@article {cho_genomic_2024,
	title = {Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses},
	journal = {PLOS Genetics},
	volume = {20},
	number = {4},
	year = {2024},
	note = {Publisher: Public Library of Science},
	pages = {e1011218},
	abstract = {Symbiomonas scintillans Guillou et Chr{\'e}tiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC247, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.},
	keywords = {Eukaryota, Gene prediction, genomics, metagenomics, RCC24, RCC257, Shotgun sequencing, Transcriptome analysis, Viral genomics, Whole genome amplification},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1011218},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011218},
	author = {Cho, Anna and Lax, Gordon and Livingston, Samuel J. and Masukagami, Yumiko and Naumova, Mariia and Millar, Olivia and Husnik, Filip and Keeling, Patrick J.}
}
@article {yung_diversity_2022,
	title = {Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species},
	journal = {Journal of Marine Science and Engineering},
	volume = {10},
	number = {2},
	year = {2022},
	note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {feb},
	pages = {240},
	abstract = {The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.},
	keywords = {Biogeography, evolution, genomics, mamiellophyceae, metagenomics, microalgae{\textendash}virus interactions, phycoDNAvirus, RCC809},
	issn = {2077-1312},
	doi = {10.3390/jmse10020240},
	url = {https://www.mdpi.com/2077-1312/10/2/240},
	author = {Yung, Charmaine C. M. and Rey Redondo, Elvira and Sanchez, Fr{\'e}d{\'e}ric and Yau, Sheree and Piganeau, Gwenael}
}
@article {akita_providing_2022,
	title = {Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {168},
	year = {2022},
	month = {mar},
	pages = {107408},
	abstract = {In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.},
	keywords = {Ectocarpales, genomics, Heterokontophytes, Phaeoexplorer, Phaeophyceae, RCC4962, RCC7086, RCC7088, RCC7090, RCC7092, RCC7094, RCC7096, RCC7098, RCC7101, RCC7104, RCC7107, RCC7108, RCC7109, RCC7112, RCC7115, RCC7116, RCC7117, RCC7120, RCC7123, RCC7124, RCC7125, RCC7127, RCC7129, RCC7131, RCC7134, RCC7137, RCC7138, RCC7139, stramenopiles},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2022.107408},
	url = {https://www.sciencedirect.com/science/article/pii/S1055790322000215},
	author = {Akita, Shingo and Vieira, Christophe and Hanyuda, Takeaki and Rousseau, Florence and Cruaud, Corinne and Couloux, Arnaud and Heesch, Svenja and Cock, J. Mark and Kawai, Hiroshi}
}
@article {Arsenieff2019,
	title = {First viruses infecting the marine diatom guinardia delicatula},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {January},
	year = {2019},
	note = {tex.mendeley-tags: RCC1000,RCC2023,RCC3046,RCC3083,RCC3093,RCC3101,RCC4657,RCC4659,RCC4660,RCC4667,RCC4834,RCC5154,RCC5777,RCC5778,RCC5779,RCC5780,RCC5781,RCC5782,RCC5783,RCC5784,RCC5785,RCC5787,RCC5788,RCC5789,RCC5790,RCC5792,RCC5793,RCC5794,RCC80},
	month = {jan},
	keywords = {diatoms, genomics, host-virus dynamics, RCC1000, RCC2023, RCC3046, RCC3083, RCC3093, RCC3101, RCC4657, RCC4659, RCC4660, RCC4667, RCC4834, RCC5154, RCC5777, RCC5778, RCC5779, RCC5780, RCC5781, RCC5782, RCC5783, RCC5784, RCC5785, RCC5787, RCC5788, RCC5789, RCC5790, RCC5792, RCC5793, RCC5794, RCC80, single-stranded RNA viruses, Western English Channel},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.03235},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03235/full},
	author = {Arsenieff, Laure and Simon, Nathalie and Rigaut-jalabert, Fabienne and Le Gall, Florence and Chaffron, Samuel and Corre, Erwan and Com, Emmanuelle and Bigeard, Estelle and Baudoux, Anne-claire}
}
@article {Cheng2018,
	title = {10KP: A phylodiverse genome sequencing plan},
	journal = {GigaScience},
	volume = {7},
	number = {3},
