Dr. Sucheta Tripathy
Ph.D Plant Molecular Biology 1998 (Center For Plant Molecular Biology, Hyderabad)
Training in Software Technology for PGDST at NCST(Now cDAC, dept. of science and Technology), Mumbai,2000
Bioinformatics Training, DSQ Biotech, Chennai, India, 2000
Scientist (Bioinformatics division) at DSQ biotech limited (2000-2001)
Scientist and Head Bioinformatics division at Avesthagengrain Pvt. Ltd.(2001-2002)
Senior scientist and Bioinformatics Team lead at Virginia Bioinformatics Institute at Virginia tech (2002-2012)
Assessing the genome sequences of Termitomyces clypeatus for novel metabolite discovery through whole genome sequencing methods and characterization of the metabolites for application in biotechnology
Termitomyces clypeatus belongs to an edible group of mushroom with prized metabolite content [Kumari et al. 2013]. In many parts of Asia, it is used for its medicinal value [Yang et al. 2012]. Termitomyces, belonging to species Basidiomycota, has about 35-40 species, prevalent in tropical parts of Asia and Africa where it has a tight obligatory mutualistic relationship with Termites. Both the Termites and Termitomyces can’t grow apart from each other. Transcriptome sequencing of Termitomyces albuminous [Yang et al 2012] has been carried out revealing about ~6000 transcriptomes. We have sequenced transcriptomes of Termitomyces clypeatus and found about 3 times more number of transcripts than that of T. albuminous [Manuscript under preparation]. Under different treatment conditions the number of transcripts expressed varied by 15% [Out unpublished results]. There are still a large number of metabolic pathway related genes that are not discovered through our transcriptomics studies. In recent years, with rapid advancement in sequencing technologies and falling prices, whole genome sequencing is one of the go to methods for rapid gene and transcript discovery.
In this study we propose to undertake whole genome sequencing of this economically important species using random shutgun methods using Illumina HiSeq platformat about 100X coverage. We will carry out mate pair sequencing with 2 KB and 10 KB insert size for scaffolding purpose. Genome assembly and annotation will be carried out with discovery of novel metabolic pathway genes. We will integrate our transcriptomics data for enriching gene collection and bridging gaps. The production, purification, characterization of the metabolites will be done by cloning and expression of novel glycosyl hydrolases (enzymes) like proteins, of T. clypeatus. The protein activities will be purified and validated by FPLC & HPGPLC and electrophoretic analyses.
Whole Genome and Transcriptome sequencing of selected Indian Cyanobacterial species for candidate Cyanobacterial species for candidate gene discovery for bio-metabolites.
None of the whole genome projects from India grown Cyanobacteria been sequenced and deposited in International Nucleotide Sequence Database collaboration (INSDC) by Indian Institutes to date. India provides 17% of the total biodiversity, and among which the water grown Cyanobacteria are least studied and understood. We have established collaboration with Dept. Of Biotechnology at Visva Bharati that has the largest exotic Cyanobacteria collection in India (Prof. Adhikary – personal communication). We are specifically interested in Cyanobacteria growing under stressed conditions to investigate their gene pool for specific metabolic pathway related genes that can have agricultural significance. We have investigated several pathways in Cyanobacteria in general including that of Nitrogen fixation, lipid metabolism and carbohydrate metabolism. We would be interested in discovery of genes from whole genome and transcriptome sequencing data that has agriculturally important properties such as growing under stress conditions and reducing soil alkalinity etc.
Currently we are interested in studying the following six Cyanobacteria species:
- Hassallia byssoidea: Majority of species are aerophytic. Distribution of this species is not very well known due to rampant mis-identifications.
- Mastigocladus laminosus: Grows in hot springs
- Scytonema tolypothrichoides: Grows on sub-acrophyte rocks
- Scytonema milli:
- Tolypothrix bouteillei:
- Tolypothrix campylonemoides:
All of these organisms are used as bio fertilizers with the ability to quench alkalinity of the soil. Lack of study in the classification and whole genetic makeup has left big lacunae that we would like to address.
- Grow the organisms and sequence the entire genome to study the genetic blue prints of these organisms.
- Use computational methods for predicting genes and constructing metabolic pathways.
- Identify gene belonging to novel pathways.
- Create a web portal and host the genomes of the organisms.
- Study the transcriptomics and profile them under control and treated conditions.
Developing diagnostic parameters for control of Phytophthora infestans by studying Genetic Diversity using Phenotypic, Moelcular and Nextgen Sequencing methods.
