Codon usage tabulated from international DNA sequence databases: status for the year 2000

Nakamura, Yasukazu; Gojobori, Takashi; Ikemura, Toshimichi

doi:10.1093/nar/28.1.292

Cited by 1,130 publications

(861 citation statements)

References 2 publications

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“…The specificity of the 269 tRNA genes and the codon usage are presented in Supplementary Tables 1 and 2 online and confirm the published usage 11 . A. oryzae has a comparable set of tRNAs (245), whereas A. nidulans and A. fumigatus contain 188 and 179 tRNAs, respectively.…”

Section: Gene Identification and Annotationsupporting

confidence: 79%

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

et al. 2007

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The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

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Section: Gene Identification and Annotationsupporting

confidence: 79%

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

et al. 2007

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“…Codon usage tables for Methylococcus capsulatus Bath, as well as alphaproteobacterial reference organisms such as Bradyrhizobium japonicum, were obtained from the Kazusa codon usage database (http://www.kazusa.or.jp/codon/) (Nakamura et al, 2000). Alternatively, a table for Methylococcus capsulatus Bath was computed based on 57 coding sequences (>21 000 codons) obtained from GenBank.…”

Section: Methodsmentioning

confidence: 99%

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

2004

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The ability to utilize dinitrogen as a nitrogen source is an important phenotypic trait in most currently known methanotrophic bacteria (MB). This trait is especially important for acidophilic MB, which inhabit acidic oligotrophic environments, highly depleted in available nitrogen compounds. Phylogenetically, acidophilic MB are most closely related to heterotrophic dinitrogen-fixing bacteria of the genus Beijerinckia. To further explore the phylogenetic linkage between these metabolically different organisms, the sequences of nifH and nifD gene fragments from acidophilic MB of the genera Methylocella and Methylocapsa, and from representatives of Beijerinckia, were determined. For reference, nifH and nifD sequences were also obtained from some type II MB of the alphaproteobacterial Methylosinus/Methylocystis group and from gammaproteobacterial type I MB. The trees constructed for the inferred amino acid sequences of nifH and nifD were highly congruent. The phylogenetic relationships among MB in the NifH and NifD trees also agreed well with the corresponding 16S rRNA-based phylogeny, except for two distinctive features. First, different methods used for phylogenetic analysis grouped the NifH and NifD sequences of strains of the gammaproteobacterial MB Methylococcus capsulatus within a clade mainly characterized by Alphaproteobacteria, including acidophilic MB and type II MB of the Methylosinus/Methylocystis group. From this and other genomic data from Methylococcus capsulatus Bath, it is proposed that an ancient event of lateral gene transfer was responsible for this aberrant branching. Second, the identity values of NifH and NifD sequences between Methylocapsa acidiphila B2 and representatives of Beijerinckia were clearly higher (98?5 and 96?6 %, respectively) than would be expected from their 16S rRNA-based relationships. Possibly, these two bacteria originated from a common acidophilic dinitrogen-fixing ancestor, and were subject to similar evolutionary pressure with regard to nitrogen acquisition. This interpretation is corroborated by the observation that, in contrast to most other diazotrophs, M. acidiphila B2 and Beijerinckia spp. are capable of active growth on nitrogen-free media under fully aerobic conditions.

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“…Sequences of 300 codons were simulated on the tree topologies of the fungi data set. Codon usage was sampled from the actual frequencies in Saccharomyces cerevisiae 95 . The κ (transition/transversion rate) was set to 1.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

et al. 2017

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Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.

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Codon usage tabulated from international DNA sequence databases: status for the year 2000

Cited by 1,130 publications

References 2 publications

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

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