Comparative analysis of complete mitochondrial genome sequences from two geographically distinct Heterosigma akashiwo (Raphidophyceae) strains

Karol, Kenneth G.; Jacobs, Michael A.; Zhou, Yang; Sims, Elizabeth H.; Gillett, Will D.; Cattolico, Rose Ann

doi:10.1127/1438-9134/2010/0136-0261

Cited by 4 publications

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“…We recently completed the sequencing of the full-length mtDNA of four H. akashiwo strains, H93616, Ha00_17, HaTj01 and NEPCC522 [27] ( figure 1 and table 2). For systematic comparison, we identified the ORFs on the mtDNA of the four newly sequenced strains and reannotated the previously sequenced strains, CCMP452 and NIES293 [28], based on the strain Y annotations [29]. The sequences and configurations of the ORFs with defined functions were well preserved in all of the strains, except for the absence of rbs4 in CCMP452 (figure 1).…”

Section: Resultsmentioning

confidence: 99%

A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

et al. 2017

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Geographical distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g. recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming alga, We compared the entire mitochondrial genome sequences of seven strains from Japanese and North American coastal waters and identified a hypervariable segment. The region codes for a hypothetical protein with no defined function, and its variations between Japanese and North American isolates were prominent, while the sequences were more conserved among Japanese strains and North American isolates. Comparison of the sequence in isolates obtained from different geographical points in the Northern Hemisphere revealed that the sequence variations largely correlated with latitude and longitude (i.e. Pacific/Atlantic oceans). Our results demonstrate the usefulness of the sequence in determining the phylogeographic history of .

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Section: Resultsmentioning

confidence: 99%

A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

et al. 2017

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“…; Karol et al. ). Our relative rate analyses of these organelle sequences , which are ~ 39 kb (mtDNA) and ~ 160 kb (ptDNA) , revealed similar trends to those observed for E. huxleyi (Table ).…”

Section: Resultsmentioning

confidence: 98%

“…; Karol et al. ). Nucleotide divergences were calculated with DnaSP v5.10.01 and MEGA5 (Librado and Rozas ; Tamura et al.…”

Section: Methodsmentioning

confidence: 98%

Twenty‐Fold Difference in Evolutionary Rates between the Mitochondrial and Plastid Genomes of Species with Secondary Red Plastids

Smith

Keeling

2012

J Eukaryotic Microbiology

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Within plastid-bearing species, the relative rates of evolution between mitochondrial and plastid genomes are poorly studied, but for the few lineages in which they have been explored, including land plants and green algae, the mitochondrial DNA mutation rate is nearly always estimated to be lower than or equal to that of the plastid DNA. Here, we show that in protists from three distinct lineages with secondary, red algal-derived plastids, the opposite is true: their mitochondrial genomes are evolving 5-30 times faster than their plastid genomes, even when the plastid is nonphotosynthetic. These findings have implications for understanding the origins and evolution of organelle genome architecture and the genes they encode.

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“…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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Comparative analysis of complete mitochondrial genome sequences from two geographically distinct Heterosigma akashiwo (Raphidophyceae) strains

Cited by 4 publications

References 0 publications

A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo

Twenty‐Fold Difference in Evolutionary Rates between the Mitochondrial and Plastid Genomes of Species with Secondary Red Plastids

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

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