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The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages
BACKGROUND: In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of g...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2006
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1578591/ https://www.ncbi.nlm.nih.gov/pubmed/16923188 http://dx.doi.org/10.1186/1471-2148-6-64 |
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author | Johnson, Deborah A Hill, Jeffrey P Thomas, Michael A |
author_facet | Johnson, Deborah A Hill, Jeffrey P Thomas, Michael A |
author_sort | Johnson, Deborah A |
collection | PubMed |
description | BACKGROUND: In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific expansion patterns? We also looked for correlations between relative EST database representation in Arabidopsis and similarity to orthologs in early lineages. RESULTS: Homologs of all seven MST subfamilies were present in land plants at least 400 million years ago. Subfamily expression levels vary across lineages with greater relative expression of the STP, ERD6-like, INT and PLT subfamilies in the vascular plants. In the large EST databases of the moss, gymnosperm, monocot and eudicot lineages, EST contig construction reveals that MST subfamilies have experienced lineage-specific expansions. Large subfamily expansions appear to be due to multiple gene duplications arising from single ancestral genes. In Arabidopsis, one or a few genes within most subfamilies have much higher EST database representation than others. Most highly represented (broadly expressed) genes in Arabidopsis have best match orthologs in early divergent lineages. CONCLUSION: The seven subfamilies of the Arabidopsis MST gene family are ancient in land plants and show differential subfamily expression and lineage-specific subfamily expansions. Patterns of gene expression in Arabidopsis and correlation of highly represented genes with best match homologs in early lineages suggests that broadly expressed genes are often highly conserved, and that most genes have more limited expression. |
format | Text |
id | pubmed-1578591 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-15785912006-09-27 The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages Johnson, Deborah A Hill, Jeffrey P Thomas, Michael A BMC Evol Biol Research Article BACKGROUND: In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific expansion patterns? We also looked for correlations between relative EST database representation in Arabidopsis and similarity to orthologs in early lineages. RESULTS: Homologs of all seven MST subfamilies were present in land plants at least 400 million years ago. Subfamily expression levels vary across lineages with greater relative expression of the STP, ERD6-like, INT and PLT subfamilies in the vascular plants. In the large EST databases of the moss, gymnosperm, monocot and eudicot lineages, EST contig construction reveals that MST subfamilies have experienced lineage-specific expansions. Large subfamily expansions appear to be due to multiple gene duplications arising from single ancestral genes. In Arabidopsis, one or a few genes within most subfamilies have much higher EST database representation than others. Most highly represented (broadly expressed) genes in Arabidopsis have best match orthologs in early divergent lineages. CONCLUSION: The seven subfamilies of the Arabidopsis MST gene family are ancient in land plants and show differential subfamily expression and lineage-specific subfamily expansions. Patterns of gene expression in Arabidopsis and correlation of highly represented genes with best match homologs in early lineages suggests that broadly expressed genes are often highly conserved, and that most genes have more limited expression. BioMed Central 2006-08-21 /pmc/articles/PMC1578591/ /pubmed/16923188 http://dx.doi.org/10.1186/1471-2148-6-64 Text en Copyright © 2006 Johnson et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Johnson, Deborah A Hill, Jeffrey P Thomas, Michael A The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
title | The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
title_full | The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
title_fullStr | The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
title_full_unstemmed | The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
title_short | The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
title_sort | monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1578591/ https://www.ncbi.nlm.nih.gov/pubmed/16923188 http://dx.doi.org/10.1186/1471-2148-6-64 |
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