	year = {2018},
	pages = {1{\textendash}9},
	keywords = {10kp, 12 february 2018, 2018, 4, accepted, access article distributed under, and reproduction in any, attribution license, biodiversity, by, c the author, creative commons, creativecommons, Distribution, genome sequencing, genomics, http, licenses, medium, mgiseq, open community, org, phylogenomics, PLANTS, press, published by oxford university, received, s, samples, the terms of the, this is an open, which permits unrestricted reuse},
	issn = {2047-217X},
	doi = {10.1093/gigascience/giy013},
	url = {https://academic.oup.com/gigascience/article/7/3/1/4880447},
	author = {Cheng, Shifeng and Melkonian, Michael and Smith, Stephen A and Brockington, Samuel and Archibald, John M and Delaux, Pierre-Marc and Li, Fay-Wei and Melkonian, Barbara and Mavrodiev, Evgeny V and Sun, Wenjing and Fu, Yuan and Yang, Huanming and Soltis, Douglas E and Graham, Sean W and Soltis, Pamela S and Liu, Xin and Xu, Xun and Wong, Gane Ka-Shu}
}
@article {Wheeler2015,
	title = {Evolution of alternative biosynthetic pathways for vitamin C following plastid acquisition in photosynthetic eukaryotes},
	journal = {eLife},
	volume = {4},
	year = {2015},
	note = {ISBN: 8196242115 tex.mendeley-tags: RCC299},
	pages = {1{\textendash}25},
	abstract = {Ascorbic acid (vitamin C) is an enzyme co-factor in eukaryotes that also plays a critical role in protecting photosynthetic eukaryotes against damaging reactive oxygen species derived from the chloroplast. Many animal lineages, including primates, have become ascorbate auxotrophs due to the loss of the terminal enzyme in their biosynthetic pathway, L-gulonolactone oxidase (GULO). The alternative pathways found in land plants and Euglena use a different terminal enzyme, L-galactonolactone dehydrogenase (GLDH). The evolutionary processes leading to these differing pathways and their contribution to the cellular roles of ascorbate remain unclear. Here we present molecular and biochemical evidence demonstrating that GULO was functionally replaced with GLDH in photosynthetic eukaryote lineages following plastid acquisition. GULO has therefore been lost repeatedly throughout eukaryote evolution. The formation of the alternative biosynthetic pathways in photosynthetic eukaryotes uncoupled ascorbate synthesis from hydrogen peroxide production and likely contributed to the rise of ascorbate as a major photoprotective antioxidant.},
	keywords = {ascorbate, evolutionary biology, Galdieria, genomics, L-gulonolactone oxidase, plant biology, Porphyra, RCC299, vitamin C},
	issn = {2050084X},
	doi = {10.7554/eLife.06369},
	author = {Wheeler, Glen and Ishikawa, Takahiro and Pornsaksit, Varissa and Smirnoff, Nicholas}
}
@article {Biller2014,
	title = {Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus},
	journal = {Scientific Data},
	volume = {1},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	month = {sep},
	pages = {1{\textendash}11},
	abstract = {The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity{\textemdash}both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.},
	keywords = {Environmental microbiology, genomics, rcc, RCC?o?dd},
	issn = {2052-4463},
	doi = {10.1038/sdata.2014.34},
	url = {http://www.nature.com/articles/sdata201434},
	author = {Biller, Steven J. and Berube, Paul M. and Berta-Thompson, Jessie W. and Kelly, Libusha and Roggensack, Sara E. and Awad, Lana and Roache-Johnson, Kathryn H. and Ding, Huiming and Giovannoni, Stephen J. and Rocap, Gabrielle and Moore, Lisa R. and Chisholm, Sallie W. and H. and Ding, Huiming and Giovannoni, Stephen J. and Moore, Lisa R. and Chisholm, Sallie W.}
}
@article {Gobler2011,
	title = {Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {108},
	number = {11},
	year = {2011},
	note = {ISBN: 0027-8424 tex.mendeley-tags: RCC,rcc},
