Dataset Information

Patterns of expansion and expression divergence in the plant polygalacturonase gene family.

ABSTRACT:

Background

Polygalacturonases (PGs) belong to a large gene family in plants and are believed to be responsible for various cell separation processes. PG activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, fruit softening and decay, xylem cell formation, and pollen tube growth, thus illustrating divergent roles for members of this gene family. A close look at phylogenetic relationships among Arabidopsis and rice PGs accompanied by analysis of expression data provides an opportunity to address key questions on the evolution and functions of duplicate genes.

Results

We found that both tandem and whole-genome duplications contribute significantly to the expansion of this gene family but are associated with substantial gene losses. In addition, there are at least 21 PGs in the common ancestor of Arabidopsis and rice. We have also determined the relationships between Arabidopsis and rice PGs and their expression patterns in Arabidopsis to provide insights into the functional divergence between members of this gene family. By evaluating expression in five Arabidopsis tissues and during five stages of abscission, we found overlapping but distinct expression patterns for most of the different PGs.

Conclusion

Expression data suggest specialized roles or subfunctionalization for each PG gene member. PGs derived from whole genome duplication tend to have more similar expression patterns than those derived from tandem duplications. Our findings suggest that PG duplicates underwent rapid expression divergence and that the mechanisms of duplication affect the divergence rate.

SUBMITTER: Kim J

PROVIDER: S-EPMC1794546 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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Publications

Patterns of expansion and expression divergence in the plant polygalacturonase gene family.

Kim Joonyup J Shiu Shin-Han SH Thoma Sharon S Li Wen-Hsiung WH Patterson Sara E SE

Genome biology 20060101 9

<h4>Background</h4>Polygalacturonases (PGs) belong to a large gene family in plants and are believed to be responsible for various cell separation processes. PG activities have been shown to be associated with a wide range of plant developmental programs such as seed germination, organ abscission, pod and anther dehiscence, pollen grain maturation, fruit softening and decay, xylem cell formation, and pollen tube growth, thus illustrating divergent roles for members of this gene family. A close l ...[more]

PMID: 17010199

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Project description:BackgroundPolygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants' developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members of PG gene family in sweetpotato (Ipomoea batatas) have not been extensively identified.ResultsIn this study, there were 103 PG genes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed these PGs according to their locations of the chromosomes. The investigation of collinearity between the PGs in sweetpotato and other four species, contained Arabidopsis thaliana, Solanum lycopersicum, Malus domestica and Ziziphus jujuba, revealed important clues about the potential evolution of the PG family in sweetpotato. Gene duplication analysis showed that IbPGs with collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins contained cis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103 IbPGs were differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment). IbPG038 and IbPG039 were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found that IbPG006, IbPG034 and IbPG099 had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes.ConclusionA total of 103 IbPGs were identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested that IbPG006, IbPG034 and IbPG099 might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of the IbPGs.

Project description:Since the development of methods for homologous gene recombination, mouse models have played a central role in research in renal pathophysiology. However, many published and unpublished results show that mice with genetic changes mimicking human pathogenic mutations do not display the human phenotype. These functional differences may stem from differences in gene expression between mouse and human kidneys. However, large scale comparison of gene expression networks revealed conservation of gene expression among a large panel of human and mouse tissues including kidneys. Because renal functions result from the spatial integration of elementary processes originating in the glomerulus and the successive segments constituting the nephron, we hypothesized that differences in gene expression profiles along the human and mouse nephron might account for different behaviors. Analysis of SAGE libraries generated from the glomerulus and seven anatomically defined nephron segments from human and mouse kidneys allowed us to identify 4644 pairs of gene orthologs expressed in either one or both species. Quantitative analysis shows that many transcripts are present at different levels in the two species. It also shows poor conservation of gene expression profiles, with less than 10% of the 4644 gene orthologs displaying a higher conservation of expression profiles than the neutral expectation (p<0.05). Accordingly, hierarchical clustering reveals a higher degree of conservation of gene expression patterns between functionally unrelated kidney structures within a given species than between cognate structures from the two species. Similar findings were obtained for sub-groups of genes with either kidney-specific or housekeeping functions. Conservation of gene expression at the scale of the whole organ and divergence at the level of its constituting sub-structures likely account for the fact that although kidneys assume the same global function in the two species, many mouse "models" of human pathologies do not display the expected phenotype.

Dataset Information

Patterns of expansion and expression divergence in the plant polygalacturonase gene family.

Background

Results

Conclusion

Publications

Patterns of expansion and expression divergence in the plant polygalacturonase gene family.

Similar Datasets

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