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

2017 Papers from the Bhattacharya Lab and Collaborators

Brodie J, Ball SG, Bouget F-Y, Chan CX, De Clerck O, Cock M, Gachon C, Grossman AR, Mock T, Raven J, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D. 2017. Biotic interactions as drivers of algal origin and evolution. New Phytol. (Invited Tansley Review) doi:10.1111/nph.14760

Brawley SH, Blouin NA, Ficko-Blean E, Wheeler GL, Lohr M, Goodson HV, Jenkins JW,  Blaby-Haas CE,  Helliwell KE, Xin Chan Cl, Marriage TK, Bhattacharya D, Klein AS, Badis Y, Brodie , Cao Y, Collén J, Dittam SM, Gachon CMM, Green BR, Karpowicz SJ, Kim JW, Kudahl UJ, Lin S, Michel G, Mittag M, Olson BJSC, Pangilinan JL, Peng Y, Qiu H, Shuh S, Singer JT, Smith AG, Sprecher BN, Wagner V, Wang W, Wang Z-Y, Yan J,  Yarish C, Zäuner-Rieka S, Zhuang Y, Zou Y, Lindquist EA, Grimwood J, Barry KW,  Rokhsar DH, Schmutz J, Stiller JW, Grossman AR, Prochnik SE. 2017. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta). Proc Natl Acad Sci USA. 114:E6361-E6370.

Kim JI, Moore CE, Archibald JM, Bhattacharya D, Yi G, Yoon HS, Shin W. 2017. Evolutionary dynamics of cryptophyte plastid genomes. Genome Biol and Evol. 9:1859-1872.

Qiu H, Zelzion E, Putnam HM, Gates RD, Wagner NE, Adams DK, Bhattacharya D. 2017. Discovery of SCORs: Anciently derived, highly conserved gene-associated repeats in stony corals. Genomics. Jun 17. doi:10.1016/j.ygeno.2017.06.003. [Epub ahead of print]

Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. 2017. The algal revolution. Trends Plant Sci. 22:726-738.

Tripp EA, Zhang N, Schneider H, Huang Y, Mueller GM, Hu Z, Häggblom M, Bhattacharya D. 2017. Reshaping Darwin's tree: impact of the symbiome. Trends Ecol Evol. 32:552-555.

Putnam HM, Adams DK, Zelzion E, Wagner NE, Qiu H, Mass T, Falkowski PG, Gates RD, Bhattacharya D. 2017. Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ. 5:e3319.

Price DC, Bhattacharya D. 2017. Robust Dinoflagellata phylogeny inferred from public transcriptome databases. J Phycol. 53:725-729.

Zhang R, Nowack EC, Price DC, Bhattacharya D, Grossman AR. 2017. Impact of light intensity and quality on chromatophore and nuclear gene expression in Paulinella chromatophora, an amoeba with nascent photosynthetic organelles. Plant J. 90:221-234.

Qiu H, Lee JM, Yoon HS, Bhattacharya D. 2017. Hypothesis: gene-rich plastid genomes in red algae may be an outcome of nuclear genome reduction. J Phycol. 53:715-719.

Cenci U, Bhattacharya D, Weber AP, Colleoni C, Subtil A, Ball SG. 2017. Biotic host-pathogen interactions as major drivers of plastid endosymbiosis. Trends Plant Sci. 22:316-328.

Pandey RS, Saxena G, Bhattacharya D, Qiu H, Azad RK. 2017. Using complementary approaches to identify trans-domain nuclear gene transfers in the extremophile Galdieria sulphuraria (Rhodophyta). J Phycol. 53:7-11.

Honig JA, Zelzion E, Wagner NE, Kubik C, Averello V, Vaiciunas J, Bhattacharya D, Bonos SA, Meyer WA. 2017. Microsatellite identification in perennial ryegrass using next-generation sequencing. Crop Sci. 57:1-10.

Bhattacharya Lab News and Events

Photo: amobae This Little Amoeba Committed Grand Theft – from amoeba to alga through endosymbiosis.
Eva C. M. Nowack, Dana C. Price, Debashish Bhattacharya, Anna Singer, Michael Melkonian, and Arthur R. Grossman. 2016. Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora, PNAS 2016: 1608016113v1-201608016
Rutgers Today | doi

Debashish Bhattacharya and Professor Juliet Brodie from the Natural History Museum in London co-organize a Theo Murphy international scientific meeting from June 8-9, 2016 funded by the Royal Society entitled, "Into the genome: advances in the world of algal genomics." The event will take place at the Kavli Royal Society Centre, Chicheley Hall, Buckinghamshire, United Kingdom.

Photo of a coral reef; Image credit: Anna Roik, King Abdullah University of Science and Technology The Bhattacharya group co-leads a major genomic analysis of reef building corals that was recently published in eLife. The research used information from 20 genomic datasets to understand how stony corals live and have survived for over 240 million years.
Bhattacharya D, Agrawal S, Aranda M, Baumgarten S, Belcaid M, Drake JL, Erwin D, Foret S, Gates RD, Gruber DF, et al. 2016. Comparative genomics explains the evolutionary success of reef-forming corals. eLife. 5:e13288.
Rutgers Today | NSF 360 | doi

Graduate student, Fatima Foflonker, publishes paper in Algal Research exploring the adaptation to salinity shock in a broadly halotolerant Picochlorum species.
Foflonker F, Ananyev G, Qiu H, Morrison A, Palenik B, Dismukes GC, Bhattacharya D. 2016. The unexpected extremophile: Tolerance to fluctuating salinity in the green alga Picochlorum. Algal Res. 16:465-472. doi

image of Huan Qiu Research associate Huan Qiu published a discovery in BMC Biology revealing how the devastating plant pathogens Magnaporthales and Colletotrichum were made in nature.
Huan Qiu, Guohong Cai, Jing Luo, Debashish Bhattacharya, Ning Zhang. Extensive horizontal gene transfers between plant pathogenic fungi. BMC Biol. 2016 May 23;14(1):41. doi

mitochondrial symbiosis Debashish and his colleagues Steven Ball and Andreas Weber propose in their new Perspectives piece in Science magazine that the endosymbioses that led to their formation were made possible by the role of pathogens.

Steven G. Ball, Debashish Bhattacharya, Andreas P. M. Weber, Pathogen to powerhouse. Science 12 Feb 2016: Vol. 351, Issue 6274, pp. 659-660
Summary | Reprint | Full Text | doi

Photo: phylogenetic tree

Research associate Huan Qiu led a study focusing on the question why the terrestrial environment become green and not red, published in the Journal of Phycology.

Huan Qiu, Dana C. Price, Eun Chan Yang, Hwan Su Yoon and Debashish Bhattacharya. 2015. Evidence of ancient genome reduction in red algae (Rhodophyta) doi

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.

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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