Publications of Komal Chenthamara

Peer-reviewed scientific articles

CAI Feng, GAO Renwai, ZHAO Zheng, DING Mingyue, JIANG Siqi, YAGTU Civan, ZHU Hong, ZHANG Jian, EBNER Thomas, MAYRHOFER-REINHARTSHUBER Michael, KAINZ Philipp, CHENTHAMARA Komal, AKCAPINAR Gunseli Bayram, SHEN Qirong, DRUZHININA Irina. Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival. ISME Journal 14(10):1-15, July 2020

GAO Renwai, DING Mingyue, JIANG Siqi, ZHAO Zheng, CHENTHAMARA Komal, SHEN Qirong, CAI Feng, DRUZHININA Irina. The evolutionary and functional paradox of cerato- platanins in the mycoparasitic fungus Trichoderma: high diversity, stabilizing selection, and a minor role in biotic interactions. Applied Environmental Microbiology, April 2020

PÉREZ-LLANO Yordanis, RODRÍGUEZ-PUPO Eya Caridad, DRUZHININA Irina, CHENTHAMARA Komal, CAI Feng, GUNDE-CIMERMAN Nina, ZALAR Polona, GOSTINČAR Cene, KOSTANJŠEK Rok, FOLCH-MALLOL Jorge Luis, BATISTA-GARCÍA Ramón Alberto and SÁNCHEZ-CARBENTE María del Rayo. Stress Reshapes the Physiological Response of Halophile Fungi to Salinity. Cells, February 2020

HATVANI Lóránt, HOMA Mónika, CHENTHAMARA Komal, KOCSUBÉ Sándor, ATANASOVA Lea, MLINARIC-MISSONI Emilija, MANIKANDAN Palanisamy, REVATHI Rajaraman, DÓCZI Ilona, IVÁNYI Béla, BOGÁTS Gábor, NARENDRAN Venkatapathy, BÜCHNER Rita, VÁGVÖLGYI Csaba, DRUZHININA Irina, KREDICS László. Agricultural systems as potential sources of emerging human mycoses caused by Trichoderma. FEMS Microbiology letters, December 2019

KUBICEK Christian§, STEINDORFF Andrei§, CHENTHAMARA Komal, MANGANIELLO Gelsomina, BERNARD Henrissat, ZHANG Jian, CAI Feng, KOPCHINSKIY Alexey, KUBICEK Eva M, KUO Alan, BARONCELLI Riccardo, SARROCCO Sabrina, NORONHA Eliane Ferreira, VANNACCI Giovanni, SHEN Qirong, GRIGORIEV Igor and DRUZHININA Irina. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics, June 2019

ZHANG Jian, MIAO Youzhi, RAHIMI Mohammad Javad, ZHU Hong, STEINDORFF Andrei, SCHIESSLER Sabine, CAI Feng, PANG Guan, CHENTHAMARA Komal, XU Yu, KUBICEK Christian, SHEN Qirong, and DRUZHININA Irina. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environmental Microbiology, February 2019

DRUZHININA Irina, CHENTHAMARA Komal, ZHANG Jian, ATANASOVA Lea, YANG Dongqing, MIAO Youzhi, RAHIMI Mohammad, GRUJIC Marica, CAI Feng, POURMEHDI Shadi, ABU SALIM Kamariah, PRETZER Carina, KOPCHINSKIY Alexey, HENRISSAT Bernard, KUO Alan, HUNDLEY Hope, WANG Mei, AERTS Andrea, SALAMOV Asaf, LIPZEN Anna, LABUTTI Kurt, BARRY Kerrie, GRIGORIEV Igor, SHEN Qirong, and KUBICEK Christian. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLOS Genetics, April 2018

QIN Yuan, PAN Xueyu, KUBICEK Christian, DRUZHININA Irina, CHENTHAMARA Komal, LABBÉ Jessy and YUAN Zhilin. Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth. Frontiers in Microbiology, February 2017

PRZYLUCKA Agnes, AKCAPINAR Gunseli Bayram, CHENTHAMARA Komal, CAI Feng, GRUJIC Marica, KARPENKO Juriy, LIVOI Miriam, SHEN Qirong, KUBICEK Christian, DRUZHININA Irina. HFB7 – A Novel Orphan Hydrophobin of the Harzianum and Virens Clades of Trichoderma, Is Involved in Response to Biotic and Abiotic Stresses. Fungal Genetics and Biology, May 2017

