The Complete Mitochondrial Genome Sequence of the Haptophyte Emiliania huxleyi and its Relation to Heterokonts

Puerta, María Virginia Sánchez

doi:10.1093/dnares/11.1.1

Cited by 54 publications

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“…UGA codons are most likely assigned for tryptophan instead of termination signal (Table S1), as reported previously 25 . This type of mt genetic code was reported in other members of Prymnesiophyceae, one of the two classes of Haptophyta 26 - 28 . We detected 26 tRNA genes and a set of small and large subunits of rRNAs; No 5S rRNA gene was identified.…”

Section: Resultssupporting

confidence: 82%

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An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

Nishimura¹,

Kamikawa²,

Hashimoto³

et al. 2014

Mobile Genetic Elements

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Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.

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Section: Resultssupporting

confidence: 82%

“…and D. lutheri are representatives of two major classes, Prymnesiophyceae and Pavlovaphyceae, in Haptophyta, respectively. This scenario suggests that multiple intron losses occurred in the cox1 genes of Emiliania huxleyi , 28 , 29 members of the genus Phaeocystis , 12 , 26 and Isochrysis galbana 30 …”

Section: Resultsmentioning

confidence: 99%

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

Nishimura¹,

Kamikawa²,

Hashimoto³

et al. 2014

Mobile Genetic Elements

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“…: NC_000894.1; Maslov et al 1992). Homologs of the plastid core ribosomal set are encoded by many Stramenopiles (including Oomycetes) and Cryptophytes (Hauth et al 2005; Kim et al 2008), but in the Haptophyte Emiliania huxleyi in a reduced manner only (Sanchez Puerta et al 2004; fig. 1).…”

Section: Resultsmentioning

confidence: 99%

Massively Convergent Evolution for Ribosomal Protein Gene Content in Plastid and Mitochondrial Genomes

Maier

Zauner

Woehle

et al. 2013

Genome Biology and Evolution

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Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force.

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“…As in other sequenced haptophytes, NCBI translation table 4 [24] was used, where UGA codes tryptophan rather than a termination codon. Comparison of the genomic content among all published haptophyte genomes ( E. huxleyi [25, 26]: [GenBank:AY342361, JN022704]; P. antarctica [27]: [GenBank:JN131834, JN131835]; P. globosa [27]: [GenBank:KC967226]; P. lutheri : [GenBank:HQ908424]) indicate that 14 energy and metabolism genes are conserved in all examined taxa. All haptophyte genomes also contain an identical complement of five ribosomal proteins ( rps 3 , rps 8 , rps 12 , rps 14 , and rpl16 ) except for P. antarctica and P. globosa which are missing the rps 8 or the rps 8 and rps 14 genes respectively (Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…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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The Complete Mitochondrial Genome Sequence of the Haptophyte Emiliania huxleyi and its Relation to Heterokonts

Cited by 54 publications

References 0 publications

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyteChrysochromulinasp. NIES-1333

Massively Convergent Evolution for Ribosomal Protein Gene Content in Plastid and Mitochondrial Genomes

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

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