@article {Lema2019731,
	title = {Inter- and Intra-Specific Transcriptional and Phenotypic Responses of Pseudo-nitzschia under Different Nutrient Conditions},
	journal = {Genome Biology and Evolution},
	volume = {11},
	number = {3},
	year = {2019},
	note = {cited By 1},
	pages = {731-747},
	publisher = {Oxford University Press},
	abstract = {Untangling thefunctionalbasis of divergencebetweenclosely relatedspecies is a steptowardunderstanding speciesdynamicswithin communities at both the evolutionary and ecological scales. We investigated cellular (i.e., growth, domoic acid production, and nutrient consumption) and molecular (transcriptomic analyses) responses to varying nutrient concentrations across several strains belonging to three species of the toxic diatomgenus Pseudo-nitzschia. Threemain resultswere obtained. First, strains fromthe same species displayed similar transcriptomic, but not necessarily cellular, responses to the experimental conditions. It showed the importance of considering intraspecific diversity to investigate functional divergence between species. Second, a major exception to the first findingwas a strain recently isolated fromthe natural environment and displaying contrasting gene expression patterns related to cell motility and domoic acid production. This result illustrated the profound modifications thatmay occurwhen transferring a cell fromthe natural to the in vitro environment and asks for future studies to better understand the influence of culture duration and life cycleon expression patterns. Third, transcriptomic responsesweremore similarbetween the two speciesdisplaying similar ecology in situ, irrespective of the genetic distance. This was especially true formolecular responses related to TCA cycle, photosynthesis, and nitrogen metabolism. However, transcripts related to phosphate uptake were variable between species. It highlighted the importance of considering both overall genetic distance and ecological divergence to explain functional divergence between species. {\textcopyright} The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.},
	keywords = {analogs and derivatives, Biological Evolution, comparative study, Diatom, Diatoms, Domoic acid, evolution, kainic acid, Metabolism, Multigene Family, Nutrients, Phenotype, Physiology},
	issn = {17596653},
	doi = {10.1093/gbe/evz030},
	url = {https://academic.oup.com/gbe/article/11/3/731/5332980},
	author = {Lema, Kimberley A. and Metegnier, G. and Qu{\'e}r{\'e}, J. and Latimier, Marie and Agn{\`e}s Youenou and Lambert, Christophe and Juliette Fauchot and Le Gac, Mickael and Costantini, M.}
}
@article {3394,
	title = {The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development.},
	journal = {Gene},
	volume = {538},
	year = {2014},
	month = {2014 Mar 15},
	pages = {164-75},
	abstract = {<p>Jumonji (Jmj) proteins are histone demethylases, which control the identity of stem cells. Jmj genes were characterized from plants to mammals where they have been implicated in the epigenetic regulation of development. Despite the Pacific oyster Crassostrea gigas representing one of the most important aquaculture resources worldwide, the molecular mechanisms governing the embryogenesis and reproduction of this lophotrochozoan species remain poorly understood. However, annotations in the C. gigas EST library suggested the presence of putative Jumonji genes, raising the question of the conservation of this family of histone demethylases in the oyster. Using Primer walking, 5{\textquoteright}-RACE PCR and in silico analyses, we characterized nine Jumonji orthologues in the oyster, called Cg-Jmj, bearing conserved domains critical for putative histone demethylase activity. Phylogenic analyses revealed that oyster Jumonji cluster into two distinct groups: {\textquoteright}single-domain Jmj{\textquoteright} and {\textquoteright}multi-domain Jmj{\textquoteright}, and define 8 subgroups corresponding to each cognate orthologues in metazoans. RT-qPCR investigations showed specific regulations of Cg-Jmj mRNAs during the early development and along the reproduction cycle. Furthermore, in situ and in toto hybridizations indicate that oyster Jumonji genes are transcribed mostly within the gonad in adult oysters whereas they display a ubiquitous expression during embryonic and larval development. Our study demonstrates the presence of nine Jumonji orthologues in the oyster C. gigas. Their domain conservation and their expression profile suggest an implication during reproduction and development, questioning about the epigenetic regulation by histone methylation in lophotrochozoans.</p>
},
	keywords = {Animals, Base Sequence, Conserved Sequence, Crassostrea, Evolution, Molecular, Gametogenesis, Gene Expression Regulation, Developmental, Jumonji Domain-Containing Histone Demethylases, Molecular Sequence Data, Multigene Family, RNA, Messenger},
	issn = {1879-0038},
	doi = {10.1016/j.gene.2013.12.016},
	author = {Alexandre Fellous and Pascal Favrel and Guo, Ximing and Guillaume Rivi{\`e}re}
}