DE MAN Tom, STAJICH Jason, KUBICEK Christian, TEILING Clotilde, CHENTHAMARA Komal, ATANASOVA Lea, DRUZHININA Irina, LEVENKOVA Natasha, BIRNBAUM Stephanie, BARRIBEAU Seth, BOZICK Brooke, SUEN Garret, CURRIE Cameron, and GERARDO Nicole. Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. PNAS, Proceedings of the National Academy of Sciences, March 2016

YANG Dongqing, POMRANING Kyle, KOPCHINSKIY Alexey, AGHCHEH Razieh Karimi, ATANASOVA Lea, CHENTHAMARA Komal, BAKER Scott E., ZHANG Ruifu, SHEN Qirong, FREITAG Michael, KUBICEK Christian, and DRUZHININA Irina. Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei. American Society for Microbiology – Genome Announcements August 2015

Book chapters

CHENTHAMARA Komal, DRUZHININA Irina, RAHIMI Mohammad, GRUJIC Marica, and CAI Feng. “Ecological genomics and evolution of Trichoderma reesei”. Springer – Trichoderma reesei ‐ Methods and Protocols, January 2021

RAHIMI Mohammad, CAI Feng, GRUJIC Marica, CHENTHAMARA Komal, and DRUZHININA Irina. Molecular Identification of Trichoderma reesei”. Springer – Trichoderma reesei ‐ Methods and Protocols, January 2021

CHENTHAMARA Komal, DRUZHININA Irina. “Ecological Genomics of Mycotrophic Fungi”. Springer – THE MYCOTA, Environmental and Microbial Relationships, Volume IV, Third Edition, March 2016

List of first author conference papers (Scientific posters)

CHENTHAMARA Komal, STEINDORFF Andrei, GOJIC Vladimir, SHELEST Ekaterina, GRIGORIEV Igor, KUBICEK Christian, DRUZHININA Irina. “The comparative genomics of the most common Trichoderma species reveals the unique pattern of the ankyrin domain-containing proteins in orphomes of individual Trichoderma species”; Poster: Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, April 2019

CHENTHAMARA Komal, CAI Feng, VON ROTZ Sebastian, CERVENKA Isabella, SHEN Qirong, DRUZHININA Irina. “The enrichment in hydrophobin-encoding genes constitutes the main genomic hallmark of Trichoderma: the pattern search revealed a plethora of unknown genes absent in other hypocrealean fungi”; Poster: Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, April 2019

CHENTHAMARA Komal, GOJIC Vladimir, BAJTELA Robert, DRUZHININA Irina. “Decoding the expanded Ankyrin-Repeat gene family in Trichoderma”; Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, March 2018

CHENTHAMARA Komal, CAI Feng, PRZYLUCKA Agnieszka, SHEN Qirong, BAYRAM AKCAPINAR Günseli, DRUZHININA Irina.: “The origin and architecture of Trichoderma hydrophobome”; Poster: Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, March 22, 2017, in “Abstract Book”, (2016), S.24

CHENTHAMARA Komal, CAI Feng, PRZYLUCKA Agnieszka, SHEN Qirong, BAYRAM AKCAPINAR Günseli, DRUZHININA Irina. “The origin and architecture of Trichoderma hydrophobome”; Short-talk and poster: Vienna young Scientists Symposium, TU WIEN, June 6, 2017; in “Abstract Book”, (2016), S90-91

DRUZHININA Irina, ATANASOVA Lea, CHENTHAMARA Komal, GRUJIC Marica, HENRISSAT Bernard, ZHANG Jian, SHEN Qirong, GRIGORIEV Igor, KUBICEK Christian. Horizontal gene transfers drove the mycoparasite Trichoderma to adapt to saprotrophy and cellulase production. Talk: 13th European Conference on Fungal Genetics, 3-6, April 2016, Paris, France; in “Abstract Book”, (2016), S.70.