The primary objective is to characterize the P.infestans populations genotypically and phenotypically primarily from West Bengal and secondarily other adjoining states in Eastern India and its correlation so that the information can be used to control future out breaks of late blight in this region. The information would include known hosts, potato and tomato and potential weed hosts if any on which the inoculum is capable of surviving, and other standard phenotypic diversity evaluations. These would include fungicide sensitivity/resistance assays of currently used and newly introduced ones, testing of virulence of the isolates, evaluation of aggressiveness and determination of mating type.
Genotypic diversity analysis would include allozyme diversity at Gpi locus, RG-57 fingerprinting if needed to allow comparisons with lineages studied in the past. However, limited analyses will be performed using RFLPs and allozymes with the major stress being on SSR profiles which will come from use of multiplexed SSR primers. Clustering of SSR profiles will be done with DarWin software and attempt will be made to correlate them to phenotypic traits.
Additionally, the isolates would be screened for sequence diversity of known candidate effectors Avr 3a, Avr–blb2 and the IPI-O family from P. infestans. Due to selection pressure from the hosts, the avirulence genes show extensive variations, including amino acid changes indicative of strong positive selection, gene truncations and deletions, and transcriptional silencing. An attempt would be made to detect this diversity among isolates.
The genotypic and phenotypic assays would be carried out in West Bengal State University, Barasat and all sequencing as well as diversity analysis of the effectors and population genetic analyses would be carried out at Indian Institute of Chemical Biology, Kolkata.
Development of comprehensive genomic resources for newly sequenced genomes
With the reduced cost and rapid pace, the next generation sequencing methods are all set to take over the new data age science. However, there exists a bottleneck since trained human resources and softwares are not developing that fast to transform this data into knowledge. We are also interested in creating novel software resources and piplelines for genome data analysis.
Understanding Genomes of Extremophiles.
Aditya Sarangi: RA, DBT.
Subhadeep Das: SRF, DBT.
Abhishek Das: SRF, ICMR.
Mathu Malar C.: SRF, DST.
Arijit Panda: SRF, CSIR-NET.
Deeksha Singh: SRF, ICMR
Pijush Das, SRF: CSIR
Mayuri Mukherjea: SRF, CSIR
Samrat Ghosh: JRF, DBT
Shashikant: JRF, CSIR
Publication at the CSIR-IICB
Elliott M, Yuzon J, C MM, Tripathy S, Bui M, Chastagner GA, Coats K, Rizzo DM, Garbelotto M, Kasuga T. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics. 2018 May 2;19(1):320. doi: 10.1186/s12864-018-4709-7. PubMed PMID: 29720102; PubMed Central PMCID: PMC5932867 [IF: 3.729]
Dey T, Saville A, Myers K, Tewari S, Cooke DEL, Tripathy S, Fry WE, Ristaino JB, Guha Roy S. Large sub-clonal variation in Phytophthora infestans from recent severe late blight epidemics in India. Sci Rep. 2018 Mar 13;8(1):4429. doi: 10.1038/s41598-018-22192-1. [IF: 4.2]
- Panda A, Sen D, Ghosh A, Gupta A, C MM, Prakash Mishra G, Singh D, Ye W, Tyler BM, Tripathy S*. EumicrobeDBLite: a lightweight genomic resource and analytic platform for draft oomycete genomes. Mol Plant Pathol. 2018 Jan;19(1):227-237. doi: 10.1111/mpp.12505. Epub 2017 Jan 3. [IF: 4.7]
- Majumder R, Sheikh L, Naskar A, Vineeta, Mukherjee M, Tripathy S*. Depletion of Cr(VI) from aqueous solution by heat dried biomass of a newly isolated fungus Arthrinium malaysianum: A mechanistic approach. Sci Rep. 2017 Sep 12;7(1):11254. doi: 10.1038/s41598-017-10160-0.[IF: 4.2]
