A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Koonin, Eugene V.; Fedorova, Natalie D.; Jackson, John D.; Jacobs, Aviva R.; Krylov, Dmitri M.; Makarova, Kira S.; Mazumder, Raja; Mekhedov, Sergei; Nikol'skaya, A. N.; Rao, Bachoti S.; Rogozin, Igor B.; Smirnov, Sergei; Sorokin, Alexander V.; Sverdlov, Alexander V.; Vasudevan, Sona; Wolf, Yuri I.; Yin, Jodie J.; Natale, Darren A.

doi:10.1186/gb-2004-5-2-r7

Cited by 833 publications

(427 citation statements)

References 138 publications

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“…Functional and structural domains were predicted in protein sequences using the InterPro software (Zdobnov and Apweiler 2001). All genes were also annotated according to Gene Ontology (Ashburner et al 2000;Harris et al 2004), eukaryotic orthologous groups (KOGs) (Koonin et al 2004), and KEGG metabolic pathways (Kanehisa et al 2004). …”

Section: Atcc 1015 Automatic Annotationmentioning

confidence: 99%

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Andersen

Salazar²,

Schaap³

et al. 2011

Genome Res.

315

276

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The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook wholegenome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.

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Section: Atcc 1015 Automatic Annotationmentioning

confidence: 99%

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Andersen

Salazar²,

Schaap³

et al. 2011

Genome Res.

315

276

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“…Gene prediction methods used for annotation of two Ostreococcus genomes included ab initio Fgenesh (40), homology-based Fgeneshϩ (SoftBerry), Genewise (41), MAGPIE (42), EST-based estExt (I.V.G., unpublished data), and a combined-approach EuGene (43). Predicted genes were annotated by using double-affine Smith-Waterman (TimeLogic) alignments against proteins from the National Center for Biotechnology Information nonredundant protein database, protein domain predictions using InterProScan (44), and their mappings to Gene Ontology (45), eukaryotic clusters of orthologous groups [KOGs (46)], and KEGG metabolic pathways (47). The available functional annotation of O. tauri (GenBank accession nos.…”

Section: Methodsmentioning

confidence: 99%

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Palenik

Grimwood

Aerts

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

573

532

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The smallest known eukaryotes, at Ϸ1-m diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.green algae ͉ picoeukaryote ͉ genome evolution ͉ selenium ͉ synteny P hytoplankton living in the oceans perform nearly half of total global photosynthesis (1). Eukaryotic phytoplankton exhibit great diversity that contrasts with the lower apparent diversity of ecological niches available to them in aquatic ecosystems. This observation, know as the ''paradox of the plankton,'' has long puzzled biologists (2). By providing molecular level information on related species, genomics is poised to provide new insights into this paradox.Picophytoplankton, with cell diameters Ͻ2 m, play a significant role in major biogeochemical processes, primary productivity, and food webs, especially in oligotrophic waters. Within this size class, the smallest known eukaryotes are Ostreococcus tauri and related species. Although more similar to flattened spheres in shape, these organisms are Ϸ1 m in diameter (3, 4) and have been isolated or detected from samples of diverse geographical origins (5-8). They belong to the Prasinophyceae, an early diverging class within the green plant lineage, and have a strikingly simple cellular organization, with no cell wall or flagella, and with a single chloroplast and mitochondrion (4). Recent work has shown that small-subunit rDNA sequences of Ostreococcus from cultures and environmental samples cluster into four different clades that are likely distinct enough to represent different species (6, 9).Here we report on the gene content, genome organization, and deduced metabolic capacity of the complete genome of Ostreococcus sp. strain CCE9901 (7), a representative of surface-ocean adapted Ostreococcus, referred to here as Ostreococcus lucimarinus. We compare it to the analogous features of the related species O. tauri strain OTH95 (10). Our results show that many process...

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“…As suggested by Curtin et al (24), coding sequences (CDSs) were predicted by the AUGUSTUS (v2.5.5) program (54) with the S. cerevisiae gene models as a reference. All predicted genes were annotated by using the NCBI KOG database (55) and Blast2GO (56) with AWRI 1499 (ϭ ST05.12/62 in our study) as a reference (24).…”

Section: Methodsmentioning

confidence: 99%

Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

Crauwels

Zhu

Steensels

et al. 2014

Appl Environ Microbiol

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e Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis.

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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

Cited by 833 publications

References 138 publications

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

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