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Das KC, Konhar R, Biswal DK. Fasciola gigantica vaccine construct: an in silico approach towards identification and design of a multi-epitope subunit vaccine using calcium binding EF-hand proteins. BMC Immunol 2023; 24:1. [PMID: 36604615 PMCID: PMC9813462 DOI: 10.1186/s12865-022-00535-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
Continuous attempts have been made to pinpoint candidate vaccine molecules and evaluate their effectiveness in order to commercialise such vaccines for the treatment of tropical fascioliasis in livestock. The pathophysiology of fascioliasis can be related to liver damage brought on by immature flukes that migrate and feed, as well as immunological reactions to chemicals produced by the parasites and alarm signals brought on by tissue damage. Future research should, in our opinion, concentrate on the biology of invasive parasites and the resulting immune responses, particularly in the early stages of infection. The goal of the current study was to use the calcium-binding proteins from F. gigantica to create a multi-epitope subunit vaccine. The adjuvant, B-cell epitopes, CTL epitopes, and HTL epitopes that make up the vaccine construct are all connected by certain linkers. The antigenicity, allergenicity, and physiochemical properties of the vaccine construct were examined. The vaccine construct was docked with toll-like receptor 2, and simulations of the molecular dynamics of the complex's stability, interaction, and dynamics were run. After performing in silico cloning and immunosimulation, it was discovered that the construct was suitable for further investigation. New vaccination technologies and adjuvant development are advancing our food safety procedures since vaccines are seen as safe and are accepted by the user community. This research is also applicable to the F. hepatica system.
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Affiliation(s)
- Kanhu Charan Das
- grid.412227.00000 0001 2173 057XBioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya India
| | - Ruchishree Konhar
- grid.412227.00000 0001 2173 057XBioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya India ,grid.417639.eInformatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Devendra Kumar Biswal
- grid.412227.00000 0001 2173 057XBioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya India
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Konhar R, Debnath M, Vishwakarma S, Bhattacharjee A, Sundar D, Tandon P, Dash D, Biswal DK. The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 2019; 7:e7756. [PMID: 31695964 PMCID: PMC6830405 DOI: 10.7717/peerj.7756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/26/2019] [Indexed: 11/21/2022] Open
Abstract
The medicinal orchid genus Dendrobium belonging to the Orchidaceae family is a huge genus comprising about 800-1,500 species. To better illustrate the species status in the genus Dendrobium, a comparative analysis of 33 available chloroplast genomes retrieved from NCBI RefSeq database was compared with that of the first complete chloroplast genome of D. nobile from north-east India based on next-generation sequencing methods (Illumina HiSeq 2500-PE150). Our results provide comparative chloroplast genomic information for taxonomical identification, alignment-free phylogenomic inference and other statistical features of Dendrobium plastomes, which can also provide valuable information on their mutational events and sequence divergence.
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Affiliation(s)
- Ruchishree Konhar
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
- Informatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Santosh Vishwakarma
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Atanu Bhattacharjee
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pramod Tandon
- Biotech Park, Kursi road, Lucknow, Uttar Pradesh, India
| | - Debasis Dash
- Informatics and Big Data, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
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Biswal DK, Roychowdhury T, Pandey P, Tandon V. De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski. PLoS One 2018; 13:e0205570. [PMID: 30325945 PMCID: PMC6191129 DOI: 10.1371/journal.pone.0205570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/27/2018] [Indexed: 11/19/2022] Open
Abstract
Many trematode parasites cause infection in humans and are thought to be a major public health problem. Their ecological diversity in different regions provides challenging questions on evolution of these organisms. In this report, we perform transcriptome analysis of the giant intestinal fluke, Fasciolopsis buski, using next generation sequencing technology. Short read sequences derived from polyA containing RNA of this organism were assembled into 30,677 unigenes that led to the annotation of 12,380 genes. Annotation of the assembled transcripts enabled insight into processes and pathways in the intestinal fluke, such as RNAi pathway and energy metabolism. The expressed kinome of the organism was characterized by identifying all protein kinases. A rough draft genome assembly for Fasciolopsis buski is also reported herewith with SRA accessions for crosschecking the findings in the analyzed transcriptome data. Transcriptome data also helped us to identify some of the expressed transposable elements. Though many Long Interspersed elements (LINEs) were identified, only two Short Interspersed Elements (SINEs) were visible. Overall transcriptome and draft genome analysis of F. buski helped us to characterize some of its important biological characteristics and provided enormous resources for development of a suitable diagnostic system and anti-parasitic therapeutic molecules.