- Mukherjee S, Chandrababunaidu MM, Panda A, Khowala S, Tripathy S*. Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. Front Microbiol. 2016 May 13;7:596. doi: 10.3389/fmicb.2016.00596. eCollection 2016. [IF: 4.07]
- Mohan A, Singh RS, Kumari M, Garg D, Upadhyay A, Ecelbarger CM, Tripathy S, Tiwari S. Urinary Exosomal microRNA-451-5p Is a Potential Early Biomarker of Diabetic Nephropathy in Rats. PLoS One. 2016 Apr 21;11(4):e0154055. doi: 10.1371/journal.pone.0154055. eCollection 2016. [IF: 2.3]
- Sheikh L, Tripathy S, Nayar S, 2016. Biomimetic matrix mediated room temperature synthesis and characterization of nano-hydroxyapatite towards targeted drug delivery. RSC Advances 6, 62556-71 [IF: 3.3]
- Mathu Malar Chandrababunaidu, Deeksha Singh, Diya Sen, Sushma Bhan, Subhadeep Das, Akash Gupta, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of Tolypothrix boutellei Strain VB521301. Genome announcements 3: 02. [IF: 1.44]
- Diya Sen, Mathu Malar Chandrababunaidu, Deeksha Singh, Neha Sanghi, Arpita Ghorai, Gyan Prakash Mishra, Madhavi Madduluri,Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India. Genome announcements 3: 03. [IF: 1.44]
- Sourav Bhattacharyya, Mathu Malar Chandrababunaidu, Deeya Sen, Arijit Panda, Arpita Ghorai, Sushma Bhan, Neha Sanghi, Sucheta Tripathy* (2015) Draft Genome Sequence of Exopolysaccharide-Producing Cyanobacterium Aphanocapsa montana BDHKU 210001. Genome announcements 3: 03. [IF: 1.44]
- Deeksha Singh, Mathu Malar Chandrababunaidu, Arijit Panda, Diya Sen, Sourav Bhattacharyya, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of Cyanobacterium Hassallia byssoidea Strain VB512170, Isolated from Monuments in India. Genome announcements 3: 03. [IF: 1.44]
- Mathu Malar Chandrababunaidu, Diya Sen, Sucheta Tripathy* (2015) Draft Genome Sequence of Filamentous Marine Cyanobacterium Lyngbya confervoides Strain BDU141951. Genome announcements 3: 03. [IF: 1.44]
- Subhadeep Das, Deeksha Singh, Madhavi Madduluri, Mathu Malar Chandrababunaidu, Akash Gupta, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Draft Genome Sequence of Bioactive-Compound-Producing Cyanobacterium Tolypothrix campylonemoides Strain VB511288. Genome announcements 3: 04. [IF: 1.44]
- Abhishek Das, Arijit Panda, Deeksha Singh, Mathu Malar Chandrababunaidu, Gyan Prakash Mishra, Sushma Bhan, Siba Prasad Adhikary, Sucheta Tripathy* (2015) Deciphering the Genome Sequences of the Hydrophobic Cyanobacterium Scytonema tolypothrichoides VB-61278. Genome announcements 3: 04. [IF: 1.44]
- Bhowmick S, Malar M, Das A, Kumar Thakur B, Saha P, Das S, Rashmi HM, Batish VK, Grover S, Tripathy S*. Genome Announc. 2014 Dec 24;2(6). pii: e01326-14. doi: 10.1128/genomeA.01326-14. [IF: 1.44]
- A Tale of Effectors; Their Secretory Mechanisms and Computational Discovery in Pathogenic, Non-Pathogenic and Commensal Microbes.S Bhowmick, S Tripathy* – Mol Biol, 2014
Publication at the Virginia Tech
- Rays H Y Jiang et al.,, Sucheta Tripathy, et al., (2013) Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica. PLoS genetics 9: 6. Jun [IF: 7.528]
- Sucheta Tripathy*, Tejal Deo, Brett M Tyler (2012) Oomycete transcriptomics database: A resource for oomycete transcriptomes. BMC Genomics. [IF: 3.867]
- Sucheta Tripathy*, Rays H Y Jiang (2012) Massively parallel sequencing technology in pathogenic microbes. Methods Mol Biol 835: 271-294. [IF: 2.2]
- Qunqing Wang, et al., Sucheta Tripathy, et al.(2011) Transcriptional programming and functional interactions within the Phytophthora sojae RXLR effector repertoire. Plant Cell 23: 6. 2064-2086 Jun. [IF: 10.5]
- M A Saghai Maroof, Dominic M Tucker, Jeffrey A Skoneczka, Brian C Bowman, Sucheta Tripathy, Sue A Tolin (2010) Fine Mapping and Candidate Gene Discovery of the Soybean Mosaic Virus Resistance Gene, Rsv4 The Plant Genome 3: 14-22. [IF: 3.933]
- C André Lévesque, et al. Sucheta Tripathy, et al. (2010) Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol 11: 7. 07. [IF: 11.313]
