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

image of Slim Karkar Post-doc Slim Karkar publishes a paper in PNAS on the evolution of metabolic connectivity in algae
Slim's collaborative paper shows that plastid transporters are mostly of host nuclear
origin with some key components provided by foreign bacteria through horizontal gene
transfer (HGTs). This work supports the hypothesis that creation of new organelles is directed
by the host cell with the endosymbiont making a smaller contribution to host-plastid connectivity.

image of Arik Harel Post-doc Arik Harel lands a faculty job in Israel
Arik is now situated in the Department of Vegetable Research, Institute of Plant Sciences, Volcani Center, in Bet Dagan. This follows on a successful stay at Rutgers where he worked in the Yana Bromberg and Bhattacharya labs on a collaborative project led by Paul Falkowski on the origin and evolution of redox enzymes in the earliest microbial life forms.

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. 2015 Feb;17(2):412-26. Epub 2014 Jul 24 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

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 2015:

Karkar S, Facchinelli F, Price DC, Weber APM, and Bhattacharya D. 2015. Metabolic connectivity as a driver of host and endosymbiont integration. Proc Natl Acad Sci U S A. 2015 Mar 30.
doi

J. Luo, H. Qiu, G. Cai, N. E. Wagner, D. Bhattacharya & N. Zhang. 2015. Phylogenomic analysis uncovers the evolutionary history of nutrition and infection mode in rice blast fungus and other Magnaporthales. Scientific Reports 5, Article number: 9448.
doi

Harel A, Karkar S, Cheng S, Falkowski PG, and Bhattacharya D. 2015. Deciphering primordial cyanobacterial genome functions from protein network analysis. Current Biology, Volume 25, Issue 5, 2 March 2015, Pages R192-R193
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

MM Perrineau, DC Price, G Mohr, D Bhattacharya. 2015. Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium. MM Perrineau, DC Price, G Mohr, D Bhattacharya. 2015. PeerJ [in press].


H Qiu, DC Price, EC Yang, HS Yoon, D Bhattacharya. 2015. Evidence of ancient genome reduction in red algae (Rhodophyta). Journal of Phycology [in press]. "Algae Highlights" upcoming.


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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