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Narh Mensah DL, Wingfield BD, Coetzee MPA. Two distinct non-ribosomal peptide synthetase-independent siderophore synthetase gene clusters identified in Armillaria and other species in the Physalacriaceae. G3 (Bethesda) 2023; 13:jkad205. [PMID: 37843963 DOI: 10.1093/g3journal/jkad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/28/2023] [Indexed: 10/18/2023]
Abstract
Siderophores are important for ferric iron solubilization, sequestration, transportation, and storage, especially under iron-limiting conditions such as aerobic conditions at high pH. Siderophores are mainly produced by non-ribosomal peptide synthetase-dependent siderophore pathway, non-ribosomal peptide synthetase-independent siderophore synthetase pathway, or the hybrid non-ribosomal peptide synthetases/non-ribosomal peptide synthetases-independent siderophore pathway. Outcompeting or inhibition of plant pathogens, alteration of host defense mechanisms, and alteration of plant-fungal interactions have been associated with fungal siderophores. To understand these mechanisms in fungi, studies have been conducted on siderophore biosynthesis by ascomycetes with limited focus on the basidiomycetes. Armillaria includes several species that are pathogens of woody plants and trees important to agriculture, horticulture, and forestry. The aim of this study was to investigate the presence of non-ribosomal peptide synthetases-independent siderophore synthetase gene cluster(s) in genomes of Armillaria species using a comparative genomics approach. Iron-dependent growth and siderophore biosynthesis in strains of selected Armillaria spp. were also evaluated in vitro. Two distinct non-ribosomal peptide synthetases-independent siderophore synthetase gene clusters were identified in all the genomes. All non-ribosomal peptide synthetases-independent siderophore synthetase genes identified putatively encode Type A' non-ribosomal peptide synthetases-independent siderophore synthetases, most of which have IucA_IucC and FhuF-like transporter domains at their N- and C-terminals, respectively. The effect of iron on culture growth varied among the strains studied. Bioassays using the CAS assay on selected Armillaria spp. revealed in vitro siderophore biosynthesis by all strains irrespective of added FeCl3 concentration. This study highlights some of the tools that Armillaria species allocate to iron homeostasis. The information generated from this study may in future aid in developing molecular based methods to control these phytopathogens.
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Affiliation(s)
- Deborah L Narh Mensah
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
- CSIR-Food Research Institute, Microbiology and Mushroom Research Division, P. O. Box, M20, Accra, Ghana
| | - Brenda D Wingfield
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
| | - Martin P A Coetzee
- Departments of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa
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Zhang Z, Cui M, Chen P, Li J, Mao Z, Mao Y, Li Z, Guo Q, Wang C, Liao X, Liu H. Insight into the phylogeny and metabolic divergence of Monascus species ( M. pilosus, M. ruber, and M. purpureus) at the genome level. Front Microbiol 2023; 14:1199144. [PMID: 37303795 PMCID: PMC10249731 DOI: 10.3389/fmicb.2023.1199144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/09/2023] [Indexed: 06/13/2023] Open
Abstract
Background Species of the genus Monascus are economically important and widely used in the production of food colorants and monacolin K. However, they have also been known to produce the mycotoxin citrinin. Currently, taxonomic knowledge of this species at the genome level is insufficient. Methods This study presents genomic similarity analyses through the analysis of the average nucleic acid identity of the genomic sequence and the whole genome alignment. Subsequently, the study constructed a pangenome of Monascus by reannotating all the genomes and identifying a total of 9,539 orthologous gene families. Two phylogenetic trees were constructed based on 4,589 single copy orthologous protein sequences and all the 5,565 orthologous proteins, respectively. In addition, carbohydrate active enzymes, secretome, allergic proteins, as well as secondary metabolite gene clusters were compared among the included 15 Monascus strains. Results The results clearly revealed a high homology between M. pilosus and M. ruber, and their distant relationship with M. purpureus. Accordingly, all the included 15 Monascus strains should be classified into two distinctly evolutionary clades, namely the M. purpureus clade and the M. pilosus-M. ruber clade. Moreover, gene ontology enrichment showed that the M. pilosus-M. ruber clade had more orthologous genes involved with environmental adaptation than the M. purpureus clade. Compared to Aspergillus oryzae, all the Monascus species had a substantial gene loss of carbohydrate active enzymes. Potential allergenic and fungal virulence factor proteins were also found in the secretome of Monascus. Furthermore, this study identified the pigment synthesis gene clusters present in all included genomes, but with multiple nonessential genes inserted in the gene cluster of M. pilosus and M. ruber compared to M. purpureus. The citrinin gene cluster was found to be intact and highly conserved only among M. purpureus genomes. The monacolin K gene cluster was found only in the genomes of M. pilosus and M. ruber, but the sequence was more conserved in M. ruber. Conclusion This study provides a paradigm for phylogenetic analysis of the genus Monascus, and it is believed that this report will lead to a better understanding of these food microorganisms in terms of classification, metabolic differentiation, and safety.
