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A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

Favre P, Bapaume L, Bossolini E, Delorenzi M, Falquet L, Reinhardt D - BMC Plant Biol. (2014)

Bottom Line: However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify.As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM.This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species.

Results: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility.

Conclusions: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

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Related in: MedlinePlus

Cluster of genes induced in both, mycorrhizal roots, and nodule symbiosis. Details from cluster shown in Additional file 8: Table S3. Numbers in the column “criteria” indicate under which conditions the gene was induced at least 3-fold (compare to Table 2). Numbers in the column “Task” indicate in which task the gene was still retained (compare to Table 1). Ranks are assigned according to gene induction in mycorrhizal roots (corresponding to the rank in Additional file 7: Table S2).
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Fig5: Cluster of genes induced in both, mycorrhizal roots, and nodule symbiosis. Details from cluster shown in Additional file 8: Table S3. Numbers in the column “criteria” indicate under which conditions the gene was induced at least 3-fold (compare to Table 2). Numbers in the column “Task” indicate in which task the gene was still retained (compare to Table 1). Ranks are assigned according to gene induction in mycorrhizal roots (corresponding to the rank in Additional file 7: Table S2).

Mentions: While gene expression patterns can be identified based on defined conditions (e.g. criteria 1-6 in this study), global expression analysis by clustering can identify groups of genes with similar expression patterns over a large set of expression data like the 254 different treatments and conditions covered by the Medicago Gene Atlas (http://mtgea.noble.org/v3). This approach can identify groups of genes that are co-regulated and therefore might be functionally related. On the other hand, this approach can lead to the discovery of common regulatory elements in promoters, which are the reason for co-regulation (see below). Hence, we decided to use pairwise average linkage and Pearson correlation in order to identify genes with shared expression pattern (Figure 2, P2; see P2_task4cytoallr.cys in Additional file 3: File S2). All proteins identified by Task4 were correlated based on their standardized gene expression score, i.e. the ratios between the individual expression levels divided by the average of all expression levels as a relative indicator of expression (see Methods). Particular attention was paid to groups of genes that comprised AM-induced genes. One conspicuous cluster of 51 genes with a significantly correlated expression pattern turned out to be highly specific for AM, resulting in apparent vertical red stripes in the visual representation of the cluster (Additional file 9: Figure S2 and Figure 4). A further relevant group comprised genes that are induced commonly in AM and in RNS (Additional file 10: Figure S3 and Additional file 11: Figure S5). These genes may encode proteins that play a general role in symbiotic interactions. Interestingly, this cluster consisted primarily of chitinases, cysteine proteases, a glucanase and several ripening-related proteins (Figure 5).Figure 4


A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

Favre P, Bapaume L, Bossolini E, Delorenzi M, Falquet L, Reinhardt D - BMC Plant Biol. (2014)

Cluster of genes induced in both, mycorrhizal roots, and nodule symbiosis. Details from cluster shown in Additional file 8: Table S3. Numbers in the column “criteria” indicate under which conditions the gene was induced at least 3-fold (compare to Table 2). Numbers in the column “Task” indicate in which task the gene was still retained (compare to Table 1). Ranks are assigned according to gene induction in mycorrhizal roots (corresponding to the rank in Additional file 7: Table S2).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4274732&req=5

Fig5: Cluster of genes induced in both, mycorrhizal roots, and nodule symbiosis. Details from cluster shown in Additional file 8: Table S3. Numbers in the column “criteria” indicate under which conditions the gene was induced at least 3-fold (compare to Table 2). Numbers in the column “Task” indicate in which task the gene was still retained (compare to Table 1). Ranks are assigned according to gene induction in mycorrhizal roots (corresponding to the rank in Additional file 7: Table S2).
Mentions: While gene expression patterns can be identified based on defined conditions (e.g. criteria 1-6 in this study), global expression analysis by clustering can identify groups of genes with similar expression patterns over a large set of expression data like the 254 different treatments and conditions covered by the Medicago Gene Atlas (http://mtgea.noble.org/v3). This approach can identify groups of genes that are co-regulated and therefore might be functionally related. On the other hand, this approach can lead to the discovery of common regulatory elements in promoters, which are the reason for co-regulation (see below). Hence, we decided to use pairwise average linkage and Pearson correlation in order to identify genes with shared expression pattern (Figure 2, P2; see P2_task4cytoallr.cys in Additional file 3: File S2). All proteins identified by Task4 were correlated based on their standardized gene expression score, i.e. the ratios between the individual expression levels divided by the average of all expression levels as a relative indicator of expression (see Methods). Particular attention was paid to groups of genes that comprised AM-induced genes. One conspicuous cluster of 51 genes with a significantly correlated expression pattern turned out to be highly specific for AM, resulting in apparent vertical red stripes in the visual representation of the cluster (Additional file 9: Figure S2 and Figure 4). A further relevant group comprised genes that are induced commonly in AM and in RNS (Additional file 10: Figure S3 and Additional file 11: Figure S5). These genes may encode proteins that play a general role in symbiotic interactions. Interestingly, this cluster consisted primarily of chitinases, cysteine proteases, a glucanase and several ripening-related proteins (Figure 5).Figure 4

Bottom Line: However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify.As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM.This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species.

Results: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility.

Conclusions: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

Show MeSH
Related in: MedlinePlus