CHENTHAMARA Komal, ATANASOVA Lea, YANG Dongqing, ZHANG Jian, KOPCHINSKIY Alexey, GRIGORIEV Igor, KUBICEK Christian, SHEN Qirong, DRUZHININA Irina. Phylogenomics of Trichoderma. Poster: ECFG12- 12th European conference on fungal genetics, Seville, Spain; 23.3.-27.3. 2014. S: 184

Dipl. Ing. Dr. Tech. Komal Chenthamara

Professional Experience

2020 – currentExternal lab member at FungiG – research group of Irina S. Druzhinina and Feng Cai in China
2019 – 2020In statutory maternal protection and then maternity leave
2015 – 2018Project Assistant (FWF) (PhD student)
 E166-05-2 – Research Group for Microbiology and Applied Genomics, Research Area Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria

Education

2018Doctoral programme, TU Wien (mit auszeichnung bestanden), Ph.D. Thesis (November 16, 2018): “Using comparative genomics to link phenotypes to genotypes of the mycotrophic fungus Trichoderma
2015Masters in Biotechnology and Bioanalytics, TU Wien, Vienna, Austria. Master Thesis: “Evolution of mycoparasitism in Hypocreales through phylogenomic approach
2011 – 2012B2 level -German, Österreichische Orient Gesellschaft, Vienna, Austria
2006 – 2010Bachelor of Technology (B-Tech) in Biotechnology, SRM University, Chennai, Tamil Nadu, India

Special Trainings

2018Trainee at the Bioinformatics unit (BIU), German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
2018Fungal Genomics Workshop, The DOE JGI Genomics of Energy and Environment Meeting, San Francisco, California, USA
2017Fungal Genomics Workshop, The DOE JGI Genomics of Energy and Environment Meeting, Walnut Creek, California, USA
KBase Workshop, The DOE JGI Genomics of Energy and Environment Meeting, Walnut Creek, California, USA
2013Intern in Research Group for Microbiology and Applied Genomics, TU Wien, TU Wien, Vienna, Austria
2013Training in Communication, BEST, Board of European Students of Technology, Vienna, Austria
2013Training in Time Management, BEST, Board of European Students of Technology, Vienna, Austria
2012Intern in Research Group for Bioprocess Technology, TU Wien, Vienna, Austria
2009IELTS (International English Language Testing System), Chennai, Tamil Nadu, India

Prizes and Awards

2017TU Wien Christiana HÖRBIGER Preis – Preis zur Förderung der internationalen Mobilität von Nachwuchswissenschaftler_innen
2016TU Wien Short-term grants for participation in conferences for PhD-students

Skills

Microbiological techniques and microscopy: axenic cultures, microbial diagnostics by DNA barcoding, fungal morphology, microbial cultivations, and phenotype microarrays. Basic molecular biological techniques for fungi and bacteria.

Molecular evolutionary analyses such as multiloci phylogenetics, phylogenomics, lateral gene transfer tests (T-Rex, Notung), natural selection pressure analyses, DNA barcoding, and protein modeling.

Basic skills in genomics (sequence similarity search, manual gene annotation), basic skills in the analyses of NGS data

Descriptive and multivariate exploratory statistical techniques(Statistica, Tableau, UpSet)

Bitmap and vector graphic skills for illustrations (CorelDraw, Affinity Designer)

Experience with citation tools like Zotero and EndNote

Experience with WorkFlow softwares like Geneious, CLC Bio

Experience with GitHub

Experience with Microsoft 365 and Acrobat

Curator of TUCIM (TU Wien Collection of Industrial Microorganisms)- A collection of over 7350 species and their respective DNAs.

Responsible for the introduction of lab techniques to new group members

Responsible for safety-training of all group members

Organized regular group meetings

Member of Journal club, – an initiative of young PostDoc researchers and Ph.D. students. A gathering dedicated to the discussion of the most paradigm-changing scientific discoveries in biotechnology and applied microbiology

Teaching Experience

2016 – 2018Lecturer for the course 166.648 “Biology and genetics of industrial microorganisms”, master Program Technical Chemistry (Biotechnology and Bioanalytics), TU Wien 
2016 – 2018Teaching Assistant for the mandatory course 166.231 “Applied Bioinformatics Lab”, master Program Technical Chemistry Biotechnology and Bioanalytics, TU Wien
2015 – 2018Tutor for mandatory laboratory course 166.222 “Biochemistry and Biotechnology”, bachelor program Technical Chemistry, TU Wien
2014Assistant for the mandatory laboratory course 166.193 “Microbiology”, master Program Technical Chemistry Biotechnology and Bioanalytics, TU Wien

