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Use of a Deviant Mitochondrial Genetic Code in Yellow-Green Algae as a Landmark for Segregating Members Within the Phylum (1997)

Ehara, Megumi ; Hayashi-Ishimaru, Yasuko ; Inagaki, Yuji ; [et al.]

Springer

Journal of molecular evolution 45 (1997), S. 119 -124

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ISSN: 1432-1432

Keywords: Key words: Deviant genetic code — Eustigmatophyta — Xanthophyta — Cytochrome oxidase subunit I

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract. Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However, due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae, on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla. We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two, Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms, especially when it is considered with the results obtained through a molecular phylogenetic tree.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/PL00006210

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2

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Algae or Protozoa: Phylogenetic Position of Euglenophytes and Dinoflagellates as Inferred from Mitochondrial Sequences (1997)

Inagaki, Yuji ; Hayashi-Ishimaru, Yasuko ; Ehara, Megumi ; [et al.]

Springer

Journal of molecular evolution 45 (1997), S. 295-300

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ISSN: 1432-1432

Keywords: Key words: Mitochondrial COXI gene — Dinoflagellata — Apicomplexa — Kinetoplastida — Euglenophyta — Endosymbiosis — Genetic code — Malarian circle

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract. The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes, but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts are remnants of endosymbiotic algae.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/PL00006233

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A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan (1997)

Hayashi-Ishimaru, Y. ; Ehara, Megumi ; Inagaki, Yuji ; [et al.]

Springer

Current genetics 32 (1997), S. 296-299

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ISSN: 1432-0983

Keywords: Key words Prymnesiophyta ; Deviant genetic code ; Cytochrome c oxidase subunit I ; The codon-capture theory

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The sequence of a representative mitochondrial gene COXI, encoding cytochrome c oxidase subunit I, was determined in five species that cover all the orders of the Prymnesiophyta with the exception of the Pavlovales. Through this analysis, we noticed that the `stop' codon UGA appears frequently and, specifically, at conserved tryptophan (Trp) sites of the gene. We showed these sites were not edited in the corresponding mRNA in one of these species, Isochrysis galbana. Therefore, it is most likely that the UGA codon is used for Trp, and not as a stop codon, in prymnesiophytes. All the analyzed prymnesiophytes made a tight cluster on the COXI phylogenetic tree which includes representative species of green-algae, land plants, yellow-green algae, eustigmatophytes and a red-alga. This suggests a monophyletic origin for the prymnesiophytes. The same deviant genetic code, i.e. UGA for Trp, has also been found in the red-alga, Chondrus crispus. In spite of the fact that this red-alga and the prymnesiophytes, share the same deviant genetic code for Trp, close affinity between the two groups was not statistically supported by the phylogenetic analysis of COXI sequences.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002940050280

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4

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Phylogenetic analysis of diatom coxI genes and implications of a fluctuating GC content on mitochondrial genetic code evolution (2000)

Ehara, Megumi ; Inagaki, Yuji ; Watanabe, Kazuo I. ; [et al.]

Springer

Current genetics 37 (2000), S. 29-33

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ISSN: 1432-0983

Keywords: Key words Bacillariophyta ; Cytochrome c oxidase subunit I ; UGA codon ; GC bias

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract In order to address the relationships among diatom groups and to investigate possible changes in their mitochondrial (mt) genetic codes, we have analyzed a 1.1-kb region of the cytochrome c oxidase subunit I (coxI) gene from eight diverse diatom species. A phylogenetic analysis of these coxI sequences including representative species of the Phaeophyta, Xanthophyta, Eustigmatophyta and Haptophyta showed that the diatoms (Bacillariophyta) formed a well-supported monophyletic group. Of the eight species investigated, four have been classified together as radial centric diatoms based on morphology. However, in our coxI tree, the two radial centrics belonging to the order Thlassiosirales (Skeletonema costatum and Thalassiosira nordenskioldii) were placed as the sister group to the multipolar centric diatoms, while the other two radial centrics (Melosira ambigua and Rhizosolenia setigera) were in another clade. Also, in two species of the Tharassiosirales we found UGA codons that occur at conserved tryptophan (Trp) sites in the coxI sequences, strongly indicating that UGA codes for Trp in these diatoms. No evidence of a deviant genetic code was detected in the other analyzed diatom species. There was no apparent relationship between the nucleotide third-position GC content of mtDNA (based on the sequenced coxI region) and the presence of a deviant genetic code.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s002940050004

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5

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The evolutionary relationships amongst excavates: a concatened protein analysis (2005)

SIMPSON, ALASTAIR G.B. ; INAGAKI, YUJI ; ROGER, ANDREW J.