- Laura Baxter+, Sucheta Tripathy+, et. al. (2010) Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 330: 6010. 1549-1551 Dec [+joint first author]. [IF: 34.661]
- H Wang, L Waller, S Tripathy, S K St Martin, L Zhou, K Krampis, D M Tucker, Y Mao, I Hoeschele, M A Saghai Maroof, B M Tyler, A E Dorrance (2010) Analysis of Genes Underlying Soybean QTL Conferring Partial Resistance to Phytophthora sojae. The Plant Genome 3: 23-40 [IF: 3.933]
- Lecong Zhou, Santiago X Mideros, Lei Bao, Regina Hanlon, Felipe D Arredondo, Sucheta Tripathy, Konstantinos Krampis, Adam Jerauld, Clive Evans, Steven K St Martin, M A Saghai Maroof, Ina Hoeschele, Anne E Dorrance, Brett M Tyler (2009) Infection and genotype remodel the entire soybean transcriptome. BMC Genomics 10: 01. [IF: 3.867]
- Rays H Y Jiang, Sucheta Tripathy, Francine Govers, Brett M Tyler (2008) RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members. Proc Natl Acad Sci U S A 105: 4874-4879 Mar. [IF: 9.423]
- Trudy A Torto-Alalibo, Sucheta Tripathy, Brian M Smith, Felipe D Arredondo, Lecong Zhou, Hua Li, Marcus C Chibucos, Dinah Qutob, Mark Gijzen, Chunhong Mao, Bruno W S Sobral, Mark E Waugh, Thomas K Mitchell, Ralph A Dean, Brett M Tyler (2007) Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection. Mol Plant Microbe Interact 20: 781-793 Jul. [IF: 4.332]
- Sucheta Tripathy, Varun N Pandey, Bing Fang, Fidel Salas, Brett M Tyler (2006) VMD: a community annotation database for oomycetes and microbial genomes. Nucleic Acids Res 34: Database issue. D379-D381 Jan. Featured in Science. [IF: 9.122]
- Brett M Tyler, Sucheta Tripathy, Xuemin Zhang, Paramvir Dehal, Rays H Y Jiang, Andrea Aerts, Felipe D Arredondo, Laura Baxter, Douda Bensasson, Jim L Beynon, et al.,(2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313: 1261-1266 Sep. [IF: 34.661]
- Xuemin Zhang, Chantel Scheuring, Sucheta Tripathy, Zhanyou Xu, Chengcang Wu, Angela Ko, S Ken Tian, Felipe Arredondo, Mi-Kyung Lee, Felipe A Santos, et. al., (2006) An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact 19: 1302-1310 Dec. [IF: 4.332]
- Sucheta Tripathy*, Brett M Tyler (2006) The repertoire of transfer RNA genes is tuned to codon usage bias in the genomes of Phytophthora sojae and Phytophthora ramorum. Mol Plant Microbe Interact 19: 1322-1328 Dec. [IF: 4.332]
- Sucheta Tripathy, G M Reddy (2002) In Vitro callus induction and plantlet regeneration from Indian cotton cultivars Plant Cell Biotechnology and Molecular Biology 3: 3&4. 137-142.
- Sucheta Tripathy, G M Reddy (2002) A Study on the influence of genotype, medium and additives on the induction of multiple shoots in Indian cotton cultivars Asian Jr. of Microbiol Biotech. Env. Sc. 4: 4. 515-519.
* Author for correspondence
- Verma S, Tripathy S., Raychaudhuri S,Swarnakar Chapter: Insights into Metalloproteinases Regulation in Gastrointestinal Cancers: Epigenetic Influences in the Book: Gastrointestinal Cancers: Prevention, Detection and Treatment. Editor, A Tyagi. Nova Publication (2016) (in press)
- Dissecting Transcriptomes of Cyanobacteria for novel metabolite production . Sucheta Tripathy*, Deeksha Singh, Mathumalar C, Abhishek Das.Genomics, Proteomics and Metabolomics in nutraceuticals and functional foods, edited byBagchi for John Wiley & Sons
- Sucheta Tripathy (2011) cancer and Diet In: Herbal Perspective: Present and Future 468 Vedam Books isbn:8189304917.
- Brett M Tyler, Rays H Y Jiang, Lecong Zhou, Sucheta Tripathy, Daolong Dou, Trudy Torto-Alalibo, Hua Li, Yongcai Mao, Bing Liu, et al (2008) Functional Genomics and Bioinformatics of the Phytophthora sojae Soybean Interaction.ISSN:1568-1009,ISBN:978-0-387-76722-2 (Print) 978-0-387-76723-9 (Online) In: Genomics of Disease Edited by:J.P. Gustafson, J.Taylor, G. Stacey. 67-78 isbn:978-0-387-76723-9.
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