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Genome Network Project: An Integrated Genomic Platform

So Nakagawa, Jose Clemente, Kazuho Ikeo, Takashi Gojobori
2009 Nature Precedings  
CoexpressionJose Carlos Clemente, So Nakagawa, Kazuho Ikeo, Takashi Gojobori Laboratory For DNA Data Analysis, CIB-DDBJ, National Institute of Genetics, Japan Summary of results by Genome Network Project  ... 
doi:10.1038/npre.2009.3180.1 fatcat:vubnhxswwrcyno37e4qbtjvmhi

The evolutionary position of nematodes

Jaime E Blair, Kazuho Ikeo, Takashi Gojobori, S Blair Hedges
2002 BMC Evolutionary Biology  
The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting
more » ... clade, Ecdysozoa, based on data from several genes. We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.
pmid:11985779 pmcid:PMC102755 fatcat:pd32iecj7fbs5p25742vkcs2fu

Molecular Evolution of Kringle Domain

Kazuho IKEO
1995 Japanese Journal of Thrombosis and Hemostasis  
doi:10.2491/jjsth.6.95 fatcat:xfylibsnqjgnfkyib3z4izmpbq

Optimized ancestral state reconstruction using Sankoff parsimony

José C Clemente, Kazuho Ikeo, Gabriel Valiente, Takashi Gojobori
2009 BMC Bioinformatics  
Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states. Although optimizations exist to reduce the computations in the number of taxa, the original algorithm takes time O(n 2 ) in the number of states, making it impractical for large values of n. Results: In this study we
more » ... oduce an optimization of Sankoff parsimony for the reconstruction of ancestral states when ultrametric or additive cost matrices are used. We analyzed its performance for randomly generated matrices, Jukes-Cantor and Kimura's two-parameter models of DNA evolution, and in the reconstruction of elongation factor-1a and ancestral metabolic states of a group of eukaryotes, showing that in all cases the execution time is significantly less than with the original implementation. Conclusion: The algorithms here presented provide a fast computation of Sankoff parsimony for a given phylogeny. Problems where the number of states is large, such as reconstruction of ancestral metabolism, are particularly adequate for this optimization. Since we are reducing the computations required to calculate the parsimony cost of a single tree, our method can be combined with optimizations in the number of taxa that aim at finding the most parsimonious tree.
doi:10.1186/1471-2105-10-51 pmid:19200389 pmcid:PMC2677398 fatcat:fpdccyhtf5ajhluqiz5pefynhu

Pax 6: mastering eye morphogenesis and eye evolution

Walter J Gehring, Kazuho Ikeo
1999 Trends in Genetics  
This work provides further support for the notion that all eyes share a common evolutionary and developmental heritage, despite what seem to be profound differences (Gehring and Ikeo, 1999).  ... 
doi:10.1016/s0168-9525(99)01776-x pmid:10461206 fatcat:nvrzxpu4yrcillgbkiwi7m7oge

Evolutionary Patterns of Recently Emerged Animal Duplogs

Kiyoshi Ezawa, Kazuho Ikeo, Takashi Gojobori, Naruya Saitou
2011 Genome Biology and Evolution  
Duplogs, or intraspecies paralogs, constitute the important portion of eukaryote genomes and serve as a major source of functional innovation. We conducted detailed analyses of recently emerged animal duplogs. Genome data of three vertebrate species (Homo sapiens, Mus musculus, and Danio rerio), Caenorhabditis elegans, and two Drosophila species (Drosophila melanogaster and D. pseudoobscura) were used. Duplication events were divided into six age-groups according to the synonymous distance (dS)
more » ... up to 0.6. Duplogs were classified into four equal-sized classes on physical distances and into three classes on relative orientations. We observed the following shared characteristics among intrachromosomal multiexon duplogs: 1) inverted duplogs account for 20-50%, and about a half of the physically most distant 25%; 2) except for C. elegans, the composition of physical distances, that of relative orientations, and the proportion of inverted duplogs in each physical distance category are more or less uniform; 3) except for C. elegans, the characteristics of the youngest (dS , 0.01) duplogs are similar to the overall characteristics of the entire set. These results suggest that intrachromosomal duplogs with fairly long physical distances were generated at once, rather than resulting from tandem duplications and subsequent genomic rearrangements. This is different from the three well-known modes of gene duplication: tandem duplication, retrotransposition, and genome duplication. We termed this new mode as "drift" duplication. The drift duplication has been producing duplicate copies at paces comparable with tandem duplications since the common ancestor of vertebrates, and it may have already operated in the common ancestor of bilateral animals.
doi:10.1093/gbe/evr074 pmid:21859807 pmcid:PMC3194840 fatcat:barwrpeazjh7hpixgn7sanc6wy

Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda

Masafumi Nozawa, Kanako Onizuka, Mai Fujimi, Kazuho Ikeo, Takashi Gojobori
2016 Nature Communications  
doi:10.1038/ncomms13659 pmid:27897175 pmcid:PMC5141340 fatcat:5hbisbh2ebcdldqwcuj44wl7xe

Effect of Wild and Cultivated Rice Genotypes on Rhizosphere Bacterial Community Composition

Matthew Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo
2016 Rice  
We acknowledge the award of a JSPS/MEXT Grant-in-Aid for Scientific Research No. 25640103 to Kazuho Ikeo.  ... 
doi:10.1186/s12284-016-0111-8 pmid:27557607 pmcid:PMC4996804 fatcat:ymwec5rwgjgkhbrattgdiccqgu

Evolutionary origin of numerous kringles in human and simian apolipoprotein(a)

