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De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways.

Hittalmani S, Mahesh HB, Mahadevaiah C, Prasannakumar MK - BMC Genomics (2016)

Bottom Line: The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins.Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway.This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.

View Article: PubMed Central - PubMed

Affiliation: Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India. shailajah_maslab@rediffmail.com.

ABSTRACT

Background: Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth.

Results: The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future.

Conclusions: Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.

No MeSH data available.


Related in: MedlinePlus

Organization of putative gene clusters involved in helvolic acid biosynthesis in S. oryzae. Genes are compared against M. anisophilae and A. fumigatus. Red arrow: cytochrome P450 genes. Yellow arrow: transferase family protein genes. Blue arrow: 3-ketosteroid-delta-1-dehydrogenase genes. Green arrow: SDR gene. Purple arrow: Squalene-hopene cyclase gene. Homologs are shown in dotted lines
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Fig5: Organization of putative gene clusters involved in helvolic acid biosynthesis in S. oryzae. Genes are compared against M. anisophilae and A. fumigatus. Red arrow: cytochrome P450 genes. Yellow arrow: transferase family protein genes. Blue arrow: 3-ketosteroid-delta-1-dehydrogenase genes. Green arrow: SDR gene. Purple arrow: Squalene-hopene cyclase gene. Homologs are shown in dotted lines

Mentions: Secondary metabolites (SMs) are small bioactive molecules and they are essential for fungal growth and development. At the same time SMs provide protection against various environmental stresses. The biosynthesis of SMs is catalyzed by either nonribosomal peptides synthases (NRPSs), polyketide synthases (PKSs), hybrid NRPS-PKS enzymes, prenyltransferases (DMATSs), and terpene cyclases (TCs). The catalytic activity of these enzymes results in production of SMs respectively like nonribosomal peptides, polyketides, NRPS-PKS hybrids, indole alkaloids, and terpenes [49]. Searching for SMs revealed that S. oryzae genome is enriched with PKSs, TCs followed by NRPSs, NRPSs-PKSs hybrid clusters (Fig. 4). Several studies have reported that S. oryzae produces helvolic acid and cerulenin SMs [50–53]. The biosynthetic pathways of these SMs were found to be different and concomitant production of these two metabolites might have synergistic effect to invade host by changing the cell permeability leading to leakage of electrolytes in the host tissue [52, 54–56]. So far, the studies on helvolic acid and cerulenin metabolites were restricted only to chromatographic assays and gene and protein level information of the pathways involved in their metabolism is unknown in S. oryzae. Based on our SM analysis, we hypothesize that PKSs, TCs and NRPSs could be the putative enzymes involved in the biosynthesis of these two metabolites in S. oryzae. We critically examined the proteome of S. oryzae to screen candidate genes involved in biosynthesis of these SMs. Helvolic acid is a steroidal antibiotic, known to be controlled by cluster of genes in Aspergillus flavus [57] and Metarhizium anisophilae [58]. Initial BLASTP searches of S. oryzae proteome against A. flavus protein sequences identified nine candidate genes in S. oryzae. The structural analysis showed these genes were single exonic genes arranged in clusters. Among these gene clusters, four (SoG_03551.T1, SoG_04319.T1, SoG_09546.T1, and SoG_03005.T1) cytochrome P450, two (SoG_03552.T1 and SoG_03554.T1) transferase family protein, one each of short chain dehydrogenase (SDR) (SoG_04320.T1), qualene-hopene-cyclase (SoG_05635.T1), and 3-ketosteroid-delta-1-dehydrogenase (SoG_03553.T1) genes (Fig. 5 and Additional file 10). The structural arrangement of gene clusters was more similar to Metarhizium aninophilae strain NwlB-02 (NCBI Locus ID: 129929) than A. flavus.Fig. 4


De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways.

Hittalmani S, Mahesh HB, Mahadevaiah C, Prasannakumar MK - BMC Genomics (2016)

Organization of putative gene clusters involved in helvolic acid biosynthesis in S. oryzae. Genes are compared against M. anisophilae and A. fumigatus. Red arrow: cytochrome P450 genes. Yellow arrow: transferase family protein genes. Blue arrow: 3-ketosteroid-delta-1-dehydrogenase genes. Green arrow: SDR gene. Purple arrow: Squalene-hopene cyclase gene. Homologs are shown in dotted lines
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Related In: Results  -  Collection

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Fig5: Organization of putative gene clusters involved in helvolic acid biosynthesis in S. oryzae. Genes are compared against M. anisophilae and A. fumigatus. Red arrow: cytochrome P450 genes. Yellow arrow: transferase family protein genes. Blue arrow: 3-ketosteroid-delta-1-dehydrogenase genes. Green arrow: SDR gene. Purple arrow: Squalene-hopene cyclase gene. Homologs are shown in dotted lines
Mentions: Secondary metabolites (SMs) are small bioactive molecules and they are essential for fungal growth and development. At the same time SMs provide protection against various environmental stresses. The biosynthesis of SMs is catalyzed by either nonribosomal peptides synthases (NRPSs), polyketide synthases (PKSs), hybrid NRPS-PKS enzymes, prenyltransferases (DMATSs), and terpene cyclases (TCs). The catalytic activity of these enzymes results in production of SMs respectively like nonribosomal peptides, polyketides, NRPS-PKS hybrids, indole alkaloids, and terpenes [49]. Searching for SMs revealed that S. oryzae genome is enriched with PKSs, TCs followed by NRPSs, NRPSs-PKSs hybrid clusters (Fig. 4). Several studies have reported that S. oryzae produces helvolic acid and cerulenin SMs [50–53]. The biosynthetic pathways of these SMs were found to be different and concomitant production of these two metabolites might have synergistic effect to invade host by changing the cell permeability leading to leakage of electrolytes in the host tissue [52, 54–56]. So far, the studies on helvolic acid and cerulenin metabolites were restricted only to chromatographic assays and gene and protein level information of the pathways involved in their metabolism is unknown in S. oryzae. Based on our SM analysis, we hypothesize that PKSs, TCs and NRPSs could be the putative enzymes involved in the biosynthesis of these two metabolites in S. oryzae. We critically examined the proteome of S. oryzae to screen candidate genes involved in biosynthesis of these SMs. Helvolic acid is a steroidal antibiotic, known to be controlled by cluster of genes in Aspergillus flavus [57] and Metarhizium anisophilae [58]. Initial BLASTP searches of S. oryzae proteome against A. flavus protein sequences identified nine candidate genes in S. oryzae. The structural analysis showed these genes were single exonic genes arranged in clusters. Among these gene clusters, four (SoG_03551.T1, SoG_04319.T1, SoG_09546.T1, and SoG_03005.T1) cytochrome P450, two (SoG_03552.T1 and SoG_03554.T1) transferase family protein, one each of short chain dehydrogenase (SDR) (SoG_04320.T1), qualene-hopene-cyclase (SoG_05635.T1), and 3-ketosteroid-delta-1-dehydrogenase (SoG_03553.T1) genes (Fig. 5 and Additional file 10). The structural arrangement of gene clusters was more similar to Metarhizium aninophilae strain NwlB-02 (NCBI Locus ID: 129929) than A. flavus.Fig. 4

Bottom Line: The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins.Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway.This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.

View Article: PubMed Central - PubMed

Affiliation: Marker Assisted Selection Laboratory, Department of Genetics and Plant Breeding, University of Agricultural Sciences, Bengaluru, 560065, India. shailajah_maslab@rediffmail.com.

ABSTRACT

Background: Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth.

Results: The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future.

Conclusions: Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.

No MeSH data available.


Related in: MedlinePlus