Language Skills

English                                                         Fluent

German                                                       Basic

Hindi and Malayalam                           Mother-tongues

Interests / Hobbies

Reading comics

DIY skin and hair care

Baking

List of Publications

Christian P. Kubicek

Christian P. Kubicek, Vienna, 2018

Christian P. Kubicek is a retired Professor for Biotechnology and Microbiology at the University of Technology in Vienna (Austria). His scientific work concentrated on both basic and applied research on filamentous fungi with most emphasis on those from the genus Trichoderma and Aspergillus. These studies comprised enzymology and protein chemistry, metabolic regulation, microbial ecology, functional gene characterization, and all “omics” approaches towards the improvement of fungal strains used in industry and agriculture by science-driven strategies. His work is documented in more than 300 original papers in peer-reviewed journals, as well as many patents and books, and was distinguished by several international honors.

Christian P. Kubicek pioneered and most advanced Trichoderma’s genomics by making the first and most significant comparative genomic studies for this genus (below). Being the first Chair of the International Commission on Trichoderma Taxonomy (now ICTT, that time ISTH), Christian was among the first scientists who implemented the DNA Barcoding and Genealogical Concordance Phylogenetic Species Recognition concept in Trichoderma taxonomy. Irina worked together with Christian for ten years from 2002 until his retirement in 2013. We highly appreciate the still ongoing cooperation with Christian on Trichoderma genetics, genomics and systems biology.

Selected publications:

Kubicek, C.P., Steindorff, A.S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F., Kopchinskiy, A.G., Kubicek, E.M., Kuo, A., Baroncelli, R., Sarrocco, S., Noronha, E.F., Vannacci, G., Shen, Q.*, Grigoriev, I.V., Druzhinina, I.S.*, 2019. Evolution and comparative genomics of the most common Trichoderma speciesBMC Genomics 20.

Druzhinina, I.S., V. Seidl-Seiboth, A. Herrera-Estrella, B.A. Horwitz, C.M. Kenerley, E. Monte, P.K. Mukherjee, S. Zeilinger, I.V. Grigoriev and C.P. Kubicek, Trichoderma: the genomics of opportunistic success (vol 9, pg 749, 2011). Nature Reviews Microbiology, 2011. 9(12): p. 896-896 doi: 10.1038/nrmicro2689. PubMed PMID: WOS:000297255800016.

Kubicek, C.P., A. Herrera-Estrella, V. Seidl-Seiboth, D.A. Martinez, I.S. Druzhinina, M. Thon, S. Zeilinger, S. Casas-Flores, B.A. Horwitz and P.K. Mukherjee, Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology, 2011. 12(4): p. R40 doi.org/10.1186/gb-2011-12-4-r40.

Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, et al. (2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet 14(4): e1007322. https://doi.org/10.1371/journal.pgen.1007322

Druzhinina, I.S., E.M. Kubicek and C.P. Kubicek, Several steps of lateral gene transfer followed by events of ‘birth-and-death’ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster. BMC Evolutionary Biology, 2016. 16: p. 269. doi: 10.1186/s12862-016-0834-6. PubMed PMID: PMC5182515.

Druzhinina, I.S. and C.P. Kubicek, Genetic engineering of Trichoderma reesei cellulases and their production. Microb Biotechnol, 2017 doi: 10.1111/1751-7915.12726. PubMed PMID: 28557371.

de Man, T.J.B., J.E. Stajich, C.P. Kubicek, C. Teiling, K. Chenthamara, L. Atanasova, I.S. Druzhinina, N. Levenkova, S.S.L. Birnbaum, S.M. Barribeau, B.A. Bozick, G. Suen, C.R. Currie and N.M. Gerardo, Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proceedings of the National Academy of Sciences of the United States of America, 2016. 113(13): p. 3567-3572 doi: 10.1073/pnas.1518501113.

Druzhinina, I.S. and C.P. Kubicek, Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. Advances in Applied Microbiology, 2016. 95: p. 69-147 doi: 10.1016/bs.aambs.2016.02.001.

Druzhinina, I.S., A.G. Kopchinskiy, E.M. Kubicek and C.P. Kubicek, A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. Biotechnology for Biofuels, 2016. 9: p. 75 doi: 10.1186/s13068-016-0488-z.

Atanasova, L., S. Le Crom, S. Gruber, F. Coulpier, V. Seidl-Seiboth, C.P. Kubicek and I.S. DruzhininaComparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC genomics, 2013. 14(1): p. 121 doi: 10.1186/1471-2164-14-121.