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In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia.

Mardi M, Karimi Farsad L, Gharechahi J, Salekdeh GH - PLoS ONE (2015)

Bottom Line: When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5).These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways.The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran.

ABSTRACT
Witches' broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia). However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes) with an average length of 530 nt. Of these, 41,805 (53.4%) were annotated against the NCBI non-redundant (nr) protein database using a BLASTx search (e-value ≤ 1e-5). When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5). These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

No MeSH data available.


Related in: MedlinePlus

Gibberellin (GA) biosynthesis pathway.GAs are synthesised using granylgranyl diphosphate as a precursor in the phenylpropanoid biosynthesis pathway. In our study, genes related to the GA biosynthesis pathway were coordinately up-regulated in phytoplasma-infected plants. In addition, the GA-catabolising enzyme gibberellin 2 oxidase (GA20oxs), which inactivates bioactive GAs and therefore reduces their cellular level, was also significantly overexpressed in diseased plants. Enzymes coloured green are those that were up-regulated, whereas enzymes shown in blue or white without a green label are those that were not identified in the present study.
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pone.0130425.g005: Gibberellin (GA) biosynthesis pathway.GAs are synthesised using granylgranyl diphosphate as a precursor in the phenylpropanoid biosynthesis pathway. In our study, genes related to the GA biosynthesis pathway were coordinately up-regulated in phytoplasma-infected plants. In addition, the GA-catabolising enzyme gibberellin 2 oxidase (GA20oxs), which inactivates bioactive GAs and therefore reduces their cellular level, was also significantly overexpressed in diseased plants. Enzymes coloured green are those that were up-regulated, whereas enzymes shown in blue or white without a green label are those that were not identified in the present study.

Mentions: Terpenoid metabolites are known as signalling molecules involved in many interactions of plants with other organisms, including pathogens. For example, certain diterpenoid and sesquiterpene metabolites are produced as plant growth regulators (gibberellins, GAs) and phytoalexins in response to pathogen infection [66]. In our study, genes related to the diterpenoid pathway, which leads to the biosynthesis and catabolism of GAs, were up-regulated by phytoplasma infection (Fig 5). These include ent-copalyl diphosphate synthase (CPS, 4 unigenes), ent-kaurene synthase (KS, 2 unigenes), ent-kaurene oxidase (KO, 2 unigenes), ent-kaurenoic acid oxidase 2 (KAO, 5 unigenes), ent-kaurenoic acid hydroxylase (6 unigenes), gibberellin 3-beta-dioxygenase (2 unigenes), gibberellin 2-oxidase (GA2oxs, 2 unigenes), gibberellin 20 oxidase (GA20oxs, 1 unigene), 2-oxoglutarate-dependent dioxygenase (4 unigenes), and casbene synthase (7 unigenes). The biosynthesis of GAs is initiated by the conversion of geranylgeranyl diphosphate, a common precursor of diterpenoids, to copalyl diphosphate in a reaction catalysed by CPS, which is then further cyclised to ent-kaurene by the enzymatic action of KS (Fig 5). Ent-kaurene is oxidised to ent-kaurenoic acid in a reaction catalysed by KO, a membrane-associated cytochrome P450 monooxygenase, and then converted to GA12 by KAO. GA12 is further converted to GA53 by 13-hydroxylation. Finally, GA12 and GA53 are converted to various bioactive GAs by a series of oxidation steps catalysed by gibberellin oxidases (GA20oxs, 2-oxoglutarate-dependent dioxygenase, and GA3oxs) [67]. In contrast, GA2oxs inactivates bioactive GAs and is therefore responsible for a reduction in the level of bioactive GAs in plants. It has been shown that rice mutants overexpressing GA2oxs show early and increased tiller, a semidwarfism phenotype, and adventitious root growth [68]. In addition, change in the level of bioactive GAs may also affect resistance to pathogen infection. For example, recently, it has been shown that overexpression of a GA-deactivating enzyme, elongated uppermost internode (EUI), in rice decreased the GA level and increased resistance to bacterial and fungal pathogens, which suggests a negative role for GAs in the development of resistance against pathogen infection [69].


