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Insights into genome plasticity and gene regulation in Orientia tsutsugamushi through genome-wide mining of microsatellite markers

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Abstract

Microsatellite markers are being used for molecular identification and characterization as well as estimation of evolution patterns due to their highly polymorphic nature. The repeats hold 40% of the entire genome of Orientia tsutsugamushi (OT), but not yet been characterized. Thus, we investigated the genome-wide presence of microsatellites within nine complete genomes of OT and analyzed their distribution pattern, composition, and complexity. The in-silico study revealed that the genome of OT enriched with microsatellites having a total of 126,187 SSRs and 10,374 cSSRs throughout the genome, of which 70% and 30% are represented within the coding and non-coding regions, respectively. The relative density (RD) and relative abundance (RA) of SSRs were 42–44.43/kb and 6.25–6.59/kb, while for cSSRs this value ranged from 7.06 to 8.1/kb and 0.50 to 0.55/kb, respectively. However, RA and RD were weakly correlated with genome size and incidence of microsatellites. The mononucleotide repeats (54.55%) were prevalent over di- (33.22%), tri- (11.88%), tetra- (0.27%), penta- (0.02%), hexanucleotide (0.04%) repeats, with poly (A/T) richness over poly (G/C). The motif composition of cSSRs revealed that maximum cSSRs were made up of two microsatellites having unique duplication patterns such as AT-x-AT and CG-x-CG. To our knowledge, this is the first study of microsatellites in the OT genome, where characterization of such variations in repeat sequences would be important in deciphering the origin, rate of mutation, and role of repeat sequences in the genome. More numbers of microsatellites represented within the coding region provide an insight into the genome plasticity that may interfere with gene regulation to mitigate host–pathogen interaction and evolution of the species.

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References

  • Alam CM, Singh AK, Sharfuddin C, Ali S (2013) In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes. Gene 530:193–200

    Article  CAS  PubMed  Google Scholar 

  • Alam CM, Singh AK, Sharfuddin C, Ali S (2014) Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses. Infect Genet Evol 21:287–294

    Article  CAS  PubMed  Google Scholar 

  • Bagshaw AT, Pitt JP, Gemmell NJ (2008) High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots. BMC Genom 9:49

    Article  Google Scholar 

  • Basharat Z, Yasmin A (2015) Survey of compound microsatellites in multiple lactobacillus genomes. Can J Microbiol 61:898–902

    Article  CAS  PubMed  Google Scholar 

  • Batty EM, Chaemchuen S, Blacksell S et al (2018) Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia Tsutsugamushi. PLoS Negl Trop Dis 12:e0006566

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen M, Tan Z, Jiang J et al (2009) Similar distribution of simple sequence repeats in diverse completed human immunodeficiency virus type 1genomes. FEBS Lett 583:2959–2963

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Tan Z, Zeng G, Peng J (2010) Comprehensive analysis of simple sequence repeats in pre-mirnas. Mol Biol Evol 27:2227–2232

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Zeng G, Tan Z et al (2011) Compound microsatellites in complete escherichia coli genomes. FEBS Lett 585:1072–1076

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Tan Z, Zeng G, Zeng Z (2012) Differential distribution of compound microsatellites in various human immunodeficiency virus type 1 complete genomes. Infect Genet Evol 12:1452–1457

    Article  CAS  PubMed  Google Scholar 

  • Du L, Zhang C, Liu Q et al (2017) Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics 34:681–683

    Article  Google Scholar 

  • Fadda Z, Daròs JA, Flores R, Duran-Vila N (2003) Identification in eggplant of a variant of citrus exocortis viroid (cevd) with a 96 nucleotide duplication in the right terminal region of the rod-like secondary structure. Virus Res 97:145–149

    Article  CAS  PubMed  Google Scholar 

  • Gao Y, Sun S-Q, Guo H-C (2016) Biological function of foot-and-mouth disease virus non-structural proteins and non-coding elements. Virol J 13:1–7

    Article  Google Scholar 

  • Garrido-Ramos MA (2012) Repetitive DNA. Karger Medical and Scientific Publishers, p 7

