Molecular insights into the novel aspects of diatom biology

Scala, Simona; Bowler, Chris

doi:10.1007/pl00000804

Cited by 60 publications

(37 citation statements)

References 43 publications

(47 reference statements)

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“…In spite of their enormous ecological importance, only recently have they begun to attract the attention of molecular biologists (Scala and Bowler, 2001). As a consequence, knowledge of genome size and structure is extremely limited and only a few genes have been isolated.…”

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confidence: 99%

Genome Properties of the Diatom Phaeodactylum tricornutum

et al. 2002

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Diatoms are a ubiquitous class of microalgae of extreme importance for global primary productivity and for the biogeochemical cycling of minerals such as silica. However, very little is known about diatom cell biology or about their genome structure. For diatom researchers to take advantage of genomics and post-genomics technologies, it is necessary to establish a model diatom species. Phaeodactylum tricornutum is an obvious candidate because of its ease of culture and because it can be genetically transformed. Therefore, we have examined its genome composition by the generation of approximately 1,000 expressed sequence tags. Although more than 60% of the sequences could not be unequivocally identified by similarity to sequences in the databases, approximately 20% had high similarity with a range of genes defined functionally at the protein level. It is interesting that many of these sequences are more similar to animal rather than plant counterparts. Base composition at each codon position and GC content of the genome were compared with Arabidopsis, maize (Zea mays), and Chlamydomonas reinhardtii. It was found that distribution of GC within the coding sequences is as homogeneous in P. tricornutum as in Arabidopsis, but with a slightly higher GC content. Furthermore, we present evidence that the P. tricornutum genome is likely to be small (less than 20 Mb). Therefore, this combined information supports the development of this species as a model system for molecular-based studies of diatom biology. The nucleotide sequence data reported has been deposited in GenBank Nucleotide Sequence Database (dbEST section) under accession nos. BI306757 through BI307753.Diatoms are important components of marine phytoplankton, being particularly important for biogeochemical cycling of minerals such as silica, and for global carbon fixation (Werner, 1977;Tréguer et al., 1995). There are well over 250 genera of living diatoms, with perhaps as many as 100,000 species (Round et al., 1990). In toto, they may contribute as much as 25% of the total primary production on earth (Van Den Hoek et al., 1997). These figures illustrate the quantitative significance of diatoms for the functioning of "ecosystem Earth."The success of diatoms is not well understood, although it is known that they are remarkably flexible in adjusting their photosynthetic reactions to allow maximal growth rates over a wide range of light intensities (Falkowski and LaRoche, 1991), and that they may perform C4 photosynthesis (Reinfelder et al., 2000). In spite of their enormous ecological importance, only recently have they begun to attract the attention of molecular biologists (Scala and Bowler, 2001). As a consequence, knowledge of genome size and structure is extremely limited and only a few genes have been isolated. In November 2001, the sequences of less than 70 protein-encoding nuclear genes from diatoms had been deposited in GenBank (GenBank release 126, October 15, 2001).Diatoms are brown algae belonging to the division Heterokonta and are thought to have ar...

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Genome Properties of the Diatom Phaeodactylum tricornutum

et al. 2002

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“…Diatoms (class Bacillariophyceae) are microscopic photosynthetic organisms (Scala & Bowler 2001, Gordon et al 2009) that live in aquatic ecosystems, both marine and freshwater (Gröger et al 2008, Trainer et al 2008. They are the most diverse group of algae, totalling about 200 000 species (Holtermann et al 2010).…”

Section: Introductionmentioning

confidence: 99%

“…They are structurally appealing because their cell walls, the frustules, are composed of amorphous silica. The morphology of the frustules (symmetry, shape, length and valve ornamentation) is used to support taxonomic classification and species identification (Scala & Bowler 2001, Chepurnov et al 2008. The frustules are observed by light microscopy (Chepurnov et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) applied to diatom identification: influence of culturing age

Nicolau¹,

Sequeira²,

Santos³

et al. 2014

Aquat. Biol.

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Diatom identification is based on classical morphological methods focused on frustule shape and ornamentation analysis and possible chain formation. Because many morphological aspects are common to several species, diatom identification and characterisation are timeconsuming and demand significant expertise. Furthermore, the use of advanced microscopy, such as transmission electron microscopy or scanning electron microscopy, is frequently necessary to differentiate these organisms. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) was used to differentiate diatom taxa, and this report presents a preliminary study of the possibility of using this technique to obtain reliable fingerprinting of diatoms in the range of 2 to 20 kDa. Seminavis robusta, Coscinodiscus sp., Thalassiosira sp. and Cyclotella meneghiniana were used. The influence of culture age on reproducibility was studied. MALDI-TOF MS spectra were shown to vary with culturing time, and the need to consider this when setting up experimental standard conditions in the identification of diatoms was clearly established. One of the most important observations was that each diatom strain presented a specific age when the mass spectrum became reproducible. For all S. robusta strains and for C. meneghiniana, this age was 9 d, and for Thalassiosira sp. and Coscinodiscus sp., this age was 13 d. Even with the limitations of culture aging versus spectra reproducibility, MALDI-TOF MS proved to be a useful complementary tool to identify and characterise diatoms at the genus level. However, it was not possible to distinguish different mating types within the same species, as evidenced by the results obtained with S. robusta isolates. KEY WORDS: Diatoms · MALDI-TOF MS · Culture ageResale or republication not permitted without written consent of the publisher

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“…Tremendous advances have been made in understanding the transcriptomes of marine diatoms in culture (Mock et al 2006(Mock et al , 2008Scala and Bowler 2001). These studies have provided insight on environmental adaptation of these organisms and specifically on the functioning of silica metabolism and deposition, a prominent oceanic biogeochemical process.…”

Section: Introductionmentioning

confidence: 99%

Creation of a pilot metatranscriptome library from eukaryotic plankton of a eutrophic bay (Tampa Bay, Florida)

John

Zielinski

Paul

2009

Limnology & Ocean Methods

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Analysis of the suite of genes expressed by natural populations of phytoplankton can potentially elucidate valuable information about the types, cellular activity, and biogeochemical impacts of organisms present in the marine environment. Here we describe the construction of a pilot metatranscriptome library created from eukaryotic planktonic organisms in Tampa Bay, FL, USA. RNA from cells greater than 2 µm was extracted and purified, and poly(A) tailed mRNA was concentrated and amplified using linear amplification chemistry. Amplified RNA was converted to double-stranded cDNA using reverse transcriptase and DNA polymerase I (Klenow fragment) and cloned, and 232 clones were sequenced. Sequences with significant GenBank BLAST homology revealed genes related to photosynthesis and nutrient acquisition, along with general cell functions. In total, 27% of sequenced transcript clones contained significant homology to GenBank sequences, 2% of the total were putatively derived from ribosomal RNA, and 1% were most similar to sequences originating from prokaryotes. About 70% of the identified transcripts were putatively derived from eukaryotic phytoplankton, including diatoms, chlorophytes, and dinoflagellates. Although small in scale, this study provides the basis for future efforts to characterize the metatranscriptome of marine phytoplankton populations.

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Molecular insights into the novel aspects of diatom biology

Cited by 60 publications

References 43 publications

Genome Properties of the Diatom Phaeodactylum tricornutum

Genome Properties of the Diatom Phaeodactylum tricornutum

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) applied to diatom identification: influence of culturing age

Creation of a pilot metatranscriptome library from eukaryotic plankton of a eutrophic bay (Tampa Bay, Florida)

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