@article {Limardo2017,
	title = {Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton},
	journal = {Environmental Microbiology},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC715,RCC716,RCC809},
	month = {jun},
	keywords = {RCC1105, RCC715, RCC716, RCC809},
	issn = {14622912},
	doi = {10.1111/1462-2920.13812},
	url = {http://doi.wiley.com/10.1111/1462-2920.13812},
	author = {Limardo, Alexander J. and Sudek, Sebastian and Choi, Chang Jae and Poirier, Camille and Rii, Yoshimi M. and Blum, Marguerite and Roth, Robyn and Goodenough, Ursula and Church, Matthew J. and Worden, Alexandra Z.}
}
@article {Simmons2016,
	title = {Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the eastern north pacific ocean},
	journal = {Applied and Environmental Microbiology},
	volume = {82},
	number = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	month = {mar},
	pages = {1693{\textendash}1705},
	abstract = {Eukaryotic algae within the picoplankton size class (<=2 ??m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus , during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 {\texttimes} 10 5 and 3.37 {\texttimes} 10 5 cells ? ml -1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 {\texttimes} 10 5 cells ? ml -1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 {\textpm} 327 18S rRNA gene copies ? ml -1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos ) and BII. These share 82\% {\textpm} 6\% nucleotide identity across homologs, while the Ostreococcus spp. share 75\% {\textpm} 8\%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 - and low-affinity NH 4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.},
	keywords = {2016, rcc},
	issn = {0099-2240},
	doi = {10.1128/AEM.02730-15},
	url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02730-15},
	author = {Simmons, Melinda P. and Sudek, Sebastian and Monier, Adam and Limardo, Alexander J. and Jimenez, Valeria and Perle, Christopher R. and Elrod, Virginia A. and Pennington, J. Timothy and Worden, Alexandra Z.},
	editor = {Schloss, P. D.}
}
@article {Simmons2015,
	title = {Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas populations.},
	journal = {Molecular biology and evolution},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	month = {may},
	abstract = {Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, recently new families of spliceosomal introns that are repeated hundreds of times in individual genomes have been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements (ILEs) in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence-absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where this alga is increasing in abundance due to climate change. The same two families were detected in metagenomic data from Antarctica - a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our work illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation and global distribution of this sentinel marine alga.},
	keywords = {rcc},
	issn = {1537-1719},
	doi = {10.1093/molbev/msv122},
	url = {http://mbe.oxfordjournals.org/cgi/content/long/msv122v1},
	author = {Simmons, Melinda P and Bachy, Charles and Sudek, Sebastian and van Baren, Marijke J and Sudek, Lisa and Ares, Manuel and Worden, Alexandra Z}
}
@article {Duanmu2014,
	title = {Marine algae and land plants share conserved phytochrome signaling systems},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {111},
	number = {44},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {15827{\textendash}15832},
	abstract = {Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte ({\textexclamdown}2 {\textmu}m cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.},
	keywords = {Micromonas, rcc},
	doi = {10.1073/pnas.1416751111},
	url = {http://www.pnas.org/content/111/44/15827.abstract},
	author = {Duanmu, Deqiang and Bachy, Charles and Sudek, Sebastian and Wong, Chee-Hong and Jimenez, Valeria and Rockwell, Nathan C and Martin, Shelley S and Ngan, Chew Yee and Reistetter, Emily N and van Baren, Marijke J and Price, Dana C and Wei, Chia-Lin and Reyes-Prieto, Adrian and Lagarias, J Clark and Worden, Alexandra Z}
}
@article {Monier2013,
	title = {Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity},
	journal = {The ISME journal},
	volume = {7},
	year = {2013},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {1764{\textendash}1774},
	keywords = {horizontal transfer, inteins, invasive elements, metagenomics, Micromonas, polymorphic introns, rcc, viridiplantae},
	doi = {10.1038/ismej.2013.70},
	url = {http://dx.doi.org/10.1038/ismej.2013.70 10.1038/ismej.2013.70},
	author = {Monier, Adam and Sudek, Sebastian and Fast, Naomi M and Worden, Alexandra Z}
}
@article {Demir-Hilton2011,
	title = {Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus},
	journal = {The ISME journal},
	volume = {5},
	year = {2011},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC745},
	pages = {1095{\textendash}1107},
	keywords = {rcc, RCC745},
	doi = {10.1038/ismej.2010.209},
	url = {http://dx.doi.org/10.1038/ismej.2010.209 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2010209s1.html http://www.nature.com/ismej/journal/v5/n7/full/ismej2010209a.html},
	author = {Demir-Hilton, Elif and Sudek, Sebastian and Cuvelier, Marie L and Gentemann, Chelle L and Zehr, Jonathan P and Worden, Alexandra Z}
}
