILN_32 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_2002 GBV_ILN_2004 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2012 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2018 GBV_ILN_2021 GBV_ILN_2088 GBV_ILN_2190 GBV_ILN_2244 AR 93 2014 2 08 431-442 |
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Enthalten in Journal of Genetics 93(2014), 2 vom: Aug., Seite 431-442 volume:93 year:2014 number:2 month:08 pages:431-442 |
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Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome |
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Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. |
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Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. |
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Abstract The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly $ 5^{′} $UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli. |
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