In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia.

Mardi M, Karimi Farsad L, Gharechahi J, Salekdeh GH - PLoS ONE (2015)

Gibberellin (GA) biosynthesis pathway.GAs are synthesised using granylgranyl diphosphate as a precursor in the phenylpropanoid biosynthesis pathway. In our study, genes related to the GA biosynthesis pathway were coordinately up-regulated in phytoplasma-infected plants. In addition, the GA-catabolising enzyme gibberellin 2 oxidase (GA20oxs), which inactivates bioactive GAs and therefore reduces their cellular level, was also significantly overexpressed in diseased plants. Enzymes coloured green are those that were up-regulated, whereas enzymes shown in blue or white without a green label are those that were not identified in the present study.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489016&req=5

pone.0130425.g005: Gibberellin (GA) biosynthesis pathway.GAs are synthesised using granylgranyl diphosphate as a precursor in the phenylpropanoid biosynthesis pathway. In our study, genes related to the GA biosynthesis pathway were coordinately up-regulated in phytoplasma-infected plants. In addition, the GA-catabolising enzyme gibberellin 2 oxidase (GA20oxs), which inactivates bioactive GAs and therefore reduces their cellular level, was also significantly overexpressed in diseased plants. Enzymes coloured green are those that were up-regulated, whereas enzymes shown in blue or white without a green label are those that were not identified in the present study.
Mentions: Terpenoid metabolites are known as signalling molecules involved in many interactions of plants with other organisms, including pathogens. For example, certain diterpenoid and sesquiterpene metabolites are produced as plant growth regulators (gibberellins, GAs) and phytoalexins in response to pathogen infection [66]. In our study, genes related to the diterpenoid pathway, which leads to the biosynthesis and catabolism of GAs, were up-regulated by phytoplasma infection (Fig 5). These include ent-copalyl diphosphate synthase (CPS, 4 unigenes), ent-kaurene synthase (KS, 2 unigenes), ent-kaurene oxidase (KO, 2 unigenes), ent-kaurenoic acid oxidase 2 (KAO, 5 unigenes), ent-kaurenoic acid hydroxylase (6 unigenes), gibberellin 3-beta-dioxygenase (2 unigenes), gibberellin 2-oxidase (GA2oxs, 2 unigenes), gibberellin 20 oxidase (GA20oxs, 1 unigene), 2-oxoglutarate-dependent dioxygenase (4 unigenes), and casbene synthase (7 unigenes). The biosynthesis of GAs is initiated by the conversion of geranylgeranyl diphosphate, a common precursor of diterpenoids, to copalyl diphosphate in a reaction catalysed by CPS, which is then further cyclised to ent-kaurene by the enzymatic action of KS (Fig 5). Ent-kaurene is oxidised to ent-kaurenoic acid in a reaction catalysed by KO, a membrane-associated cytochrome P450 monooxygenase, and then converted to GA12 by KAO. GA12 is further converted to GA53 by 13-hydroxylation. Finally, GA12 and GA53 are converted to various bioactive GAs by a series of oxidation steps catalysed by gibberellin oxidases (GA20oxs, 2-oxoglutarate-dependent dioxygenase, and GA3oxs) [67]. In contrast, GA2oxs inactivates bioactive GAs and is therefore responsible for a reduction in the level of bioactive GAs in plants. It has been shown that rice mutants overexpressing GA2oxs show early and increased tiller, a semidwarfism phenotype, and adventitious root growth [68]. In addition, change in the level of bioactive GAs may also affect resistance to pathogen infection. For example, recently, it has been shown that overexpression of a GA-deactivating enzyme, elongated uppermost internode (EUI), in rice decreased the GA level and increased resistance to bacterial and fungal pathogens, which suggests a negative role for GAs in the development of resistance against pathogen infection [69].

Bottom Line: When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5).These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways.The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran.

ABSTRACT
Witches' broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia). However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes) with an average length of 530 nt. Of these, 41,805 (53.4%) were annotated against the NCBI non-redundant (nr) protein database using a BLASTx search (e-value ≤ 1e-5). When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5). These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.

No MeSH data available.


Related in: MedlinePlus