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

Department 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 2014 and 2015:

Harel A, Karkar S, Cheng S, Falkowski PG, and Bhattacharya D. 2015. Deciphering primordial cyanobacterial genome functions from protein network analysis. Current Biology.
doi

Bhattacharya D, Qiu H, Price DC, Yoon HS. 2015. Why we need more algal genomes. J Phycol. [epub ahead of print]
doi

Levitan O, Dinamarca J, Zelzion E, Lun DS, Guerra LT, Kim MK, Kim J, Van Mooy BA, Bhattacharya D, Falkowski PG. 2015. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. Proc Natl Acad Sci USA 112(2):412-417.
doi

Rockwell NC, Lagarias JC, and Bhattacharya D. 2014. Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes. Front Ecol Evol 2:66.
doi

Rockwell NC, Duanmu D, Martin SS, Bachy C, Price DC, Bhattacharya D, Worden AZ, and Lagarias JC. 2014. Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci USA 111:3871-3876.
doi

Foflonker F, Price DC, Qiu H, Palenik B, Wang S, and Bhattacharya D. 2014. Genome of the halotolerant green alga Picochlorum SENEW3 reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiology in press.
doi

Harel A, Bromberg Y, Falkowski PG, and Bhattacharya D. 2014. Evolutionary history of redox metal-binding domains across the tree of life. Proceedings of the National Academy of Sciences USA 111:7042-7047.
doi

Perrineau MM, Zelzion E, Gross J, Price DC, Boyd J, and Bhattacharya D. 2014. Evolution of salt tolerance in a laboratory reared population of Chlamydomonas reinhardtii. Environmental Microbiology 16:1755-1766.
doi

Perrineau MM, Gross J, Zelzion E, Price DC, Levitan O, Boyd J, and Bhattacharya D. 2014. Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii. PLoS One 9:e92533.
doi

Roy RS, Price DC, Schliep A, Cai G, Korobeynikov A, Yoon HS, Yang EC, and Bhattacharya D. 2014. Single cell genome analysis of an uncultured heterotrophic stramenopile. Nature Scientific Reports 4:4780.
doi

Roy RS, Bhattacharya D, Schliep A. 2014. Turtle: Identifying frequent k-mers with cache-efficient algorithms. Bioinformatics 30(14):1950-1957.
doi

Kim KM, Park J-H, Bhattacharya D, Yoon HS. 2014. Applications of next-generation sequencing to unravelling the evolutionary history of algae. International Journal of Systematic and Evolutionary Microbiology 64(2):333-345.
doi

Cheng S, Price DC, Karkar S, Bhattacharya D. 2014. Exploring biotic interactions within protist cell populations using network methods. J Eukaryot Microbiol 61(4):399-403.
doi

Polashock J, Zelzion E, Fajardo D, Zalapa J, Georgi L, Bhattacharya D, Vorsa N. 2014. The American cranberry: first insights into the whole genome of a species adapted to bog habitat. BMC Plant Biol 14:165.
doi

Cheng S, Karkar S, Bapteste E, Yee N, Falkowski P, Bhattacharya D. 2014. Sequence similarity network reveals the imprints of major diversification events in the evolution of microbial life. Frontiers in Ecology and Evolution 2:72.
doi

DePriest MS, Bhattacharya D, López-Bautista JM. 2014. The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of red algae. Biol Bull 227(2):191-200.


Book Chapters

Bhattacharya D, Price D, Chan CX, Gross J, Steiner JM, Löffelhardt W. 2014. Analysis of the Genome of Cyanophora paradoxa: An Algal Model for Understanding Primary Endosymbiosis, Endosymbiosis, pp.135-148, Springer. Vienna

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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