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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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Phylogenetic analysis of AM-related genes relative to house-keeping genes. Phylograms of AM-induced RAM1 (a) and PT4 (b), in relation to the housekeeping genes cyclin D6 (c) and RPL5 (d).
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Fig1: Phylogenetic analysis of AM-related genes relative to house-keeping genes. Phylograms of AM-induced RAM1 (a) and PT4 (b), in relation to the housekeeping genes cyclin D6 (c) and RPL5 (d).

Mentions: In order to explore the potential for differential conservation of AM-related genes, we established the phylogeny of two central AM-related proteins, the GRAS-type transcription factor REQUIRED FOR ARBUSCULAR MYCORRHIZA1 (RAM1), which is an essential regulator of AM symbiosis [21], and PHOSPHATE TRANSPORTER4 (PT4), which is required for symbiotic phosphate transfer and arbuscule functioning [23,24] (Additional file 1: File S1). A phylogenetic tree of RAM1 shows a clear bisection between mycorrhizal plants (group A and B), and non-mycorrhizal plants (group C) (Figure 1a). Notably, the sequences of AM-competent dicots and monocots (groups A and B) grouped significantly closer together than the dicots among each other (groups A and C). A similar pattern was observed in a phylogenetic tree of PT4 and its closest homologues in various monocot and dicot species (Figure 1b). As with RAM1, the homologues from AM-competent dicots (group A) and monocots (group B) grouped more closely together than the homologues of the phylogenetically related groups of the AM-competent dicots (group A) and the non-mycorrhizal dicots (group C).Figure 1


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)

Phylogenetic analysis of AM-related genes relative to house-keeping genes. Phylograms of AM-induced RAM1 (a) and PT4 (b), in relation to the housekeeping genes cyclin D6 (c) and RPL5 (d).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Phylogenetic analysis of AM-related genes relative to house-keeping genes. Phylograms of AM-induced RAM1 (a) and PT4 (b), in relation to the housekeeping genes cyclin D6 (c) and RPL5 (d).
Mentions: In order to explore the potential for differential conservation of AM-related genes, we established the phylogeny of two central AM-related proteins, the GRAS-type transcription factor REQUIRED FOR ARBUSCULAR MYCORRHIZA1 (RAM1), which is an essential regulator of AM symbiosis [21], and PHOSPHATE TRANSPORTER4 (PT4), which is required for symbiotic phosphate transfer and arbuscule functioning [23,24] (Additional file 1: File S1). A phylogenetic tree of RAM1 shows a clear bisection between mycorrhizal plants (group A and B), and non-mycorrhizal plants (group C) (Figure 1a). Notably, the sequences of AM-competent dicots and monocots (groups A and B) grouped significantly closer together than the dicots among each other (groups A and C). A similar pattern was observed in a phylogenetic tree of PT4 and its closest homologues in various monocot and dicot species (Figure 1b). As with RAM1, the homologues from AM-competent dicots (group A) and monocots (group B) grouped more closely together than the homologues of the phylogenetically related groups of the AM-competent dicots (group A) and the non-mycorrhizal dicots (group C).Figure 1

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