@article {Lu2016,
	title = {Transcriptomic profiling of Alexandrium fundyense during physical interaction with or exposure to chemical signals from the parasite Amoebophrya.},
	journal = {Molecular ecology},
	volume = {25},
	number = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC3037},
	pages = {1294{\textendash}307},
	abstract = {Toxic microalgae have their own pathogens, and understanding the way in which these microalgae respond to antagonistic attacks may provide information about their capacity to persist during harmful algal bloom events. Here, we compared the effects of the physical presence of the parasite Amoebophrya sp. and exposure to waterborne cues from cultures infected with this parasite, on gene expression by the toxic dinoflagellates, Alexandrium fundyense. Compared with control samples, a total of 14,882 Alexandrium genes were differentially expressed over the whole-parasite infection cycle at three different time points (0, 6 and 96 h). RNA sequencing analyses indicated that exposure to the parasite and parasitic waterborne cues produced significant changes in the expression levels of Alexandrium genes associated with specific metabolic pathways. The observed upregulation of genes associated with glycolysis, the tricarboxylic acid cycle, fatty acid β-oxidation, oxidative phosphorylation and photosynthesis suggests that parasite infection increases the energy demand of the host. The observed upregulation of genes correlated with signal transduction indicates that Alexandrium could be sensitized by parasite attacks. This response might prime the defence of the host, as indicated by the increased expression of several genes associated with defence and stress. Our findings provide a molecular overview of the response of a dinoflagellate to parasite infection.},
	keywords = {2016, Animals, Dinoflagellida, Dinoflagellida: genetics, Dinoflagellida: parasitology, Gene Expression Profiling, Harmful Algal Bloom, Host-Parasite Interactions, Metabolic Networks and Pathways, Microalgae, Microalgae: genetics, Microalgae: parasitology, Parasites, Parasites: chemistry, RCC3037, RNA, Sequence Analysis, Signal Transduction, Transcriptome},
	issn = {1365-294X},
	doi = {10.1111/mec.13566},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/26841307},
	author = {Lu, Yameng and Wohlrab, Sylke and Groth, Marco and Gl{\"o}ckner, Gernot and Guillou, Laure and John, Uwe}
}
@article {Waters2007,
	title = {Evolutionary analysis of the small heat shock proteins in five complete algal genomes},
	journal = {Journal of Molecular Evolution},
	volume = {65},
	number = {2},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {162{\textendash}174},
	abstract = {Small heat shock proteins (sHSPs) are chaperones that are crucial in the heat shock response but also have important nonstress roles within the cell. sHSPs are found in all three domains of life (Bacteria, Archaea, and Eukarya). These proteins are particularly diverse within land plants and the evolutionary origin of the land plant sHSP families is still an open question. Here we describe the identification of 17 small sHSPs from the complete genome sequences of five diverse algae: Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ostreococcus lucimarinus, Ostreococcus tauri, and Thalassiosira pseudonana. Our analysis indicates that the number and diversity of algal sHSPs are not correlated with adaptation to extreme conditions. While all of the algal sHSPs identified are members of this large and important superfamily, none of these sHSPs are members of the diverse land plant sHSP families. The evolutionary relationships among the algal sHSPs and homologues from bacteria and other eukaryotes are consistent with the hypothesis that the land plant chloroplast and mitochondrion sHSPs did not originate from the endosymbionts of the chloroplast and mitochondria. In addition the evolutionary history of the sHSPs is very different from that of the HSP70s. Finally, our analysis of the algal sHSPs sequences in light of the known sHSP crystal structures and functional data suggests that the sHSPs possess considerable structural and functional diversity.},
	keywords = {*Evolution, *Genome, algae, Algae/classification/*genetics, Algal Proteins/*genetics, Amino Acid Sequence, Animals, Chlamydomonas reinhardtii/genetics, Diatoms/genetics, Green/genetics, Heat-Shock Proteins, Molecular, Molecular Sequence Data, phylogeny, Protein, rcc, Red/genetics, Sequence Alignment, Sequence Analysis, Small/*genetics, Species Specificity},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17684698},
	author = {Waters, E R and Rioflorido, I}
}
@article {Khan2007,
	title = {Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny},
	journal = {Molecular Biology and Evolution},
	volume = {24},
	number = {8},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1832{\textendash}1842},
	abstract = {Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other{\textquoteright}s closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.},
	keywords = {*DNA Replication, *Gene Transfer, *Genome, Bacteria/*genetics, Cryptophyta/*genetics, DNA, evolution, genes, Horizontal, Molecular, phylogeny, Plant, Plastids/*genetics, rcc, Sequence Analysis, symbiosis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17522086},
	author = {Khan, H and Parks, N and Kozera, C and Curtis, B A and Parsons, B J and Bowman, S and Archibald, J M}
}
@article {Fawley2000,
	title = {Phylogenetic analyses of 18S rDNA sequences reveal a new coccoid lineage of the Prasinophyceae (Chlorophyta)},
	journal = {Journal of Phycology},
	volume = {36},
	number = {2},
	year = {2000},
	note = {ISBN: 0022-3646 Publisher: Phycological Soc Amer Inc tex.address: 810 East 10Th St, Lawrence, KS 66044, USA tex.mendeley-tags: RCC,rcc},
	pages = {387{\textendash}393},
	abstract = {Phylogenetic analyses of 18S rDNA sequences from 25 prasinophytes, including 10 coccoid isolates, reveals that coccoid organisms are-found in at least three prasinophyte lineages, The coccoid Ostreococcus tauri is included in the Mamiellales lineage and Pycnococcus provasolii is allied with the f dfellate Pseudoscourfieldia marina. A previously undescribed prasinophyte lineage is comprised of the coccoid Prasinococcus cf. Capsulatus (CCMP 1407) and other isolates tentatively identified as Prasinococcussp. (CCMP 1202, CCMP 1614, and CCMP 1194), as well as three unnamed coccoids (CCMP 1193, CCMP 1413, and CCMP 1220). No flagellate organisms are known from this lineage. Organisms of this new lineage share some characteristics of both the Pycnococcaceae and the Mamiellales, although relationships among these separate lineages were not supported by bootstrap analyses. An additional unnamed coccoid isolate (CCMP 1205) is separate from all major prasinophyte lineages. The analyses did not resolve the relationships among the major prasinophyte lineages, although they support previous conclusions that the Prasinophyceae are not monophyletic.},
	keywords = {ALGAL CAROTENOIDS, coccoid algae, EVOLUTIONARY TREES, Gen, GREEN-ALGAE, LIGHT-HARVESTING COMPLEX, MICROMONADOPHYCEAE CHLOROPHYTA, Prasinophyceae, PRASINOXANTHIN, PSEUDOSCOURFIELDIA-MARINA, rcc, RDNA, RIBOSOMAL-RNA SEQUENCES, Sequence Analysis, sp-nov},
	doi = {10.1046/j.1529-8817.2000.99105.x},
	author = {Fawley, M W and Yun, Y and Qin, M}
}
