Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana

Secq, Marie-Pierre Oudot–Le; Green, Beverley R.

doi:10.1016/j.gene.2011.02.001

Cited by 71 publications

(61 citation statements)

References 45 publications

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“…The homoplasmic nature of organelle genomes was consistent with the mitochondrial genome of allopolyploid yeast (Sipiczki, 2008). It should be noted that the mitochondrial genome assembly is incomplete, possibly due to the large inverted repeats commonly found in the mitochondrial genomes of diatoms (Oudot-Le Secq and Green, 2011). The sequenced region of the mitochondrial genome with no long repeat sequences is 38.6 kb, similar in size to the nonrepeat regions of the mitochondrial genomes of T. pseudonana (38.8 kb with 5.0-kb repeat region) and P. tricornutum (42.0 kb with 35.4-kb repeat region).…”

Section: Genome Sequencing and Assemblysupporting

confidence: 65%

Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome

et al. 2015

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Oleaginous photosynthetic organisms such as microalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy. However, the metabolic mechanisms driving high-rate lipid production in these oleaginous organisms remain unclear, thus impeding efforts to improve productivity through genetic modifications. We analyzed the genome and transcriptome of the oleaginous diatom Fistulifera solaris JPCC DA0580. Next-generation sequencing technology provided evidence of an allodiploid genome structure, suggesting unorthodox molecular evolutionary and genetic regulatory systems for reinforcing metabolic efficiencies. Although major metabolic pathways were shared with nonoleaginous diatoms, transcriptome analysis revealed unique expression patterns, such as concomitant upregulation of fatty acid/triacylglycerol biosynthesis and fatty acid degradation (b-oxidation) in concert with ATP production. This peculiar pattern of gene expression may account for the simultaneous growth and oil accumulation phenotype and may inspire novel biofuel production technology based on this oleaginous microalga.

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Section: Genome Sequencing and Assemblysupporting

confidence: 65%

Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome

et al. 2015

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“…The three large tandem repeats are separated from each other within the repeat region by spacers (consisting of a C-A-A pattern). Interestingly, this direct repeat arrangement is strikingly similar to the larger (35 kb) repeat structure found in the diatom Phaeodactylum tricornutum [29]. The cryptophytes, Hemiselmis andersenii and Rhodomonas salina , and the chlorophytes Pedinomonas minor and Acutodesmus obliquus also contain large tandem repeat regions (>4 kb) that differ from the minimal repeat embellishment seen in most mitochondrial genomes of other algae.…”

Section: Resultsmentioning

confidence: 53%

“…Unfortunately, the use of short read, high throughput sequencing techniques do not easily facilitate solving these complex repeat structures. The first E. huxleyi mitochondrial genome published in 2004 [25], the stramenopile, Heterosigma akashiwo [30], as well as the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana [29] utilized fosmid sequencing, that supported assembly and primer walking for the resolution of longer repeats.…”

Section: Resultsmentioning

confidence: 99%

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

et al. 2014

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BackgroundHaptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation.ResultsThe complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent ‘CheY-like’ two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes - algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs) - a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade.ConclusionThe Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-604) contains supplementary material, which is available to authorized users.

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“…We were unable to bridge the final gap in both genomes, despite numerous attempts using different long-range PCR protocols under different conditions, buffer systems, and primers. This is most likely due to the presence of a large intervening sequence, as is common to other diatom mitochondrial genomes (for example the 35 kb insertion in P. tricornutum [29]), and/or to the presence of repetitive elements that may form complex secondary structures that inhibit PCR. Since all the other sequenced diatom mitochondrial genomes map as circular molecules [28], [29], it is likely that the D. baltica and K. foliaceum genomes share the same configuration.…”

Section: Resultsmentioning

confidence: 99%

“…Sequenced diatom mitochondrial genomes range from 43 to 77 kbp, have a circular map, and encode about 60 genes. While generally compact, they usually feature one large intergenic spacer composed of repetitive sequences (from nearly 5 kbp in the centric diatom Thalassiosira pseudonana and the araphid pennate diatom Synedra acus, to about 35 kbp in the raphid pennate diatom Phaeodactylum tricornutum) [28], [29]. In contrast, dinoflagellate mitochondria encode only three protein-coding genes (cox1, cox3 and cob) and many fragments of ribosomal RNA (rRNA), and these appear to be organised on multiple chromosomes that may be linear, and which are greatly expanded in number and include numerous incomplete copies or pseudogenes along with highly dispersed short or long stretches of non-coding and repetitive sequences [30]–[32].…”

Section: Introductionmentioning

confidence: 99%

Tertiary Endosymbiosis in Two Dinotoms Has Generated Little Change in the Mitochondrial Genomes of Their Dinoflagellate Hosts and Diatom Endosymbionts

et al. 2012

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BackgroundMitochondria or mitochondrion-derived organelles are found in all eukaryotes with the exception of secondary or tertiary plastid endosymbionts. In these highly reduced systems, the mitochondrion has been lost in all cases except the diatom endosymbionts found in a small group of dinoflagellates, called ‘dinotoms’, the only cells with two evolutionarily distinct mitochondria. To investigate the persistence of this redundancy and its consequences on the content and structure of the endosymbiont and host mitochondrial genomes, we report the sequences of these genomes from two dinotoms.Methodology/Principal FindingsThe endosymbiont mitochondrial genomes of Durinskia baltica and Kryptoperidinium foliaceum exhibit nearly identical gene content with other diatoms, and highly conserved gene order (nearly identical to that of the raphid pennate diatom Fragilariopsis cylindrus). These two genomes are differentiated from other diatoms' by the fission of nad11 and by an insertion within nad2, in-frame and unspliced from the mRNA. Durinskia baltica is further distinguished from K. foliaceum by two gene fusions and its lack of introns. The host mitochondrial genome in D. baltica encodes cox1 and cob plus several fragments of LSU rRNA gene in a hugely expanded genome that includes numerous pseudogenes, and a trans-spliced cox3 gene, like in other dinoflagellates. Over 100 distinct contigs were identified through 454 sequencing, but intact full-length genes for cox1, cob and the 5′ exon of cox3 were present as a single contig each, suggesting most of the genome is pseudogenes. The host mitochondrial genome of K. foliaceum was difficult to identify, but fragments of all the three protein-coding genes, corresponding transcripts, and transcripts of several LSU rRNA fragments were all recovered.Conclusions/SignificanceOverall, the endosymbiont and host mitochondrial genomes in the two dinotoms have changed surprisingly little from those of free-living diatoms and dinoflagellates, irrespective of their long coexistence side by side in dinotoms.

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Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana

Cited by 71 publications

References 45 publications

Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome

Oil Accumulation by the Oleaginous Diatom Fistulifera solaris as Revealed by the Genome and Transcriptome

The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles

Tertiary Endosymbiosis in Two Dinotoms Has Generated Little Change in the Mitochondrial Genomes of Their Dinoflagellate Hosts and Diatom Endosymbionts

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