    Book  Google Scholar 

  • George B, Alam CM, Kumar RV et al (2015) Potential linkage between compound microsatellites and recombination in geminiviruses: evidence from comparative analysis. Virology 482:41–50

    Article  CAS  PubMed  Google Scholar 

  • Haasl RJ, Payseur BA (2010) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 106:158–171

    Article  PubMed  PubMed Central  Google Scholar 

  • Houng H-SH, Lott L, Gong H et al (2009) Adenovirus microsatellite reveals dynamics of transmission during a recent epidemic of human adenovirus serotype 14 infection. J Clin Microbiol 47:2243–2248

    Article  PubMed  PubMed Central  Google Scholar 

  • Jain A, Sharma PC (2021) Occurrence and distribution of compound microsatellites in the genomes of three economically important virus families. Infect Genet Evol 92:104853

    Article  CAS  PubMed  Google Scholar 

  • Karaoglu H, Lee CM, Meyer W (2004) Survey of simple sequence repeats in completed fungal genomes. Mol Biol Evol 22:639–649

    Article  PubMed  Google Scholar 

  • Kashi Y, King D (2006) Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22:253–259

    Article  CAS  PubMed  Google Scholar 

  • Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167

    Article  CAS  PubMed  Google Scholar 

  • Kelly DJ, Fuerst PA, Ching W, Richards AL (2009) Scrub typhus: the geographic distribution of phenotypic and genotypic variants of orientia tsutsugamushi. Clin Infect Dis 48:203–230

    Article  Google Scholar 

  • Kofler R, Schlotterer C, Luschutzky E, Lelley T (2008) Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites. BMC Genom 9:612

    Article  Google Scholar 

  • Ledenyova ML, Tkachenko GA, Shpak IM (2019) Imperfect and compound microsatellites in the genomes of burkholderia pseudomallei strains. Mol Biol 53:127–137

    Article  CAS  Google Scholar 

  • Liti G, Louis EJ (2005) Yeast evolution and comparative genomics. Annu Rev Microbiol 59:135–153

    Article  CAS  PubMed  Google Scholar 

  • Mrázek J, Guo X, Shah A (2007) Simple sequence repeats in prokaryotic genomes. Proc Natl Acad Sci 104:8472–8477

    Article  PubMed  PubMed Central  Google Scholar 

  • Napierala M, Parniewski P, Pluciennik A, Wells RD (2002) Long CTG· CAG repeat sequences markedly stimulate intramolecular recombination. J Biol Chem 277:34087–34100

    Article  CAS  PubMed  Google Scholar 

  • Nasrin T, Hoque M, Ali S (2023) Microsatellite signature analysis of twenty-one virophage genomes of the family Lavidaviridae. Gene 851:147037

    Article  CAS  PubMed  Google Scholar 

  • Power PM, Sweetman WA, Gallacher NJ et al (2009) Simple sequence repeats in haemophilus influenzae. Infect Genet Evol 9:216–228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qi W-H, Lu T, Zheng C-L et al (2020) Distribution patterns of Microsatellites and development of its marker in different genomic regions of forest musk deer genome based on high throughput sequencing. Aging 12:4445–4462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rathbun MM, Szpara ML (2021) A holistic perspective on herpes simplex virus (HSV) ecology and evolution. Adv Virus Res 110:27–57

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Richard G-F, Kerrest A, Dujon B (2008) Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 72:686–727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sahoo L, Sahu BP, Das SP, Swain SK, Bej D, Patel A et al (2014) Limited genetic differentiation in Labeo rohita (Hamilton 1822) populations as revealed by microsatellite markers. Biochem Syst Ecol 57:427–431

    Article  CAS  Google Scholar 

  • Sahoo L, Patel A, Sahu BP, Mitra S, Meher PK, Mahapatra KD et al (2015) Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers. J Genet 94:271–277

    Article  CAS  PubMed  Google Scholar 

  • Sahu BP, Majee P, Singh RR et al (2020) Comparative analysis, distribution, and characterization of microsatellites in ORF virus genome. Sci Rep 10:1–3

