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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.

Show MeSH
Predicted regulatory elements in the promoters of AM-responsive genes. Promoter elements were identified by MEME from 190 promoters of genes represented in Task4 that are significantly upregulated (>3x) in mycorrhizal roots or in microdissected cells with arbuscules (red and blue domains in Figure 3, Additional file 8: Table S3). The search was set to palindromic sequences of 6-30 nucleotides.
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Fig9: Predicted regulatory elements in the promoters of AM-responsive genes. Promoter elements were identified by MEME from 190 promoters of genes represented in Task4 that are significantly upregulated (>3x) in mycorrhizal roots or in microdissected cells with arbuscules (red and blue domains in Figure 3, Additional file 8: Table S3). The search was set to palindromic sequences of 6-30 nucleotides.

Mentions: Phylogenetic sequence analysis for Figures 1 and 9 was performed using the protein sequences provided in Additional file 1: File S1. To obtain these sequences, the first sequence for each group (marked in bold in Additional file 1: File S1; e.g. M. truncatula RAM1 for the RAM1 group) was used as a query for a protein blast at NCBI against the non-redundant protein database. From the results of this blast, the first hit for each plant species was retrieved. Phylogenetic analysis was performed as described [77] with the basic function (“One-click”). Red numbers on the branches of phylogenetic trees represent indices from an approximate Likelyhood Ratio Test (aLRT) [78]. aLRT vales are equivalent to bootstrap values and indicate well supported branches (close to 1) or weakly supported branches (close to 0).Figure 9


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)

Predicted regulatory elements in the promoters of AM-responsive genes. Promoter elements were identified by MEME from 190 promoters of genes represented in Task4 that are significantly upregulated (>3x) in mycorrhizal roots or in microdissected cells with arbuscules (red and blue domains in Figure 3, Additional file 8: Table S3). The search was set to palindromic sequences of 6-30 nucleotides.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig9: Predicted regulatory elements in the promoters of AM-responsive genes. Promoter elements were identified by MEME from 190 promoters of genes represented in Task4 that are significantly upregulated (>3x) in mycorrhizal roots or in microdissected cells with arbuscules (red and blue domains in Figure 3, Additional file 8: Table S3). The search was set to palindromic sequences of 6-30 nucleotides.
Mentions: Phylogenetic sequence analysis for Figures 1 and 9 was performed using the protein sequences provided in Additional file 1: File S1. To obtain these sequences, the first sequence for each group (marked in bold in Additional file 1: File S1; e.g. M. truncatula RAM1 for the RAM1 group) was used as a query for a protein blast at NCBI against the non-redundant protein database. From the results of this blast, the first hit for each plant species was retrieved. Phylogenetic analysis was performed as described [77] with the basic function (“One-click”). Red numbers on the branches of phylogenetic trees represent indices from an approximate Likelyhood Ratio Test (aLRT) [78]. aLRT vales are equivalent to bootstrap values and indicate well supported branches (close to 1) or weakly supported branches (close to 0).Figure 9

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