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Affiliation(s)
| | - Tanmoy Roychowdhury
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyatama Pandey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Veena Tandon
- Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya, India
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Konhar R, Debnath M, Marbaniang JV, Biswal DK, Tandon P. Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction. J Bioinform Comput Biol 2017; 14:1660001. [DOI: 10.1142/s0219720016600015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points.
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Affiliation(s)
- Ruchishree Konhar
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
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Biswal DK, Debnath M, Kharumnuid G, Thongnibah W, Tandon V. Northeast India Helminth Parasite Information Database (NEIHPID): Knowledge Base for Helminth Parasites. PLoS One 2016; 11:e0157459. [PMID: 27285615 PMCID: PMC4902196 DOI: 10.1371/journal.pone.0157459] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 05/31/2016] [Indexed: 11/19/2022] Open
Abstract
Most metazoan parasites that invade vertebrate hosts belong to three phyla: Platyhelminthes, Nematoda and Acanthocephala. Many of the parasitic members of these phyla are collectively known as helminths and are causative agents of many debilitating, deforming and lethal diseases of humans and animals. The North-East India Helminth Parasite Information Database (NEIHPID) project aimed to document and characterise the spectrum of helminth parasites in the north-eastern region of India, providing host, geographical distribution, diagnostic characters and image data. The morphology-based taxonomic data are supplemented with information on DNA sequences of nuclear, ribosomal and mitochondrial gene marker regions that aid in parasite identification. In addition, the database contains raw next generation sequencing (NGS) data for 3 foodborne trematode parasites, with more to follow. The database will also provide study material for students interested in parasite biology. Users can search the database at various taxonomic levels (phylum, class, order, superfamily, family, genus, and species), or by host, habitat and geographical location. Specimen collection locations are noted as co-ordinates in a MySQL database and can be viewed on Google maps, using Google Maps JavaScript API v3. The NEIHPID database has been made freely available at http://nepiac.nehu.ac.in/index.php.
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Affiliation(s)
| | - Manish Debnath
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | | | - Welfrank Thongnibah
- Bioinformatics Centre, North-Eastern Hill University, Shillong, Meghalaya, India
| | - Veena Tandon
- Department of Zoology, North-Eastern Hill University, Shillong, Meghalaya, India
- Biotech Park, Lucknow, Uttar Pradesh, India
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Biswal DK, Konhar R, Debnath M, Tandon V. Complete mitochondrial genome annotation of the giant intestinal fluke, Fasciolopsis buski (Indian isolate) as revealed by ion torrent and illuminanext-generation sequencing. Mitochondrial DNA B Resour 2016; 1:693-695. [PMID: 34395880 PMCID: PMC7875049 DOI: 10.1080/23802359.2016.1222249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The complete mitogenome sequences of the intestinal fluke Fasciolopsis buski are presented for the first time in this study. It is 14,119 bp long and is thus the shortest trematode mitochondrial genome sequenced to date. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The overall base composition of F. buski mitogenome is 17.89% for A, 9.16% for C, 27.59% for G and 45.36% for T, and has a GC content of 36.75%. The assembled mitogenome (GenBank accession number KX449331) consists of 12 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNA genes. The mtDNA for the intestinal fluke reported herein would help investigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data.
