Neutral Polymorphisms in Putative Housekeeping Genes and Tandem Repeats Unravels the Population Genetics and Evolutionary History of Plasmodium vivax in India

Prajapati, Surendra Kumar; Joshi, Hema; Carlton, Jane M.; Rizvi, Abbas

doi:10.1371/journal.pntd.0002425

Cited by 7 publications

(4 citation statements)

References 60 publications

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“…larvae in North America. It could be implied that ilvD1 , tri , pyre , sucC and glpK are especially free from directed selection pressure, and therefore will be most useful for understanding demographic events and bacterial population history [ 36 ].…”

Section: Discussionmentioning

confidence: 99%

Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae

Krongdang

Evans²,

Pettis³

et al. 2017

PLoS ONE

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Paenibacillus larvae is a Gram positive bacterium and the causative agent of the most widespread fatal brood disease of honey bees, American foulbrood (AFB). A total of thirty-three independent Paenibacillus larvae isolates from various geographical origins in North America and five reference strains were investigated for genetic diversity using multilocus sequence typing (MLST). This technique is regarded to be a powerful tool for epidemiological studies of pathogenic bacteria and is widely used in genotyping assays. For MLST, seven housekeeping gene loci, ilvD (dihydroxy-acid dyhydrogenase), tri (triosephosphate isomerase), purH (phospharibosyl-aminoimidazolecarboxamide), recF (DNA replication and repair protein), pyrE (orotate phosphoribosyltransferase), sucC (succinyl coenzyme A synthetase β subunit) and glpF (glycerol uptake facilitator protein) were studied and applied for primer designs. Previously, ERIC type DNA fingerprinting was applied to these same isolates and the data showed that almost all represented the ERIC I type, whereas using BOX-PCR gave an indication of more diversity. All isolates were screened for resistance to four antibiotics used by U.S. beekeepers, showing extensive resistance to tetracycline and the first records of resistance to tylosin and lincomycin. Our data highlight the intraspecies relationships of P. larvae and the potential application of MLST methods in enhancing our understanding of epidemiological relationships among bacterial isolates of different origins.

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Section: Discussionmentioning

confidence: 99%

Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae

Krongdang

Evans²,

Pettis³

et al. 2017

PLoS ONE

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“…Nonetheless publication of the genome 10 and the transcriptome of the blood stage life cycle 11 12 in 2008 provided invaluable insights into P. vivax biology. The subsequent high throughput sequencing 13 and the assembly of a genetic map helped us to understand the genetic diversity of this pathogen 9 14 15 16 17 18 showing specific differences from other parasites 10 19 20 21 . Altogether these genomic studies provided a broader platform for identifying new molecular targets for malaria intervention strategies 22 23 24 25 .…”

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confidence: 99%

New insights into the Plasmodium vivax transcriptome using RNA-Seq

Zhu

Mok

Imwong

et al. 2016

Sci Rep

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Historically seen as a benign disease, it is now becoming clear that Plasmodium vivax can cause significant morbidity. Effective control strategies targeting P. vivax malaria is hindered by our limited understanding of vivax biology. Here we established the P. vivax transcriptome of the Intraerythrocytic Developmental Cycle (IDC) of two clinical isolates in high resolution by Illumina HiSeq platform. The detailed map of transcriptome generates new insights into regulatory mechanisms of individual genes and reveals their intimate relationship with specific biological functions. A transcriptional hotspot of vir genes observed on chromosome 2 suggests a potential active site modulating immune evasion of the Plasmodium parasite across patients. Compared to other eukaryotes, P. vivax genes tend to have unusually long 5′ untranslated regions and also present multiple transcription start sites. In contrast, alternative splicing is rare in P. vivax but its association with the late schizont stage suggests some of its significance for gene function. The newly identified transcripts, including up to 179 vir like genes and 3018 noncoding RNAs suggest an important role of these gene/transcript classes in strain specific transcriptional regulation.

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“…Sites are shown as coloured circles whose size is proportional to the number of samples collected. Dark blue circles show 98 samples collected between 2003 and 2006 from Kamrup (Assam, n = 20), Delhi ( n = 20), Nadiad (Gujarat, n = 18), Panna (Madhya Pradesh, n = 20) and Chennai (Tamil Nadu, n = 20) [ 57 ]. Pink circles show 73 samples collected between 2014 and 2019 from Sonapur (Assam, n = 10), Delhi ( n = 28), Panaji (Goa, n = 7), Surat and Nadiad (Gujarat, n = 8 and 20, respectively).…”

Section: Methodsmentioning

confidence: 99%

Global distribution of single amino acid polymorphisms in Plasmodium vivax Duffy-binding-like domain and implications for vaccine development efforts

et al. 2020

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Plasmodium vivax ( Pv ) malaria continues to be geographically widespread with approximately 15 million worldwide cases annually. Along with other proteins, Duffy-binding proteins (DBPs) are used by plasmodium for RBC invasion and the parasite-encoded receptor binding regions lie in their Duffy-binding-like (DBL) domains—thus making it a prime vaccine candidate. This study explores the sequence diversity in Pv DBL globally, with an emphasis on India as it remains a major contributor to the global Pv malaria burden. Based on 1358 Pv DBL protein sequences available in NCBI, we identified 140 polymorphic sites within 315 residues of Pv DBL. Alarmingly, country-wise mapping of SAAPs from field isolates revealed varied and distinct polymorphic profiles for different nations. We report here 31 polymorphic residue positions in the global SAAP profile, most of which map to the Pv DBL subdomain 2 ( α 1– α 6). A distinct clustering of SAAPs distal to the DARC-binding sites is indicative of immune evasive strategies by the parasite. Analyses of Pv DBL-neutralizing antibody complexes revealed that between 24% and 54% of interface residues are polymorphic. This work provides a framework to recce and expand the polymorphic space coverage in Pv DBLs as this has direct implications for vaccine development studies. It also emphasizes the significance of surveying global SAAP distributions before or alongside the identification of vaccine candidates.

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Neutral Polymorphisms in Putative Housekeeping Genes and Tandem Repeats Unravels the Population Genetics and Evolutionary History of Plasmodium vivax in India

Cited by 7 publications

References 60 publications

Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae

Multilocus sequence typing, biochemical and antibiotic resistance characterizations reveal diversity of North American strains of the honey bee pathogen Paenibacillus larvae

New insights into the Plasmodium vivax transcriptome using RNA-Seq

Global distribution of single amino acid polymorphisms in Plasmodium vivax Duffy-binding-like domain and implications for vaccine development efforts

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