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Affiliation(s)
- Zhiyu Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Mengfei Cui
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Panting Chen
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Juxing Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Zhitao Mao
- Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yufeng Mao
- Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhenjing Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Qingbin Guo
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Changlu Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
| | - Xiaoping Liao
- Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Haihe Laboratory of Synthetic Biology, Tianjin, China
| | - Huanhuan Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, China
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, Tianjin, China
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Nkosi BVZ, Padayachee T, Gront D, Nelson DR, Syed K. Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters. Int J Mol Sci 2022; 23:5057. [PMID: 35563448 DOI: 10.3390/ijms23095057] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Species belonging to the bacterial phyla Bacteroidetes and Firmicutes represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were found to have contrasting health effects, including obesity and inflammatory diseases. Despite the availability of many bacterial genomes, comparative genomic studies on the gene pools of these two bacterial groups concerning cytochrome P450 monooxygenases (P450s), ferredoxins, and secondary metabolite biosynthetic gene clusters (smBGCs) are not reported. This study is aimed to address this research gap. The study revealed the presence of diverse sets of P450s, ferredoxins, and smBGCs in their genomes. Bacteroidetes species have the highest number of P450 families, ferredoxin cluster-types, and smBGCs compared to Firmicutes species. Only four P450 families, three ferredoxin cluster types, and five smBGCs are commonly shared between these two bacterial groups. Considering the above facts, we propose that the contrasting effects of these two bacterial groups on the host are partly due to the distinct nature of secondary metabolites produced by these organisms. Thus, the cause of the contrasting health effects of these two bacterial groups lies in their gene pools.
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Płachetka M, Krawiec M, Zakrzewska-Czerwińska J, Wolański M. AdpA Positively Regulates Morphological Differentiation and Chloramphenicol Biosynthesis in Streptomyces venezuelae. Microbiol Spectr 2021; 9:e0198121. [PMID: 34878326 PMCID: PMC8653842 DOI: 10.1128/spectrum.01981-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 11/22/2022] Open
Abstract
In members of genus Streptomyces, AdpA is a master transcriptional regulator that controls the expression of hundreds of genes involved in morphological differentiation, secondary metabolite biosynthesis, chromosome replication, etc. However, the function of AdpASv, an AdpA ortholog of Streptomyces venezuelae, is unknown. This bacterial species is a natural producer of chloramphenicol and has recently become a model organism for studies on Streptomyces. Here, we demonstrate that AdpASv is essential for differentiation and antibiotic biosynthesis in S. venezuelae and provide evidence suggesting that AdpASv positively regulates its own gene expression. We speculate that the different modes of AdpA-dependent transcriptional autoregulation observed in S. venezuelae and other Streptomyces species reflect the arrangement of AdpA binding sites in relation to the transcription start site. Lastly, we present preliminary data suggesting that AdpA may undergo a proteolytic processing and we speculate that this may potentially constitute a novel regulatory mechanism controlling cellular abundance of AdpA in Streptomyces. IMPORTANCEStreptomyces are well-known producers of valuable secondary metabolites which include a large variety of antibiotics and important model organisms for developmental studies in multicellular bacteria. The conserved transcriptional regulator AdpA of Streptomyces exerts a pleiotropic effect on cellular processes, including the morphological differentiation and biosynthesis of secondary metabolites. Despite extensive studies, the function of AdpA in these processes remains elusive. This work provides insights into the role of a yet unstudied AdpA ortholog of Streptomyces venezuelae, now considered a novel model organism. We found that AdpA plays essential role in morphological differentiation and biosynthesis of chloramphenicol, a broad-spectrum antibiotic. We also propose that AdpA may undergo a proteolytic processing that presumably constitutes a novel mechanism regulating cellular abundance of this master regulator.
