A protein similarity network obtained by translating genes from a reference genome (Bigelowiella natans) and 5 single-cell genome datasets from heterotrophic Paulinella (Rhizaria)

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Debashish Bhattacharya

Rutgers University

Department of Ecology, Evolution, and Natural Resources

Institute of Marine and Coastal Sciences

Faculty Member (Evolutionary/Comparative
Genetics): Faculty of 1000

102 Foran Hall, 59 Dudley Rd
New Brunswick, NJ 08901- 8520, USA
Tel: (848) 932-6218
Fax: (732) 932-8746
Email: Bhattacharya@AESOP.Rutgers.edu

Bhattacharya Lab News and Events

NSF Fuels IGERT program-funded graduate student Fatima Foflonker publishes a paper about the genome of the halotolerant green alga Picochlorum that provides insights into how horizontal gene transfer can lead to adaptation to stressful environments. This alga also offers promise for biofuel and other biotechnological applications. The work was done in collaboration with the group of Brian Palenik at the Scripps Institution of Oceanography, University of California, San Diego.
Foflonker F, Price DC, Qiu H, Palenik B, Wang S, Bhattacharya D. 2014. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiol. Jun 25. [Epub ahead of print] PMID: 24965277 doi

image of Rajat S. Roy Read about the newest developments in single cell genomics (SCG) in this invited review at Biochemist Magazine. Graduate student Rajat S. Roy who is co-supervised by Debashish and Alex Schliep in Computer Science has led the SCG research in our group.
Debashish Bhattacharya, Rajat S. Roy, Dana C. Price and Alexander Schliep. 2014. Single-cell genomics of marine plankton. Biochemist Magazine – Journal of the Biochemical Society, 36:1 February 16–22. pdf
Marie-Mathilde Perrineau publishes the lab's first two papers on algal experimental evolution.
Perrineau MM, Gross J, Zelzion E, Price DC, Levitan O, Boyd J, Bhattacharya D. 2014. Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii.
PLoS One: March 21, 2014. doi| pdf
Perrineau MM, Zelzion E, Gross J, Price DC, Boyd J, Bhattacharya D. 2014. Evolution of salt tolerance in a laboratory reared population of Chlamydomonas reinhardtii. Environ Microbiol. 2013 Dec 24. doi

Genome cooperative bioinformaticist Udi ZelZion contributes to papers in PNAS and Current Biology in collaboration with the Falkowski group.
Jeana L. Drake, Tali Mass, Liti Haramaty, Ehud Zelzion, Debashish Bhattacharya, and Paul G. Falkowski. Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. PNAS 2013 110 (10) 3788-3793; published ahead of print February 19, 2013. doi| pdf

Tali Mass, Jeana L. Drake, Liti Haramaty, J. Dongun Kim, Ehud Zelzion, Debashish Bhattacharya, and Paul G. Falkowski. Cloning and Characterization of Four Novel Coral Acid-Rich Proteins that Precipitate Carbonates In Vitro. Current Biology, Volume 23, Issue 12, 17 June 2013, Pages 1126–1131. doi | RU news release

Arik Harel publishes paper in PNAS about the metal-binding domains in the tree of life.
image of Arik Harel Harel A, Bromberg Y, Falkowski PG, Bhattacharya D. 2014. The evolutionary history of redox metal-binding domains across the tree of life. Proc Natl Acad Sci USA doi.

image of protein similarity networkImage of a protein similarity network obtained by translating genes from a reference genome (Bigelowiella natans) and 5 single-cell genome datasets from heterotrophic Paulinella.

Article in Smithsonianmag.com explains Bhattacharya lab findings on the origin of photosynthesis.
How Did Plants Develop Photosynthesis?
Smithsonian magazine, March 2013. By Henry Fountain.

Bhattacharya Lab Papers in 2013:

S Nyati, D Bhattacharya, S Werth, R Honegger. Phylogenetic analysis of LSU and SSU rDNA group I introns of lichen photobionts associated with the genera Xanthoria and Xanthomendoza (Teloschistaceae, lichenized Ascomycetes). Journal of Phycology 49 (6), 1154-1166, 11 Nov 2013.

Huan Qiu, Dana C. Price, Andreas P.M. Weber, Fabio Facchinelli, Hwan Su Yoon, and Debashish Bhattacharya. Accepted. Assessing the bacterial contribution to the plastid proteome. Trends in Plant Science. 16 Oct 2013. S1360-1385(13)00198-2.

Huan Qiu, Dana C. Price, Andreas P.M. Weber, Valérie Reeb, Eun Chan Yang, Jun Mo Lee, Su Yeon Kim, Hwan Su Yoon, and Debashish Bhattacharya, Adaptation through horizontal gene transfer in the cryptoendolithic red alga Galdieria phlegrea. Current Biology. 7 Oct 2013; 23(19):R865-6.

Ugo Cenci, Malika Chabi, Mathieu Ducatez, Catherine Tirtiaux, Jennifer Nirmal-Raj, Yoshinori Utsumi, Daiki Kobayashi, Satoshi Sasaki, Eiji Suzuki, Yasunori Nakamura, Jean-Luc Putaux, Xavier Roussel, Amandine Durand-Terrasson, Debashish Bhattacharya, Anne-Sophie Vercoutter-Edouart, Emmanuel Maes, Maria Cecilia Arias, Monica Palcic, Lyann Sim, Steven G. Ball and Christophe Colleoni. 2013. Convergent Evolution of Polysaccharide Debranching Defines a Common Mechanism for Starch Accumulation in Cyanobacteria and Plants. The Plant Cell October 2013 tpc.113.118174

C. X. Chan, F. L. Baglivi, C. E. Jenkins, and D. Bhattacharya. Foreign gene recruitment to the fatty acid biosynthesis pathway in diatoms. Mobile Genetic Elements 3, e27313; September/October 2013.