    Article  Google Scholar 

  • Sahu BP, Majee P, Singh RR et al (2022a) Genome-wide identification and characterization of microsatellite markers within the avipoxviruses. 3 Biotech 12:1–7

    Article  Google Scholar 

  • Sahu BP, George B, Majee P, Singh RR, Mishra A, Tiwari R et al (2022b) A comprehensive analysis of simple sequence repeats in Picorna viruses. Res Sq. https://doi.org/10.21203/rs.3.rs-1557265/v1

    Article  Google Scholar 

  • Salje J (2017) Orientia tsutsugamushi: a neglected but fascinating obligate intracellular bacterial pathogen. PLoS Pathog 13(12):e1006657

    Article  PubMed  PubMed Central  Google Scholar 

  • Singh AK, Alam CM, Sharfuddin C, Ali S (2014) Frequency and distribution of simple and compound microsatellites in forty-eight human papillomavirus (HPV) genomes. Infect Genet Evol 24:92–98

    Article  CAS  PubMed  Google Scholar 

  • Soong L (2018) Dysregulated th1 immune and vascular responses in scrub typhus pathogenesis. J Immunol 200:1233–1240

    Article  CAS  PubMed  Google Scholar 

  • Sreenu VB, Kumar P, Nagaraju J, Nagarajaram HA (2006) Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: Implications on genome evolution and plasticity. BMC Genom. https://doi.org/10.1186/1471-2164-7-78

    Article  Google Scholar 

  • Swain SK, Sahu BP, Das SP, Sahoo L, Das PC, Das P (2022) Population genetic structure of fringe-lipped carp, Labeo fimbriatus from the peninsular rivers of India. 3 Biotech 12:300

    Article  PubMed  PubMed Central  Google Scholar 

  • Tilak R, Kunte R (2019) Scrub typhus strikes back: are we ready? Medical J Armed Forces India 75:8–17

    Article  Google Scholar 

  • Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res 10:967–981

    Article  PubMed  PubMed Central  Google Scholar 

  • Tycowski KT, Guo YE, Lee N et al (2015) Viral noncoding RNAS: more surprises. Genes Dev 29:567–584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Usdin K (2008) The biological effects of simple tandem repeats: lessons from the repeat expansion diseases: Table 1. Genome Res 18:1011–1019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Yu X, Zhao K et al (2012) Microsatellite development for an endangered Bream Megalobrama Pellegrini (Teleostei, Cyprinidae) using 454 sequencing. Int J Mol Sci 13:3009–3021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu G, Walker DH, Jupiter D et al (2017) A review of the global epidemiology of scrub typhus. PLoS Negl Trop Dis 11(11):e0006062

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors would like to acknowledge the Medical Research Laboratory of the Institute of Medical Sciences and SUM Hospital for providing the laboratory facility. They would also like to thank Siksha ‘O’ Anusandhana (deemed to be) University and SOA University for providing financial support in the form of a Ph.D. fellowship.

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Authors and Affiliations

  1. Department of Pediatrics, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha, 751003, India

    Subhasmita Panda

  2. Medical Research Laboratory, IMS and SUM Hospital, Siksha ‘O’ Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha, 751003, India

    Subrat Kumar Swain

  3. School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong

    Basanta Pravas Sahu

  4. Department of Pediatrics, IMS and SUM Hospital, Siksha “O” Anusandhan (Deemed to be University), K8, Kalinga Nagar, Bhubaneswar, Odisha, 751003, India

    Rachita Sarangi

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Contributions

SP and SKS performed the bioinformatics analysis and wrote the manuscript. SP and SKS created the figures. BPS generated the circos plot. RS designed the study, and BPS executed the study and reviewed the manuscript.

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Correspondence to Rachita Sarangi.

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Panda, S., Swain, S.K., Sahu, B.P. et al. Insights into genome plasticity and gene regulation in Orientia tsutsugamushi through genome-wide mining of microsatellite markers. 3 Biotech 13, 366 (2023). https://doi.org/10.1007/s13205-023-03795-6

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