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Indian Journal of Microbiology

, Volume 59, Issue 4, pp 468–475 | Cite as

Genome-Wide Analysis of Putative G-Quadruplex Sequences (PGQSs) in Onion Yellows Phytoplasma (Strain OY-M): An Emerging Plant Pathogenic Bacteria

  • Amrita Singh
  • Suman LakhanpaulEmail author
Original Research article

Abstract

Phytoplasma, an emerging plant pathogen is an endocellular obligate parasite of plant phloem tissues with highly reduced genomes and low GC content. They contain a minimal set of genes essential for survival as an intracellular parasite. The role of G-Quadruplexes in pathogenicity has been reported in a variety of microbial pathogens. Detailed investigation on the genome wide occurrence and distribution of Putative G-Quadruplex forming Sequences (PGQSs) in the AT-rich genome of Onion yellows phytoplasma (strain OY-M) was carried out. Relative enrichment and depletion of these putative secondary structures in different genomic regions of OY-M was investigated with an aim to unravel their association with functionally important genomic locations. PGQSs density of 0.4407/Kbp was detected in the genome of OY-M phytoplasma, which is significantly higher than the average PGQSs density (0.136/Kbp) reported for other members of its phylum, namely Tenericutes. A non-random distribution of PGQSs across the length of the genome was observed. Putative promoter regions of OY-M were found to be particularly enriched in PGQSs followed by genic regions. The repeat rich regions were identified to have minimum PGQSs density. Presence of PGQSs in important genes such as those involved in secretory pathways of virulent factors, transport related functions, rRNA and tRNA was particularly intriguing. Our study reports for the first time a detailed investigation on the genome-wide locations of putative G-Quadruplexes in phytoplasma and highlights the need to further investigate their role in the metabolism and also in the mechanism of pathogenicity.

Keywords

Phytoplasma G-Quadruplexes Genic regions Regulatory regions Repeat-rich regions 

Notes

Acknowledgements

Authors are grateful to financial support from National Agricultural Science Fund (NASF, ICAR), Government of India and R&D Grant, University of Delhi.UGC (Grant No. 2121330649) Fellowship awarded to AS by Ministry of Human Resource Development is gratefully acknowledged.

Compliance with Ethical Standards

Conflict of interest

Both authors declare that they have no conflict of interest.

Ethical Approval

This manuscript is original and has not been published elsewhere in any form or language. The authors discussed the result, read and approved the final article. The authors confirm that there are no ethical issues in publication of the manuscript.

Research Involving Human Participants and/or Animals

This study does not involve studies with human participants or animals performed by any of the authors.

Informed Consent

This article is original and has not been submitted or published elsewhere.

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Copyright information

© Association of Microbiologists of India 2019

Authors and Affiliations

  1. 1.Department of BotanyUniversity of DelhiDelhiIndia

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