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The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.

ABSTRACT: The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.

SUBMITTER: Palenik B

PROVIDER: S-EPMC1863510 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature

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The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.

Palenik Brian B Grimwood Jane J Aerts Andrea A Rouzé Pierre P Salamov Asaf A Putnam Nicholas N Dupont Chris C Jorgensen Richard R Derelle Evelyne E Rombauts Stephane S Zhou Kemin K Otillar Robert R Merchant Sabeeha S SS Podell Sheila S Gaasterland Terry T Napoli Carolyn C Gendler Karla K Manuell Andrea A Tai Vera V Vallon Olivier O Piganeau Gwenael G Jancek Séverine S Heijde Marc M Jabbari Kamel K Bowler Chris C Lohr Martin M Robbens Steven S Werner Gregory G Dubchak Inna I Pazour Gregory J GJ Ren Qinghu Q Paulsen Ian I Delwiche Chuck C Schmutz Jeremy J Rokhsar Daniel D Van de Peer Yves Y Moreau Hervé H Grigoriev Igor V IV

Proceedings of the National Academy of Sciences of the United States of America 20070425 18

The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms actin ...[more]

PMID: 17460045

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Project description:The bicolor Asiatic hybrid lily cultivar "Tiny Padhye" is an attractive variety because of its unique color pattern. During its bicolor tepal development, the upper tepals undergo a rapid color change from green to white, while the tepal bases change from green to purple. However, the molecular mechanisms underlying these changes remain largely uncharacterized. To systematically investigate the dynamics of the lily bicolor tepal transcriptome during development, we generated 15 RNA-seq libraries from the upper tepals (S2-U) and basal tepals (S1-D, S2-D, S3-D, and S4-D) of Lilium "Tiny Padhye." Utilizing the Illumina platform, a total of 295,787 unigenes were obtained from 713.12 million high-quality paired-end reads. A total of 16,182 unigenes were identified as differentially expressed genes during tepal development. Using Kyoto Encyclopedia of Genes and Genomes pathway analysis, candidate genes involved in the anthocyanin biosynthetic pathway (61 unigenes), and chlorophyll metabolic pathway (106 unigenes) were identified. Further analyses showed that most anthocyanin biosynthesis genes were transcribed coordinately in the tepal bases, but not in the upper tepals, suggesting that the bicolor trait of "Tiny Padhye" tepals is caused by the transcriptional regulation of anthocyanin biosynthetic genes. Meanwhile, the high expression level of chlorophyll degradation genes and low expression level of chlorophyll biosynthetic genes resulted in the absence of chlorophylls from "Tiny Padhye" tepals after flowering. Transcription factors putatively involved in the anthocyanin biosynthetic pathway and chlorophyll metabolism in lilies were identified using a weighted gene co-expression network analysis and their possible roles in lily bicolor tepal development were discussed. In conclusion, these extensive transcriptome data provide a platform for elucidating the molecular mechanisms of bicolor tepals in lilies and provide a basis for similar research in other closely related species.

Dataset Information

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.

Publications

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation.

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