Oxford, UK : Blackwell Science Inc

The @journal of eukaryotic microbiology 52 (2005), S. 0

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ISSN: 1550-7408

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: Morphological studies and phylogenies of ribosomal RNA, taken together, suggest that excavate protists may be related to each other, but many of the deepest level relationships amongt these organisms remain poorly understood. We have assembled a data set of six slowly evolving nuclear-encoded protein genes that include nine of the 10 recognized excavate groups. Maximum likelihood analyses demonstrate that diplomonads and Carpediemonas than parabasalids are related to each other. They also confirm that Trimastix is specifically related to oxymonads, forming the taxon Preaxostyla. There is strong support for a clade of Euglenozoa, Heterolobsea and jakobids, but, unexpectedly, jakobids and Heterolobosea are robustly recovered as sister taxa. Malawimonas is placed either as sister to Preaxostyla or as sister to the (Euglenozoa, Heterolobosea, jakobid) clade. The original data set strongly supports an association between the (diplomonad, Carpediemonas, parabasalid) clade and Opisthokonts. However, this grouping is not recovered when α-tubulin is excluded from the analysis, suggesting that the signal for this relationship lies within this one protein and might be suspect. All other important nodes in the tree are, by contrast, robust to the removal of any one gene. With α-tubulin excluded, excavates tend to form just two clades, with no strong nodes separating them. Jakobids, with their apparently ancestral bacterial-type mitrochondrial RNA polymerase are nonetheless nested within a clade with normal phage-type RNA polymerases, complicating any understanding of deep-level mitochondrial evolution The position of jakobids also seriously challenges the now well-accepted concept of a taxon Discicristata.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_68.x

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6

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Directionally Evolving Genetic Code: The UGA Codon from Stop to Tryptophan in Mitochondria (1998)

Inagaki, Yuji ; Ehara, Megumi ; Watanabe, Kazuo I. ; [et al.]

Springer

Journal of molecular evolution 47 (1998), S. 378-384

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ISSN: 1432-1432

Keywords: Key words: COXI phylogenetic tree — UGA codon — Deviant genetic code — Directional codon reassignment

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract. For the comprehensive analyses of deviant codes in protistan mitochondria (mt), we sequenced about a 1.1-kb region of a mitochondrial (mt) gene, the cytochrome c oxidase subunit I (coxI) in two chlorarachniophytes, the filose amoeba Euglypha rotunda, the cryptomonad Cryptomonas ovata, the prymnesiophyte (haptophyte) Diacronema vlkianum (Pavlovales), and the diatom Melosira ambigua. As a result of this analysis, we noticed that the UGA codon is assigned to tryptophan (Trp) instead of being a signal for translational termination in two chlorarachniophytes and in E. rotunda. The same type of deviant code was reported previously in animals, fungi, ciliates, kinetoplastids, Chondrus crispus (a red alga), Acanthamoeba castellanii (an amoeboid protozoon), and three of the four prymnesiophyte orders with the exception of the Pavlovales. A phylogenetic analysis based on the COXI sequences of 56 eukaryotes indicated that the organisms bearing the modified code, UGA for Trp, are not monophyletic. Based on these studies, we propose that the ancestral mitochondrion was bearing the universal genetic code and subsequently reassigned the codon to Trp independently, at least in the lineage of ciliates, kinetoplastids, rhodophytes, prymnesiophytes, and fungi. We also discuss how this codon was directionally captured by Trp tRNA.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/PL00006395

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Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis (2020)

Sarai, Chihiro ; Tanifuji, Goro ; Nakayama, Takuro ; [et al.]

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences of the United States of America. 2020; 117(10): 5364-5375. Published 2020 Feb 24. doi: 10.1073/pnas.1911884117.

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Publication Date: 2020-02-24

Description: Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggest that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making it difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which endosymbiont-to-host DNA transfer is on-going and for which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide evidence for the presence of DNA in the two nucleomorphs and the transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both the MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. With the combined evidence, we conclude that the host–endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as models for elucidating organellogenesis.

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

Published by National Academy of Sciences

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Single-cell genomics unveiled a cryptic cyanobacterial lineage with a worldwide distribution hidden by a dinoflagellate host (2019)

Nakayama, Takuro ; Nomura, Mami ; Takano, Yoshihito ; [et al.]

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences of the United States of America. 2019; 116(32): 15973-15978. Published 2019 Jun 24. doi: 10.1073/pnas.1902538116.

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Publication Date: 2019-06-24

Description: Cyanobacteria are one of the most important contributors to oceanic primary production and survive in a wide range of marine habitats. Much effort has been made to understand their ecological features, diversity, and evolution, based mainly on data from free-living cyanobacterial species. In addition, symbiosis has emerged as an important lifestyle of oceanic microbes and increasing knowledge of cyanobacteria in symbiotic relationships with unicellular eukaryotes suggests their significance in understanding the global oceanic ecosystem. However, detailed characteristics of these cyanobacteria remain poorly described. To gain better insight into marine cyanobacteria in symbiosis, we sequenced the genome of cyanobacteria collected from a cell of a pelagic dinoflagellate that is known to host cyanobacterial symbionts within a specialized chamber. Phylogenetic analyses using the genome sequence revealed that the cyanobacterium represents an underdescribed lineage within an extensively studied, ecologically important group of marine cyanobacteria. Metagenomic analyses demonstrated that this cyanobacterial lineage is globally distributed and strictly coexists with its host dinoflagellates, suggesting that the intimate symbiotic association allowed the cyanobacteria to escape from previous metagenomic studies. Furthermore, a comparative analysis of the protein repertoire with related species indicated that the lineage has independently undergone reductive genome evolution to a similar extent as Prochlorococcus, which has the most reduced genomes among free-living cyanobacteria. Discovery of this cyanobacterial lineage, hidden by its symbiotic lifestyle, provides crucial insights into the diversity, ecology, and evolution of marine cyanobacteria and suggests the existence of other undiscovered cryptic cyanobacterial lineages.

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General