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Hybrid Genome Assembly for Predicting Functional Potential of a Novel Streptomyces Strain as Plant Biomass Valorisation Agent

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Abstract

Environmental bioremediation relies heavily on the realized potential of efficient bioremediation agents or microbial strains of interest. Identifying suitable microbial agents for plant biomass waste valorization requires (i) high-quality genome assemblies to predict the full metabolic and functional potential, (ii) accurate mapping of lignocellulose metabolizing enzymes. However, fragmented nature of the sequenced genomes often limits the prediction ability due to breaks occurring in coding sequences. To address these challenges and as part of our ongoing agri-culturomics efforts, we have performed a hybrid genome assembly using Illumina and Nanopore reads with modified assembly protocol, for a novel Streptomyces strain isolated from the rhizosphere niche of green leafy vegetables grown in a commercial urban farm. High-quality genome was assembled with the size of 8.6 Mb in just two contigs with N50 of 8,542,030 and coverage of 383X. This facilitated identification and complete arrangement of approximately 248 CAZymes and 38 biosynthetic gene clusters in the genome. Multiple gene clusters consisting of cellulases and hemicellulases associated with substrate recognition domain were identified in the genome. Genes for lignin, chitin, and even some aromatic compounds degradation were found in the Streptomyces sp. genome which makes it a promising candidate for lignocellulosic waste valorization.

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Data Availability

The assembled genome was submitted in NCBI under accession no. JAEMGU000000000.

Code Availability

Custom scripts were not used to generate or process this dataset. Software versions and non-default parameters used have been appropriately specified where required.

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Acknowledgements

This work was funded by the National Research Foundation, Prime Minister’s Office, Singapore under its Competitive Research Programme grant NRF—CRP16—2015—04. Computational work was done using resources available at the High Performance Computing facility at National University of Singapore, Singapore (https://nusit.nus.edu.sg/hpc/).

Funding

The project is funded by National Research Foundation, Prime Minister's Office, Singapore with Grant ID NRF-CRP16-2015–04, titled as "Novel integrated agrotechnologies, plant nutrients and microbials for improved production of green leafy vegetables in Singapore".

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Correspondence to Sanjay Swarup.

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Tikariha, H., Pavagadhi, S., Mayalagu, S. et al. Hybrid Genome Assembly for Predicting Functional Potential of a Novel Streptomyces Strain as Plant Biomass Valorisation Agent. Indian J Microbiol 61, 283–290 (2021). https://doi.org/10.1007/s12088-021-00935-5

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