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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

Conservation ratios of potentially AM-related proteins in comparison with housekeeping genes averaged for relevant groups of plant species. Conservation ratios were generated as for Figure 6 (see legend of Figure 6). However, no statistics were performed and all ratios are shown. Conservation ratios are compared for potential AM-related proteins extracted by Task3 (green), and for potential house-keeping genes identified by Task9 (red). For comparison, the position of the proteins represented in Figure 1 is indicated (RAM1: AES78316; PT4: AAM76743; cyclin D6: AES67335; RPL5: AES80278). (a) Ratios for log10(group C)/log10(group A). (b) Ratios for log10(group C)/log10(group B).
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Fig7: Conservation ratios of potentially AM-related proteins in comparison with housekeeping genes averaged for relevant groups of plant species. Conservation ratios were generated as for Figure 6 (see legend of Figure 6). However, no statistics were performed and all ratios are shown. Conservation ratios are compared for potential AM-related proteins extracted by Task3 (green), and for potential house-keeping genes identified by Task9 (red). For comparison, the position of the proteins represented in Figure 1 is indicated (RAM1: AES78316; PT4: AAM76743; cyclin D6: AES67335; RPL5: AES80278). (a) Ratios for log10(group C)/log10(group A). (b) Ratios for log10(group C)/log10(group B).

Mentions: Global comparison of the conservation ratios of proteins identified by Task3 and Task9, revealed considerably higher values for the former group (Figure 7), reflecting the different conservation patterns among proteins selected by Task3 and Task9. In the comparison between group A (AM-competent dicots) and group C (non-mycorrhizal dicots), the AM-related genes RAM1 and PT4 were clearly seprated from the housekeeping controls cyclin D6 and RPL5 (Figure 7a), while this distinction was much less clear in the comparison between group B (AM-competent monocots) and group C (Figure 7b). These results show that the conservation ratio can be used as a comparative proxy to evaluate the relative degree of conservation of a given protein among AM-competent species relative to the non-mycorrhizal species.Figure 7


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)

Conservation ratios of potentially AM-related proteins in comparison with housekeeping genes averaged for relevant groups of plant species. Conservation ratios were generated as for Figure 6 (see legend of Figure 6). However, no statistics were performed and all ratios are shown. Conservation ratios are compared for potential AM-related proteins extracted by Task3 (green), and for potential house-keeping genes identified by Task9 (red). For comparison, the position of the proteins represented in Figure 1 is indicated (RAM1: AES78316; PT4: AAM76743; cyclin D6: AES67335; RPL5: AES80278). (a) Ratios for log10(group C)/log10(group A). (b) Ratios for log10(group C)/log10(group B).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig7: Conservation ratios of potentially AM-related proteins in comparison with housekeeping genes averaged for relevant groups of plant species. Conservation ratios were generated as for Figure 6 (see legend of Figure 6). However, no statistics were performed and all ratios are shown. Conservation ratios are compared for potential AM-related proteins extracted by Task3 (green), and for potential house-keeping genes identified by Task9 (red). For comparison, the position of the proteins represented in Figure 1 is indicated (RAM1: AES78316; PT4: AAM76743; cyclin D6: AES67335; RPL5: AES80278). (a) Ratios for log10(group C)/log10(group A). (b) Ratios for log10(group C)/log10(group B).
Mentions: Global comparison of the conservation ratios of proteins identified by Task3 and Task9, revealed considerably higher values for the former group (Figure 7), reflecting the different conservation patterns among proteins selected by Task3 and Task9. In the comparison between group A (AM-competent dicots) and group C (non-mycorrhizal dicots), the AM-related genes RAM1 and PT4 were clearly seprated from the housekeeping controls cyclin D6 and RPL5 (Figure 7a), while this distinction was much less clear in the comparison between group B (AM-competent monocots) and group C (Figure 7b). These results show that the conservation ratio can be used as a comparative proxy to evaluate the relative degree of conservation of a given protein among AM-competent species relative to the non-mycorrhizal species.Figure 7

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