Huan Qiu, Hwan Su Yoon, and Debashish Bhattacharya. 2013. Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes. Frontiers in Plant Science, 19 September 2013.

D Bhattacharya, KN Pelletreau, DC Price, KE Sarver, ME Rumpho. Genome analysis of Elysia chlorotica egg DNA provides no evidence for horizontal gene transfer into the germ line of this kleptoplastic mollusc. Molecular biology and Evolution 30(8), 1843–1852. 11 July 2013.

Depriest MS, Bhattacharya D, López-Bautista JM. 2013. The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One. 19 Jul 2013;8(7):e68246.

Skorupa DJ, Reeb V, Castenholz RW, Bhattacharya D, McDermott TR. 2013. Cyanidiales diversity in Yellowstone National Park Lett Appl Microbiol. 19 Jul 2013. [Epub ahead of print]

Debashish contributes to the first completed genome of a dinoflagellate.
Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, Takeuchi T, Hisata K, Tanaka M, Fujiwara M, Hamada M, Seidi A, Fujie M, Usami T, Goto H, Yamasaki S, Arakaki N, Suzuki Y, Sugano S, Toyoda A, Kuroki Y, Fujiyama A, Medina M, Coffroth MA, Bhattacharya D, Satoh N. 2013. Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure. Curr Biol. 9 Jul 2013.

Two recent papers from our lab on genomics of algae.
Bhattacharya D, Price DC, Chan CX, Qiu H, Rose N, Ball S, Weber AP, Cecilia Arias M, Henrissat B, Coutinho PM, Krishnan A, Zäuner S, Morath S, Hilliou F, Egizi A, Perrineau MM, Yoon HS. 2013. Genome of the red alga Porphyridium purpureum. Nat Commun. 17 Jun 2013;4:1941.
Jeferson Gross, Sana Wajid, Dana C. Price, Ehud Zelzion, Junyi Li, Cheong Xin Chan, Debashish Bhattacharya. 2013. Evidence for Widespread Exonic Small RNAs in the Glaucophyte Alga Cyanophora paradoxa. PLoS ONE 8(7): e67669.
doi| pdf

Drake JL, Massa T, Haramaty L, Zelzion E, Bhattacharya D, Falkowski PG.
Reply to Ramos-Silva et al.: Regarding coral skeletal proteome. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):E2147-8.

Bhattacharya, D., D.C. Price, C. Bicep, E. Bapteste, M. Sarwade, V.D. Rajah, and H. S. Yoon. 2013. Identification of a marine cyanophage in a protist single cell metagenome assembly. Journal of Phycology Volume 49, Issue 1, pages 207–212, February.

Facchinelli, F., M. Pribil, U. Oster, N. Ebert, D. Bhattacharya, D. Leister, and A. Weber. 2013. Proteomic analysis of the Cyanophora paradoxa muroplast provides clues on early events in plastid endosymbiosis. Planta: 2013 Feb;237(2):637-51, epub ahead of print

Ball, S.G., A. Subtil, D. Bhattacharya, A. Moustafa, A.P.M. Weber, L. Gehre, C. Colleoni, M.-C. Arias, U. Cenci, and D. Dauvillée. 2013. Metabolic effectors secreted by bacterial pathogens: essential facilitators of plastid endosymbiosis? The Plant Cell. Jan;25(1):7-21

Select Papers:

schematic image of cyanophora paradoxaPrice et al. publish paper in Science
Price D.C., Chan C.X., Yoon H.S., Yang E.C., Qiu H., Weber A.P., Schwacke R., Gross J., Blouin N.A., Lane C., Reyes-Prieto A., Durnford D.G., Neilson J.A., Lang F.B., Gertraud Burger G., Steiner J.M., Löffelhardt W., Meuser J.E., Posewitz M.C., Ball S., Arias M.C., Henrissat B., Coutinho P.M., Rensing S.A., Symeonidi A., Doddapaneni H., Green B.R., Rajah V.D., Boore J., and Bhattacharya D. 2012.Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science 17 February 2012: Vol. 335 no. 6070 pp. 843-847
doi|full text|Nature news|ScientificAmerican.com|biotechnologie.de [German]|RU news|Cyanophora BLAST and data download
See commentary by Spiegel FW. 2012. Contemplating the first Plantae. Science 17 February 2012: Vol. 335 no. 6070 pp. 809-810 |doi

Bhattacharya, Price, Yoon et al. publish a paper in Scientific Reports
This paper shows that cyanobacteria that gave rise to a novel plastid in Paulinella chromatophora are eaten by its phagotrophic sister Paulinella ovalis and that this food is the source of horizontally transferred genes in P. ovalis. The results, for the first time, connect food, foreign gene transfer, and primary endposymbiosis in a single lineage.
Bhattacharya D., Price D.C., Yoon H.S., Yang E.C., Poulton N.J., Andersen R.A., Das S.P. Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis. doi

Funding sources: National Science Foundation logo Department of Energy logo Gordon and Betty Moore Foundation logo JGI logo NIH logo
This material is based upon work supported by the National Science Foundation. Any opinions, findings,
and conclusions or recommendations expressed in this material are those of the author(s) and do not
necessarily reflect the views of the NSF.

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