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Affiliation(s)
| | - Ruchishree Konhar
- Bioinformatics Centre, North Eastern Hill University, Shillong, India
| | - Manish Debnath
- Bioinformatics Centre, North Eastern Hill University, Shillong, India
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Biswal DK, Ghatani S, Shylla JA, Sahu R, Mullapudi N, Bhattacharya A, Tandon V. An integrated pipeline for next generation sequencing and annotation of the complete mitochondrial genome of the giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899. PeerJ 2013; 1:e207. [PMID: 24255820 PMCID: PMC3828612 DOI: 10.7717/peerj.207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/21/2013] [Indexed: 11/20/2022] Open
Abstract
Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear genome houses suitable genetic markers (e.g., in ribosomal (r) DNA) for species identification and molecular characterization, the mitochondrial (mt) genome consistently provides a rich source of novel markers for informative systematics and epidemiological studies. In the last decade, there have been some important advances in mtDNA genomics of helminths, especially lung flukes, liver flukes and intestinal flukes. Fasciolopsis buski, often called the giant intestinal fluke, is one of the largest digenean trematodes infecting humans and found primarily in Asia, in particular the Indian subcontinent. Next-generation sequencing (NGS) technologies now provide opportunities for high throughput sequencing, assembly and annotation within a short span of time. Herein, we describe a high-throughput sequencing and bioinformatics pipeline for mt genomics for F. buski that emphasizes the utility of short read NGS platforms such as Ion Torrent and Illumina in successfully sequencing and assembling the mt genome using innovative approaches for PCR primer design as well as assembly. We took advantage of our NGS whole genome sequence data (unpublished so far) for F. buski and its comparison with available data for the Fasciola hepatica mtDNA as the reference genome for design of precise and specific primers for amplification of mt genome sequences from F. buski. A long-range PCR was carried out to create an NGS library enriched in mt DNA sequences. Two different NGS platforms were employed for complete sequencing, assembly and annotation of the F. buski mt genome. The complete mt genome sequences of the intestinal fluke comprise 14,118 bp and is thus the shortest trematode mitochondrial genome sequenced to date. The noncoding control regions are separated into two parts by the tRNA-Gly gene and don’t contain either tandem repeats or secondary structures, which are typical for trematode control regions. The gene content and arrangement are identical to that of F. hepatica. The F. buski mtDNA genome has a close resemblance with F. hepatica and has a similar gene order tallying with that of other trematodes. The mtDNA for the intestinal fluke is reported herein for the first time by our group that would help investigate Fasciolidae taxonomy and systematics with the aid of mtDNA NGS data. More so, it would serve as a resource for comparative mitochondrial genomics and systematic studies of trematode parasites.
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Kumar S, Biswal DK, Tandon V. In-silico analysis of caspase-3 and -7 proteases from blood-parasitic Schistosoma species (Trematoda) and their human host. Bioinformation 2013; 9:456-63. [PMID: 23847399 PMCID: PMC3705615 DOI: 10.6026/97320630009456] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/21/2012] [Accepted: 04/17/2013] [Indexed: 12/24/2022] Open
Abstract
Proteolytic enzymes of the caspase family, which reside as latent precursors in most nucleated metazoan cells, are core effectors of
apoptosis. Of them, the executioner caspases- 3 and -7 exist within the cytosol as inactive dimers and are activated by a process
called dimerization. Caspase inhibition is looked upon as a promising approach for treating multiple diseases. Though caspases
have been extensively studied in the human system, their role in eukaryotic pathogens and parasites of human hosts has not drawn
enough attention. In protein sequence analysis, caspases of blood flukes (Schistosoma spp) were revealed to have a low sequence
identity with their counterparts in human and other mammalian hosts, which encouraged us to analyse interacting domains that
participate in dimerization of caspases in the parasite and to reveal differences, if any, between the host-parasite systems.
Significant differences in the molecular surface arrangement of the dimer interfaces reveal that in schistosomal caspases only eight
out of forty dimer conformations are similar to human caspase structures. Thus, the parasite-specific dimer conformations (that are
different from caspases of the host) may emerge as potential drug targets of therapeutic value against schistosomal infections.
Three important factors namely, the size of amino acids, secondary structures and geometrical arrangement of interacting domains
influence the pattern of caspase dimer formation, which, in turn, is manifested in varied structural conformations of caspases in the
parasite and its human hosts.