	pages = {4352{\textendash}4357},
	abstract = {Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.},
	keywords = {brown-tide blooms, comparative genomics, eutrophication, evolution, genome, genomics, long-island, marine-phytoplankton, multidrug, proteins, proteome, rcc, repeat, responses, san-francisco bay, signal-transduction, transporters},
	doi = {10.1073/pnas.1016106108},
	author = {Gobler, C J and Berry, D L and Dyhrman, S T and Wilhelm, S W and Salamov, A and Lobanov, A V and Zhang, Y and Collier, J L and Wurch, L L and Kustka, A B and Dill, B D and Shah, M and VerBerkmoes, N C and Kuo, A and Terry, A and Pangilinan, J and Lindquist, E A and Lucas, S and Paulsen, I T and Hattenrath-Lehmann, T K and Talmage, S C and Walker, E A and Koch, F and Burson, A M and Marcoval, M A and Tang, Y Z and LeCleir, G R and Coyne, K J and Berg, G M and Bertrand, E M and Saito, M A and Gladyshev, V N and Grigoriev, I V}
}
@article {Vaulot2008,
	title = {The diversity of small eukaryotic phytoplankton ({\textexclamdown}3 {\textmu}m) in marine ecosystems},
	volume = {32},
	number = {5},
	year = {2008},
	note = {Publication Title: FEMS microbiology reviews tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {795{\textendash}820},
	abstract = {Small cells dominate photosynthetic biomass and primary production in many marine ecosystems. Traditionally, picoplankton refers to cells {\textexclamdown} or =2 microm. Here we extend the size range of the organisms considered to 3 microm, a threshold often used operationally in field studies. While the prokaryotic component of picophytoplankton is dominated by two genera, Prochlorococcus and Synechococcus, the eukaryotic fraction is much more diverse. Since the discovery of the ubiquitous Micromonas pusilla in the early 1950s, just over 70 species that can be {\textexclamdown}3 microm have been described. In fact, most algal classes contain such species. Less than a decade ago, culture-independent approaches (in particular, cloning and sequencing, denaturing gradient gel electrophoresis, FISH) have demonstrated that the diversity of eukaryotic picoplankton is much more extensive than could be assumed from described taxa alone. These approaches revealed the importance of certain classes such as the Prasinophyceae but also unearthed novel divisions such as the recently described picobiliphytes. In the last couple of years, the first genomes of photosynthetic picoplankton have become available, providing key information on their physiological capabilities. In this paper, we discuss the range of methods that can be used to assess small phytoplankton diversity, present the species described to date, review the existing molecular data obtained on field populations, and end up by looking at the promises offered by genomics.},
	keywords = {2008, diversity, genomics, Marine ecosystems, Micro-algae, picoplankton, rcc, sbr?hyto$_\textrmd$ipo, taxonomy},
	author = {Vaulot, Daniel and Eikrem, Wenche and Viprey, Manon and Moreau, Herv{\'e}}
}
@article {palenik_genome_2006,
	title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {103},
	number = {36},
	year = {2006},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	pages = {13555{\textendash}13559},
	abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.},
	keywords = {cyanobacteria, genomics, Marine, RCC1086},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.0602963103},
	url = {https://www.pnas.org/content/103/36/13555},
	author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L. and Myers, Garry S. and Heidelberg, John F. and Badger, Jonathan H. and Madupu, Ramana and Nelson, William C. and Brinkac, Lauren M. and Dodson, Robert J. and Durkin, A. Scott and Daugherty, Sean C. and Sullivan, Stephen A. and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T.}
}
