The Complete Mitochondrial Genome ofYarrowia lipolytica

We here report the complete nucleotide sequence of the 47.9 kb mitochondrial (mt) genome from the obligate aerobic yeastYarrowia lipolytica. It encodes, all on the same strand, seven subunits of NADH: ubiquinone oxidoreductase (ND1-6, ND4L), apocytochromeb(COB), three subunits of cytochrome oxidase (COX1, 2, 3), three subunits of ATP synthetase (ATP6, 8 and 9), small and large ribosomal RNAs and an incomplete set of tRNAs. TheY. lipolyticamt genome is very similar to theHansenula wingeimt genome, as judged from blocks of conserved gene order and from sequence homology. The extra DNA in theY. lipolyticamt genome consists of 17 group 1 introns and stretches of A+Trich sequence, interspersed with potentially transposable GC clusters. The usual mould mt genetic code is used. Interestingly, there is no tRNA able to read CGN (arginine) codons. CGN codons could not be found in exonic open reading frames, whereas they do occur in intronic open reading frames. However, several of the intronic open reading frames have accumulated mutations and must be regarded as pseudogenes. We propose that this may have been triggered by the presence of untranslatable CGN codons. This sequence is available under EMBL Accession No. AJ307410.

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The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides

FEMS Yeast Research ◽

10.1093/femsyr/foaa048 ◽

2020 ◽

Vol 20 (6) ◽

Author(s):

Renhui Zhou ◽

Zhiwei Zhu ◽

Sufang Zhang ◽

Zongbao Kent Zhao

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Nuclear Genome ◽

Open Reading Frames ◽

Circular Dna ◽

Transfer Rnas ◽

Fundamental Information ◽

Significant Genetic Divergence ◽

Reading Frames

ABSTRACT Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.

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Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris

Plants ◽

10.3390/plants9040469 ◽

2020 ◽

Vol 9 (4) ◽

pp. 469

Author(s):

Denis O. Omelchenko ◽

Maxim S. Makarenko ◽

Artem S. Kasianov ◽

Mikhail I. Schelkunov ◽

Maria D. Logacheva ◽

...

Keyword(s):

Amino Acids ◽

Rna Editing ◽

Complete Mitochondrial Genome ◽

Open Reading Frames ◽

Protein Coding ◽

Third Generation Sequencing ◽

Rnaseq Data ◽

Complete Mitogenome ◽

Generation Sequencing ◽

Reading Frames

Shepherd’s purse (Capsella bursa-pastoris) is a cosmopolitan annual weed and a promising model plant for studying allopolyploidization in the evolution of angiosperms. Though plant mitochondrial genomes are a valuable source of genetic information, they are hard to assemble. At present, only the complete mitogenome of C. rubella is available out of all species of the genus Capsella. In this work, we have assembled the complete mitogenome of C. bursa-pastoris using high-precision PacBio SMRT third-generation sequencing technology. It is 287,799 bp long and contains 32 protein-coding genes, 3 rRNAs, 25 tRNAs corresponding to 15 amino acids, and 8 open reading frames (ORFs) supported by RNAseq data. Though many repeat regions have been found, none of them is longer than 1 kbp, and the most frequent structural variant originated from these repeats is present in only 4% of the mitogenome copies. The mitochondrial DNA sequence of C. bursa-pastoris differs from C. rubella, but not from C. orientalis, by two long inversions, suggesting that C. orientalis could be its maternal progenitor species. In total, 377 C to U RNA editing sites have been detected. All genes except cox1 and atp8 contain RNA editing sites, and most of them lead to non-synonymous changes of amino acids. Most of the identified RNA editing sites are identical to corresponding RNA editing sites in A. thaliana.

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Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Strain MS-FC-4

Genome Announcements ◽

10.1128/genomea.00429-18 ◽

2018 ◽

Vol 6 (20) ◽

Author(s):

Ryan P. Bartelme ◽

Paul Barbier ◽

Ryan S. Lipscomb ◽

Scott E. LaPatra ◽

Ryan J. Newton ◽

...

Keyword(s):

Draft Genome ◽

Open Reading Frames ◽

Flavobacterium Columnare ◽

Fish Pathogen ◽

Content Type ◽

Genomic Analyses ◽

Highly Virulent ◽

Model Strain ◽

Reading Frames ◽

Group 1

ABSTRACT Flavobacterium columnare MS-FC-4 is a highly virulent genetic group 1 (formerly genomovar I) strain isolated from rainbow trout (Oncorhynchus mykiss). The draft genome consists of three contigs totaling 3,449,277 bp with 2,811 predicted open reading frames. F. columnare MS-FC-4 is a model strain for functional genomic analyses.

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The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi

Canadian Journal of Microbiology ◽

10.1139/cjm-2017-0605 ◽

2018 ◽

Vol 64 (5) ◽

pp. 339-348 ◽

Cited By ~ 3

Author(s):

Talal George Abboud ◽

Abdullah Zubaer ◽

Alvan Wai ◽

Georg Hausner

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Open Reading Frames ◽

Dutch Elm Disease ◽

Protein Coding ◽

Protein Coding Genes ◽

Statistical Support ◽

Size Variability ◽

Reading Frames

Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.

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Nadh: Ubiquinone oxidoreductase in obligate aerobic yeasts

Yeast ◽

10.1002/yea.320100406 ◽

1994 ◽

Vol 10 (4) ◽

pp. 475-479 ◽

Cited By ~ 24

Author(s):

Rainer Büschges ◽

Gregor Bahrenberg ◽

Martin Zimmermann ◽

Klaus Wolf

Keyword(s):

Ubiquinone Oxidoreductase ◽

Nadh Ubiquinone Oxidoreductase ◽

Obligate Aerobic

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AmfS, an Extracellular Peptidic Morphogen in Streptomyces griseus

Journal of Bacteriology ◽

10.1128/jb.184.5.1488-1492.2002 ◽

2002 ◽

Vol 184 (5) ◽

pp. 1488-1492 ◽

Cited By ~ 55

Author(s):

Kenji Ueda ◽

Ken-Ichi Oinuma ◽

Go Ikeda ◽

Kuniaki Hosono ◽

Yasuo Ohnishi ◽

...

Keyword(s):

Wild Type Strain ◽

Streptomyces Griseus ◽

Aerial Mycelium ◽

Gene Organization ◽

Open Reading Frames ◽

Wild Type ◽

Amino Acid Peptide ◽

Regulatory Molecule ◽

Conserved Gene ◽

Reading Frames

ABSTRACT The amf gene cluster was previously identified as a regulator for the onset of aerial-mycelium formation in Streptomyces griseus. The nucleotide sequences of amf and its counterparts in other species revealed a conserved gene organization consisting of five open reading frames. A nonsense mutation in amfS, encoding a 43-amino-acid peptide, caused significant blocking of aerial-mycelium formation and streptomycin production, suggesting its role as a regulatory molecule. Extracellular-complementation tests for the aerial-mycelium-deficient phenotype of the amfS mutant demonstrated that AmfS was secreted by the wild-type strain. A null mutation in amfBA, encoding HlyB-like membrane translocators, abolished the extracellular AmfS activity without affecting the wild-type morphology, which suggests that AmfBA is involved not in production but in export of AmfS. A synthetic C-terminal octapeptide partially induced aerial-mycelium formation in the amfS mutant, which suggests that an AmfS derivative, but not AmfS itself, serves as an extracellular morphogen.

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