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Affiliation(s)
- Shakti Kumar
- Bioinformatics Centre, North-Eastern Hill University, Shillong 793022, Meghalaya, India ; Department of Zoology, North-Eastern Hill University, Shillong 793022, Meghalaya, India
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Biswal DK, Debnath M, Kumar S, Tandon P. Phylogenetic reconstruction in the order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding. BMC Bioinformatics 2012; 13 Suppl 17:S26. [PMID: 23282079 PMCID: PMC3521246 DOI: 10.1186/1471-2105-13-s17-s26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Nymphaeales (waterlilly and relatives) lineage has diverged as the second branch of basal angiosperms and comprises of two families: Cabombaceae and Nymphaceae. The classification of Nymphaeales and phylogeny within the flowering plants are quite intriguing as several systems (Thorne system, Dahlgren system, Cronquist system, Takhtajan system and APG III system (Angiosperm Phylogeny Group III system) have attempted to redefine the Nymphaeales taxonomy. There have been also fossil records consisting especially of seeds, pollen, stems, leaves and flowers as early as the lower Cretaceous. Here we present an in silico study of the order Nymphaeales taking maturaseK (matK) and internal transcribed spacer (ITS2) as biomarkers for phylogeny reconstruction (using character-based methods and Bayesian approach) and identification of motifs for DNA barcoding. RESULTS The Maximum Likelihood (ML) and Bayesian approach yielded congruent fully resolved and well-supported trees using a concatenated (ITS2+ matK) supermatrix aligned dataset. The taxon sampling corroborates the monophyly of Cabombaceae. Nuphar emerges as a monophyletic clade in the family Nymphaeaceae while there are slight discrepancies in the monophyletic nature of the genera Nymphaea owing to Victoria-Euryale and Ondinea grouping in the same node of Nymphaeaceae. ITS2 secondary structures alignment corroborate the primary sequence analysis. Hydatellaceae emerged as a sister clade to Nymphaeaceae and had a basal lineage amongst the water lilly clades. Species from Cycas and Ginkgo were taken as outgroups and were rooted in the overall tree topology from various methods. CONCLUSIONS MatK genes are fast evolving highly variant regions of plant chloroplast DNA that can serve as potential biomarkers for DNA barcoding and also in generating primers for angiosperms with identification of unique motif regions. We have reported unique genus specific motif regions in the Order Nymphaeles from matK dataset which can be further validated for barcoding and designing of PCR primers. Our analysis using a novel approach of sequence-structure alignment and phylogenetic reconstruction using molecular morphometrics congrue with the current placement of Hydatellaceae within the early-divergent angiosperm order Nymphaeales. The results underscore the fact that more diverse genera, if not fully resolved to be monophyletic, should be represented by all major lineages.
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Affiliation(s)
- Devendra Kumar Biswal
- Bioinformatics Centre, North Eastern Hill University, Shillong 793022, Meghalaya, India
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Malsawmtluangi C, Prasad PK, Biswal DK, Tandon V. Morphological and molecular identification of the metacestode parasitizing the liver of rodent hosts in bamboo growing areas of mizoram, northeast India. Bioinformation 2011; 7:393-9. [PMID: 22347781 PMCID: PMC3280439 DOI: 10.6026/97320630007393] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/07/2011] [Indexed: 11/29/2022] Open
Abstract
In Mizoram (Northeast India), rodent outbreaks are known to occur periodically with the onset of bamboo flowering causing a tremendous destruction to food grains and as per the folk belief, often resulting in famine. In an exploratory survey of rodent pests in bamboo growing atreas for their helminth parasite spectrum, metacestodes of tapeworms were frequently encountered infecting the liver lobes and body cavity of the host. The morphological criteria were found to be closely consistent with the metacestode of Taenia species. In molecular characterization of the parasite, the ribosomal DNA (ITS1, ITS2) and mitochondrial COI were amplified and sequenced. Based upon both morphological data and molecular analysis using bioinformatic tools, the metacestode is identified as confirmed to be representing Cysticercus fasciolaris. The adult form of which (Taenia taeniaeformis) commonly occurs in felid and canid mammalian hosts.
