EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

Lanier, William P.; Moustafa, Ahmed; Bhattacharya, Debashish; Comeron, Josep M.

doi:10.1371/journal.pone.0002171

Cited by 29 publications

(19 citation statements)

References 42 publications

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“…In contrast to metazoans, high-expression genes in plants and unicellular eukaryotes have longer intron sequence than low-expression genes (Vinogradov 2001;Ren et al, 2006). On the other hand, positive correlation between intron density and gene expression level has been proposed in metazoans, plants, and unicellular eukaryotes (Comeron 2004;Fahey and Higgins, 2007;Lanier et al, 2008). So, highexpression genes in metazoans have a tendency to have shorter intron sequence and higher intron density.…”

Section: Discussionmentioning

confidence: 99%

Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

Ogino

Tsuneki

Furuya

2010

Gene

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Section: Discussionmentioning

confidence: 99%

Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

Ogino

Tsuneki

Furuya

2010

Gene

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“…The O. tauri NOS sequence contains the characteristic oxygenase and reductase domains joined by a CaM binding domain. O. lucimarinus, another species of the Ostreococcus genus, also contains a NOS gene, the expression of which was validated by EST analysis (Lanier et al, 2008). Whereas the O. lucimarinus NOS sequence has just one intron (Lanier et al, 2008), that of the predicted O. tauri NOS sequence (Derelle et al, 2006) NO production was determined by the oxyhemoglobin method.…”

Section: Nos Is Present In Photosynthetic Organismsmentioning

confidence: 99%

“…O. lucimarinus, another species of the Ostreococcus genus, also contains a NOS gene, the expression of which was validated by EST analysis (Lanier et al, 2008). Whereas the O. lucimarinus NOS sequence has just one intron (Lanier et al, 2008), that of the predicted O. tauri NOS sequence (Derelle et al, 2006) NO production was determined by the oxyhemoglobin method. Activity was measured for 3 min at 258C in reaction containing 20 mM oxyhemoglobin, 5 mM DTT, 100 mM L-Arg, 1 mM NADPH, 10 mM CaCl 2 , 10 mM CaM, 100 mM H 4 B, 100 units/mL catalase, and 0.5 mM O. tauri NOS or commercial iNOS (Sigma-Aldrich).…”

Section: Nos Is Present In Photosynthetic Organismsmentioning

confidence: 99%

Characterization of a Nitric Oxide Synthase from the Plant Kingdom: NO Generation from the Green Alga Ostreococcus tauri Is Light Irradiance and Growth Phase Dependent

et al. 2010

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The search for a nitric oxide synthase (NOS) sequence in the plant kingdom yielded two sequences from the recently published genomes of two green algae species of the Ostreococcus genus, O. tauri and O. lucimarinus. In this study, we characterized the sequence, protein structure, phylogeny, biochemistry, and expression of NOS from O. tauri. The amino acid sequence of O. tauri NOS was found to be 45% similar to that of human NOS. Folding assignment methods showed that O. tauri NOS can fold as the human endothelial NOS isoform. Phylogenetic analysis revealed that O. tauri NOS clusters together with putative NOS sequences of a Synechoccocus sp strain and Physarum polycephalum. This cluster appears as an outgroup of NOS representatives from metazoa. Purified recombinant O. tauri NOS has a K m for the substrate L-Arg of 12 6 5 mM. Escherichia coli cells expressing recombinant O. tauri NOS have increased levels of NO and cell viability. O. tauri cultures in the exponential growth phase produce 3-fold more NOS-dependent NO than do those in the stationary phase. In O. tauri, NO production increases in high intensity light irradiation and upon addition of L-Arg, suggesting a link between NOS activity and microalgal physiology.

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“…EST analyses are especially useful when knowledge about the genome under investigation is limited, such as in the case of the green microalgae, Scherffelia dubia [23], Mesostigma viride [24], Ostreococcus lucimarinus [25], Nannochloropsis oculata [26] and Dunaliella salina [27]. Catalogs of ESTs are also valuable resources for the development of molecular tools and analysis methods.…”

mentioning

confidence: 99%

Expressed sequence tags analysis revealing the taxonomic position and fatty acid biosynthesis in an oleaginous green microalga, Myrmecia incisa Reisigl (Trebouxiophyceae, Chlorophyta)

Ouyang

et al. 2012

Chin. Sci. Bull.

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cDNA library of Myrmecia incisa H4301 was constructed using λ phage vectors. The library consisted of 1.5×10 6 clones with a recombination rate of 90%, and 1942 clones were randomly sequenced. All 1854 readable expressed sequence tags (ESTs) were clustered into 596 non-redundant sequences (NRSs), among which 126 NRSs were from 1384 ESTs, showing a high redundancy. Among the 596 NRSs, 30 were ribosomal RNA, and 152 significantly matched with those available in NCBI database and JGI Genome Portal, the latter were divided into nine subcategories. Overall, 59 NRSs were involved in photosynthesis, the respiratory electron transport chain, ATP synthesis, oxidation reduction, fatty acid biosynthesis, glucose metabolism, protein metabolism, and small molecular metabolism, suggesting that these genes were abundantly transcribed during energy and substance metabolism. Acyl-carrier protein, ferrodoxin and fatty acid elongase genes obtained from this cDNA library enabled presumption of a possible biosynthesis pathway of ArA in M. incisa. Codon usage analysis of 142 NRSs with 17798 codons in the predicted coding regions showed that the average G+C content level of the total codons was 55.39%, and that of the third position in base trimers was 66.42%, indicating a strong bias toward cytosine and/or guanosine in this algal genome. Among all synonymous codons, NAG was most favored, while NUA was most avoided. Phylogenic trees inferred from ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit genes and the extra partial sequences of 18S rRNA obtained from this library demonstrated that M. incisa belonged to Trebouxiophyceae and was significantly clustered with M. incisa SAG 2007, Lobosphaera tirolensis, M. bisecta, and Parietochloris incisa, but was clearly distant from P. pseudoalveolaris and P. alveolar. Transmission electron microscopy revealed pyrenoids traversed by many parallel thylakoids membranes, while starch grains were only clearly observed when cells were grown under nitrogen stress. Based on combined investigation of the phylogeny and morphological characteristics, it is proposed that M. incisa be kept in the genus Myrmecia in which there might be two parallel groups, one living freely and another symbiotic species.

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EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

Cited by 29 publications

References 42 publications

Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

Unique genome of dicyemid mesozoan: Highly shortened spliceosomal introns in conservative exon/intron structure

Characterization of a Nitric Oxide Synthase from the Plant Kingdom: NO Generation from the Green Alga Ostreococcus tauri Is Light Irradiance and Growth Phase Dependent

Expressed sequence tags analysis revealing the taxonomic position and fatty acid biosynthesis in an oleaginous green microalga, Myrmecia incisa Reisigl (Trebouxiophyceae, Chlorophyta)

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