Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential
Abstract Background Gongronella butleri is a fungus with many industrial applications including the composting of solid biowaste. Kerala Agricultural University, India, has developed a microbial consortium of which GbKAU strain of G. butleri is a major component. Even with great industrial significa...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-05-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | https://doi.org/10.1186/s43141-022-00351-2 |
| _version_ | 1827280236930138112 |
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| author | Ravisankar Valsalan Deepu Mathew Girija Devaki |
| author_facet | Ravisankar Valsalan Deepu Mathew Girija Devaki |
| author_sort | Ravisankar Valsalan |
| collection | DOAJ |
| description | Abstract Background Gongronella butleri is a fungus with many industrial applications including the composting of solid biowaste. Kerala Agricultural University, India, has developed a microbial consortium of which GbKAU strain of G. butleri is a major component. Even with great industrial significance, genome of this fungus is not published, and the genes and pathways contributing to the applications are not understood. This study had the objective to demonstrate the solid biowaste decomposing capability of the strain, to sequence and annotate the genome, and to reveal the genes and pathways contributing to its biodegradation potential. Results Strain GbKAU of G. butleri isolated and purified from the organic compost was found to produce higher levels of laccase and amylase, compared to Bacillus subtilis which is being widely used in biosolid waste management. Both were shown to be equally efficient in the in vivo composting capabilities. Whole genome sequencing has given ~11 million paired-end good quality reads. De novo assembly using dual-fold approach has yielded 44,639 scaffolds with draft genome size of 29.8 Mb. A total of 11,428 genes were predicted and classified into 359 groups involved in diverse pathways, of which 14 belonged to the enzymes involved in the degradation of macromolecules. Seven previously sequenced strains of the fungus were assembled and annotated. A direct comparison showed that the number of genes present in those strains was comparable to our strain, while all the important biodegrading genes were conserved across the genomes. Gene Ontology analysis had classified the genes according to their molecular function, biological process, and cellular component. A total of 104,718 SSRs were mined and classified to mono- to hexa-nucleotide repeats. The variant analysis in comparison with the closely related genus Cunninghamella has revealed 1156 variants. Conclusions Apart from demonstrating the biodegradation capabilities of the GbKAU strain of G. butleri, the genome of this industrially important fungus was sequenced, de novo assembled, and annotated. GO analysis has classified the genes based on their functions, and the genes involved in biodegradation were revealed. Biodegradation potential, genome features in comparison with other strains, and the functions of the identified genes are discussed. |
| first_indexed | 2024-04-12T15:31:26Z |
| format | Article |
| id | doaj.art-72ff271a466f4c8a82dc6de8f9db924a |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:33:29Z |
| publishDate | 2022-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-72ff271a466f4c8a82dc6de8f9db924a2024-04-16T18:23:55ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202022-05-0120111110.1186/s43141-022-00351-2Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potentialRavisankar Valsalan0Deepu Mathew1Girija Devaki2Bioinformatics Centre, Kerala Agricultural UniversityBioinformatics Centre, Kerala Agricultural UniversityDepartment of Agricultural Microbiology, College of Agriculture, Kerala Agricultural UniversityAbstract Background Gongronella butleri is a fungus with many industrial applications including the composting of solid biowaste. Kerala Agricultural University, India, has developed a microbial consortium of which GbKAU strain of G. butleri is a major component. Even with great industrial significance, genome of this fungus is not published, and the genes and pathways contributing to the applications are not understood. This study had the objective to demonstrate the solid biowaste decomposing capability of the strain, to sequence and annotate the genome, and to reveal the genes and pathways contributing to its biodegradation potential. Results Strain GbKAU of G. butleri isolated and purified from the organic compost was found to produce higher levels of laccase and amylase, compared to Bacillus subtilis which is being widely used in biosolid waste management. Both were shown to be equally efficient in the in vivo composting capabilities. Whole genome sequencing has given ~11 million paired-end good quality reads. De novo assembly using dual-fold approach has yielded 44,639 scaffolds with draft genome size of 29.8 Mb. A total of 11,428 genes were predicted and classified into 359 groups involved in diverse pathways, of which 14 belonged to the enzymes involved in the degradation of macromolecules. Seven previously sequenced strains of the fungus were assembled and annotated. A direct comparison showed that the number of genes present in those strains was comparable to our strain, while all the important biodegrading genes were conserved across the genomes. Gene Ontology analysis had classified the genes according to their molecular function, biological process, and cellular component. A total of 104,718 SSRs were mined and classified to mono- to hexa-nucleotide repeats. The variant analysis in comparison with the closely related genus Cunninghamella has revealed 1156 variants. Conclusions Apart from demonstrating the biodegradation capabilities of the GbKAU strain of G. butleri, the genome of this industrially important fungus was sequenced, de novo assembled, and annotated. GO analysis has classified the genes based on their functions, and the genes involved in biodegradation were revealed. Biodegradation potential, genome features in comparison with other strains, and the functions of the identified genes are discussed.https://doi.org/10.1186/s43141-022-00351-2Catalysis mechanismsComposting pathwayGenome annotationNGSSolid biowaste |
| spellingShingle | Ravisankar Valsalan Deepu Mathew Girija Devaki Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential Journal of Genetic Engineering and Biotechnology Catalysis mechanisms Composting pathway Genome annotation NGS Solid biowaste |
| title | Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential |
| title_full | Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential |
| title_fullStr | Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential |
| title_full_unstemmed | Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential |
| title_short | Draft genome of Gongronella butleri reveals the genes contributing to its biodegradation potential |
| title_sort | draft genome of gongronella butleri reveals the genes contributing to its biodegradation potential |
| topic | Catalysis mechanisms Composting pathway Genome annotation NGS Solid biowaste |
| url | https://doi.org/10.1186/s43141-022-00351-2 |
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