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Affiliation(s)
| | - Michał Krawiec
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | | | - Marcin Wolański
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Kwon MJ, Steiniger C, Cairns TC, Wisecaver JH, Lind AL, Pohl C, Regner C, Rokas A, Meyer V. Beyond the Biosynthetic Gene Cluster Paradigm: Genome-Wide Coexpression Networks Connect Clustered and Unclustered Transcription Factors to Secondary Metabolic Pathways. Microbiol Spectr 2021; 9:e0089821. [PMID: 34523946 DOI: 10.1128/Spectrum.00898-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Fungal secondary metabolites are widely used as therapeutics and are vital components of drug discovery programs. A major challenge hindering discovery of novel secondary metabolites is that the underlying pathways involved in their biosynthesis are transcriptionally silent under typical laboratory growth conditions, making it difficult to identify the transcriptional networks that they are embedded in. Furthermore, while the genes participating in secondary metabolic pathways are typically found in contiguous clusters on the genome, known as biosynthetic gene clusters (BGCs), this is not always the case, especially for global and pathway-specific regulators of pathways’ activities. To address these challenges, we used 283 genome-wide gene expression data sets of the ascomycete cell factory Aspergillus niger generated during growth under 155 different conditions to construct two gene coexpression networks based on Spearman’s correlation coefficients (SCCs) and on mutual rank-transformed Pearson’s correlation coefficients (MR-PCCs). By mining these networks, we predicted six transcription factors, named MjkA to MjkF, to regulate secondary metabolism in A. niger. Overexpression of each transcription factor using the Tet-On cassette modulated the production of multiple secondary metabolites. We found that the SCC and MR-PCC approaches complemented each other, enabling the delineation of putative global (SCC) and pathway-specific (MR-PCC) transcription factors. These results highlight the potential of coexpression network approaches to identify and activate fungal secondary metabolic pathways and their products. More broadly, we argue that drug discovery programs in fungi should move beyond the BGC paradigm and focus on understanding the global regulatory networks in which secondary metabolic pathways are embedded. IMPORTANCE There is an urgent need for novel bioactive molecules in both agriculture and medicine. The genomes of fungi are thought to contain vast numbers of metabolic pathways involved in the biosynthesis of secondary metabolites with diverse bioactivities. Because these metabolites are biosynthesized only under specific conditions, the vast majority of the fungal pharmacopeia awaits discovery. To discover the genetic networks that regulate the activity of secondary metabolites, we examined the genome-wide profiles of gene activity of the cell factory Aspergillus niger across hundreds of conditions. By constructing global networks that link genes with similar activities across conditions, we identified six putative global and pathway-specific regulators of secondary metabolite biosynthesis. Our study shows that elucidating the behavior of the genetic networks of fungi under diverse conditions harbors enormous promise for understanding fungal secondary metabolism, which ultimately may lead to novel drug candidates.
