Abstract
Arbuscular mycorrhizal (AM) fungi are ubiquitous endosymbionts of terrestrial plants. It helps plants to extract more nutrients from the soil and enhances the plant tolerance to various ecological stress factors. The AM fungal genome sequence helps to identify the gene repertoires that are crucial for adaptation to different habitat and mechanisms for interaction with host plant. The present work comprises the first draft of the genome sequence of Rhizophagus proliferus, which is an important AM species present in biofertilizer consortia for agricultural purpose. The estimated genome size of R. proliferus is ~ 110 Mbps and its genomic assembly is 94.35% complete. Genome mining was carried out to identify putative gene families important for biological functions. A total of 22,526 protein-coding genes were estimated in the genome, with an abundance of kinases and reduced number of glycoside hydrolases as compared to other fungal classes. A striking finding in the R. proliferus genome was higher number of carbohydrate esterases (CE), which may suggest towards presence of higher saprotrophic activity in this species as compared to the previously reported AM fungi, which may indicate towards its role as a link between plants and soil mineral nutrients. The genome sequence and annotation of R. proliferus presented here would serve as an important reference for functional genomics studies required for developing biofertilizer formulations in future. In addition, the findings from this work may also prove important in deciphering molecular mechanisms in AM fungi that govern the host-specific interaction and associated agriculture benefits.
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Data availability
The whole genome project has been deposited at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA392539 under Bioproject number PRJNA392539. The R. proliferus Internal Transcribed Spacer (ITS) gene sequence is deposited at Genbank with Accession number OK030706. All data generated and analysed during this study are included in this report and its supplementary information files.
Abbreviations
- CMCC:
-
Centre for mycorrhizal culture collection
- HMW:
-
High molecular weight
- NCBI:
-
National center for biotechnology information
- KOG:
-
Eukaryotic orthologous groups
- CAZyme:
-
Carbohydrate active enzyme
- BLAST:
-
Basic local alignment search tool
- GPCRs:
-
G-protein-coupled receptors
- Blastp:
-
Protein BLAST: search protein databases using a protein query
- CDD:
-
NCBI conserved domain database
- SMART:
-
Simple modular architecture research tool database
- AA:
-
Auxiliary activity
- CBM:
-
Carbohydrate-binding modules
- CE:
-
Carbohydrate esterases
- EXPN:
-
Expansins
- GH:
-
Glycoside hydrolases
- GT:
-
Glycosyltransferases
- PL:
-
Polysaccharide lyases
- DMAT:
-
DiMethylAllyl tryptophan synthase
- NRPS:
-
Non-ribosomal peptide synthetases
- PKS:
-
PolyKetide synthetases
- TS:
-
Terpene synthases
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Acknowledgements
We are thankful to Ms. Pratima Vasistha for supporting by providing spores from monosporal culture of R. proliferus and carrying out morphological analysis. We thank Dr. Alok Adholeya for initial discussions regarding the project idea.
Funding
This work was supported by the grant-in-aid for research to Dr. Pushplata Prasad Singh by the Science and Engineering Research Board (SERB), Department of Science and Technology (DST), India, under the grant number “EMR/2017/000657”. Funders had no role in the study.
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All authors have read and approved the final manuscript. PPS was involved in conceptualization of the project, study design, data analysis, data compilation, manuscript writing, critical inputs and finalization of the manuscript. DS was involved in genomics data analysis, data compilation and manuscript writing. SS carried out DNA extraction and molecular characterization. V was involved in raising monosporal cultures and morphology-based characterization of spores.
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Singh, P.P., Srivastava, D., Shukla, S. et al. Rhizophagus proliferus genome sequence reiterates conservation of genetic traits in AM fungi, but predicts higher saprotrophic activity. Arch Microbiol 204, 105 (2022). https://doi.org/10.1007/s00203-021-02651-6
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DOI: https://doi.org/10.1007/s00203-021-02651-6