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Affiliation(s)
| | - Pramod Kumar Prasad
- Department of Science & Technology, Technology Bhavan, Mehrauli Road, New Delhi-110016
| | | | - Veena Tandon
- Department of Zoology, North-Eastern Hill University, Shillong-793022, Meghalaya
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Tandon V, Biswal DK, Prasad PK, Malsawmtluangi C. Reconstructing the Phylogenetic Relationships of the Cyclophyllidean Cestodes: A Case Study Using ITS2 rDNA and Sequence-Structure Alignment. Biomedical Engineering Systems and Technologies 2011. [DOI: 10.1007/978-3-642-18472-7_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Prasad PK, Tandon V, Biswal DK, Goswami LM, Chatterjee A. Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species. BMC Genomics 2009; 10 Suppl 3:S25. [PMID: 19958489 PMCID: PMC2788378 DOI: 10.1186/1471-2164-10-s3-s25] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information, not found in the primary sequence. In several mountainous regions of Northeastern India, foci of Paragonimus (lung fluke) infection reportedly involve species that are known to prevail in neighbouring countries. The present study was undertaken to demonstrate the sequence analysis of the ribosomal DNA (ITS2) of the infective (metacercarial) stage of the lung fluke collected from the edible crab hosts that are abundant in a mountain stream of the area (Miao, Changlang District in Arunachal Pradesh) and to construct its phylogeny. Using the approach of molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates of Paragonimus species that are prevalent in the neighbouring Near-eastern countries have been discussed. RESULTS Initially, ten predicted RNA secondary structures were reconstructed and the topology based only on the predicted RNA secondary structure of the ITS2 region resolved most relationships among the species studied. We obtained three similar topologies for seven species of the genus Paragonimus on the basis of traditional primary sequence analysis using MEGA and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics; each data partition was allowed to have a different evolution rate. Paragonimus westermani was found to group with P. siamensis of Thailand; this was best supported by both the molecular morphometrics and combined analyses. P. heterotremus, P. proliferus, P. skrjabini, P. bangkokensis and P. harinasutai formed a separate clade in the molecular phylogenies, and were reciprocally monophyletic with respect to other species. ITS2 sequence motifs allowed an accurate in-silico distinction of lung flukes. CONCLUSION Data indicate that ITS2 motifs (<or= 50 bp in size) can be considered a promising tool for trematode species identification. RNA secondary structure analysis could be a valuable tool for distinguishing new species and completing Paragonimus systematics, more so because ITS2 secondary structure contains more information than the usual primary sequence alignment.
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Affiliation(s)
- Pramod Kumar Prasad
- Department of Zoology, North-Eastern Hill University, Shillong-793022, Meghalaya, India.
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Prasad PK, Tandon V, Biswal DK, Goswami LM, Chatterjee A. Use of sequence motifs as barcodes and secondary structures of internal transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae). Bioinformation 2009; 3:314-20. [PMID: 19294000 PMCID: PMC2655052 DOI: 10.6026/97320630003314] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 01/16/2009] [Accepted: 02/07/2009] [Indexed: 11/23/2022] Open
Abstract
Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA
secondary structures are particularly useful in systematics because they include characteristics that give
“morphological” information which is not found in the primary sequence. Also DNA sequence motifs from the
internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver
flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing
in the large biliary ducts of herbivorous mammals. While Fasciola hepatica has a cosmopolitan distribution, the
other major species, i.e., F. gigantica is reportedly prevalent in the tropical and subtropical regions of
Africa and Asia. To determine the Fasciola sp. of Assam (India) origin based on rDNA molecular data, ribosomal
ITS2 region was sequenced (EF027103) and analysed. NCBI databases were used for sequence homology analysis and the phylogenetic
trees were constructed based upon the ITS2 using MEGA and a Bayesian analysis of the combined data. The latter approach allowed
us to include both primary sequence and RNA molecular morphometrics and revealed a close relationship with isolates of
F. gigantica from China, Indonesia and Japan, the isolate from China with significant bootstrap values being
the closest. ITS2 sequence motifs allowed an accurate in silico distinction of liver flukes. The data indicate that ITS2 motifs
(≤ 50 bp in size) can be considered promising tool for trematode species identification. Using the novel approach of
molecular morphometrics that is based on ITS2 secondary structure homologies, phylogenetic relationships of the various isolates
of fasciolid species have been discussed.
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Affiliation(s)
- P K Prasad
- Department of Zoology, North Eastern Hill University, Shillong, Meghalaya, 793022, India
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