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Droste J, Rückert C, Kalinowski J, Hamed MB, Anné J, Simoens K, Bernaerts K, Economou A, Busche T. Extensive Reannotation of the Genome of the Model Streptomycete Streptomyces lividans TK24 Based on Transcriptome and Proteome Information. Front Microbiol 2021; 12:604034. [PMID: 33935985 PMCID: PMC8079986 DOI: 10.3389/fmicb.2021.604034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Streptomyces lividans TK24 is a relevant Gram-positive soil inhabiting bacterium and one of the model organisms of the genus Streptomyces. It is known for its potential to produce secondary metabolites, antibiotics, and other industrially relevant products. S. lividans TK24 is the plasmid-free derivative of S. lividans 66 and a close genetic relative of the strain Streptomyces coelicolor A3(2). In this study, we used transcriptome and proteome data to improve the annotation of the S. lividans TK24 genome. The RNA-seq data of primary 5'-ends of transcripts were used to determine transcription start sites (TSS) in the genome. We identified 5,424 TSS, of which 4,664 were assigned to annotated CDS and ncRNAs, 687 to antisense transcripts distributed between 606 CDS and their UTRs, 67 to tRNAs, and 108 to novel transcripts and CDS. Using the TSS data, the promoter regions and their motifs were analyzed in detail, revealing a conserved -10 (TAnnnT) and a weakly conserved -35 region (nTGACn). The analysis of the 5' untranslated region (UTRs) of S. lividans TK24 revealed 17% leaderless transcripts. Several cis-regulatory elements, like riboswitches or attenuator structures could be detected in the 5'-UTRs. The S. lividans TK24 transcriptome contains at least 929 operons. The genome harbors 27 secondary metabolite gene clusters of which 26 could be shown to be transcribed under at least one of the applied conditions. Comparison of the reannotated genome with that of the strain Streptomyces coelicolor A3(2) revealed a high degree of similarity. This study presents an extensive reannotation of the S. lividans TK24 genome based on transcriptome and proteome analyses. The analysis of TSS data revealed insights into the promoter structure, 5'-UTRs, cis-regulatory elements, attenuator structures and novel transcripts, like small RNAs. Finally, the repertoire of secondary metabolite gene clusters was examined. These data provide a basis for future studies regarding gene characterization, transcriptional regulatory networks, and usage as a secondary metabolite producing strain.
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Affiliation(s)
- Julian Droste
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Mohamed Belal Hamed
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium.,Molecular Biology Department, National Research Centre, Dokii, Egypt
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium
| | - Kenneth Simoens
- Bio- and Chemical Systems Technology, Reactor Engineering, and Safety (CREaS) Section, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Kristel Bernaerts
- Bio- and Chemical Systems Technology, Reactor Engineering, and Safety (CREaS) Section, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Saha P, Sarkar A, Sabnam N, Shirke MD, Mahesh HB, Nikhil A, Rajamani A, Gowda M, Roy-Barman S. Comparative analysis of secondary metabolite gene clusters in different strains of Magnaporthe oryzae. FEMS Microbiol Lett 2020; 368:6045507. [PMID: 33355334 DOI: 10.1093/femsle/fnaa216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
Rice blast caused by Magnaporthe oryzae continues to be a major constraint in rice production worldwide. Rice is one of the staple crops in India and rice blast causes huge economic losses. Interestingly, the Indian subcontinent is the centre for origin and diversity of rice as well as the Magnaporthe species complex. Secondary metabolites are known to play important role in pathogenesis and M. oryzae has high potential of genes involved in secondary metabolism but, unfortunately most of them remain uncharacterized. In the present study, we analysed the draft genome assemblies of M. oryzae strains isolated from different parts of India, for putative secondary metabolite key gene (SMKG) clusters encoding polyketide synthases, non-ribosomal peptide synthetases, diterpene cyclases and dimethylallyl tryptophan synthase. Based on the complete genome sequence of 70-15 strain and its previous reports of identified SMKGs, we have identified the key genes for the interrogated strains. Expression analysis of these genes amongst different strains indicates how they have evolved depending on the host and environmental conditions. To our knowledge, this study is first of its kind where the secondary metabolism genes and their role in functional adaptation were studied across several strains of M. oryzae.
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Affiliation(s)
- Pallabi Saha
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Rd, A-zone, Durgapur, West Bengal-713209, India
| | - Atrayee Sarkar
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Rd, A-zone, Durgapur, West Bengal-713209, India
| | - Nazmiara Sabnam
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Rd, A-zone, Durgapur, West Bengal-713209, India.,Department of Life Sciences, Presidency University, 86/1 College street, Kolkata, West Bengal-700073, India
| | - Meghana D Shirke
- Centre for Functional Genomics and Bioinformatics, The University of Trans-Disciplinary Health Sciences and Technology, 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru-560064, India
| | - H B Mahesh
- Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru-560065, India
| | - Aman Nikhil
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Rd, A-zone, Durgapur, West Bengal-713209, India
| | - Anantharamanan Rajamani
- Genome Analysis Laboratory, Rubber Research Institute of India, Kottayam, Kerala-686009, India
| | - Malali Gowda
- Centre for Functional Genomics and Bioinformatics, The University of Trans-Disciplinary Health Sciences and Technology, 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru-560064, India
| | - Subhankar Roy-Barman
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Rd, A-zone, Durgapur, West Bengal-713209, India
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