Kazuho Ikeo, Kei Takahashi, Takashi Gojobori
1991 FEBS Letters  
Human apoIipoprotein(a) has a great size heterogeneity and consists of 38 kringle domains in the amino terminal and a serine proteasc domain in the carboxyl terminal. All but one kringle of apolipoprotein(a) are homologous to the fourth kringle of plasminogen. Howsever. the 38th kringle resembles the fifth kringle of plasminogen and it seems to have been deleted in simian species. The phylogenetic trees suggest that an ancestral apolipoprotein(a) may have started with a duplicate of a
more » ... type protein. It also implies that deletion of the three kringles in the amino terminus followed. and that one of the remaining two kringles was duplicated in both human and simian species and the other was processed by a deletion in simian species after species separation. Thus. the number of kringles in other mammals not yet studied may vary considerably from species to species.
doi:10.1016/0014-5793(91)80036-3 pmid:1879523 fatcat:xqymvvteznbotokvndzdw4hkl4

Evolutionary Transitions of MicroRNA-Target Pairs

Masafumi Nozawa, Mai Fujimi, Chie Iwamoto, Kanako Onizuka, Nana Fukuda, Kazuho Ikeo, Takashi Gojobori
2016 Genome Biology and Evolution  
How newly generated microRNA (miRNA) genes are integrated into gene regulatory networks during evolution is fundamental in understanding the molecular and evolutionary bases of robustness and plasticity in gene regulation. A recent model proposed that after the birth of a miRNA, the miRNA is generally integrated into the network by decreasing the number of target genes during evolution. However, this decreasing model remains to be carefully examined by considering in vivo conditions. In this
more » ... dy, we therefore compared the number of target genes among miRNAs with different ages, combining experiments with bioinformatics predictions. First, we focused on three Drosophila miRNAs with different ages. As a result, we found that an older miRNA has a greater number of target genes than a younger miRNA, suggesting the increasing number of targets for each miRNA during evolution (increasing model). To further confirm our results, we also predicted all target genes for all miRNAs in D. melanogaster, considering coexpression of miRNAs and mRNAs in vivo. The results obtained also do not support the decreasing model but are reasonably consistent with the increasing model of miRNA-target pairs. Furthermore, our large-scale analyses of currently available experimental data of miRNA-target pairs also showed a weak but the same trend in humans. These results indicate that the current decreasing model of miRNA-target pairs should be reconsidered and the increasing model may be more appropriate to explain the evolutionary transitions of miRNA-target pairs in many organisms.
doi:10.1093/gbe/evw092 pmid:27189995 pmcid:PMC4898806 fatcat:vhk2aacddnetzcqteoalqknvm4

Effective gene collection from the metatranscriptome of marine microorganisms

Atsushi Ogura, Mengjie Lin, Yuya Shigenobu, Atushi Fujiwara, Kazuho Ikeo, Satoshi Nagai
2011 BMC Genomics  
Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species. This approach, however, cannot be used to identify active functional genes under actual environmental conditions. Metatranscriptomics, which is similar in approach to metagenomics except that it utilizes RNA samples, is a powerful tool for the
more » ... tomic study of environmental samples. Unlike metagenomic studies, metatranscriptomic studies have not been popular to date due to problems with reliability, repeatability, redundancy and cost performance. Here, we propose a normalized metatranscriptomic method that is suitable for the collection of genes from samples as a platform for comparative transcriptomics. Results: We constructed two libraries, one non-normalized and the other normalized library, from samples of marine microorganisms taken during daylight hours from Hiroshima bay in Japan. We sequenced 0.6M reads for each sample on a Roche GS FLX, and obtained 0.2M genes after quality control and assembly. A comparison of the two libraries showed that the number of unique genes was larger in the normalized library than in the nonnormalized library. Functional analysis of genes revealed that a small number of gene groups, ribosomal RNA genes and chloroplast genes, were dominant in both libraries. Taxonomic distribution analysis of the libraries suggests that Stramenopiles form a major taxon that includes diatoms. The normalization technique thus increases unique genes, functional categories of genes, and taxonomic richness. Conclusions: Normalization of the marine metatranscriptome could be useful in increasing the number of genes collected, and in reducing redundancies among highly expressed genes. Gene collection through the normalization method was effective in providing a foundation for comparative transcriptomic analysis.
doi:10.1186/1471-2164-12-s3-s15 pmid:22369384 pmcid:PMC3333174 fatcat:esr5kigqxjefhfdaiw7fopwxgy

DDBJ Activities: Contribution to the Research in Information Biology

Jun Mashima, Yoshio Tateno, Takashi Gojobori, Takehide Kosuge, Toshihisa Okido, Yuichi Kodama, Kazuho Ikeo, Hideaki Sugawara
2009 Nature Precedings  
Ikeo, Hideaki Sugawara, Yoshio Tateno and Takashi Gojobori ■ ClustalW Multiple alignment 20 DBs Ex) MAP kinase ■ ARSA Database Search Phylogenetics Structure and Function Genome Analyses  ...  2005 100 Gbp over 1986 ~ 2008 200 Gbp over http://www.ddbj.nig.ac.jp/whatsnew/2008/080606-e.html DDBJ top page http://www.ddbj.nig.ac.jp/ Jun Mashima, Takehide Kosuge, Toshihisa Okido, Yuichi Kodama, Kazuho  ... 
doi:10.1038/npre.2009.3211.1 fatcat:6kqo3wol6rfopdiyqnkbhtdvm4

Two-step evolution of endosymbiosis between hydra and algae

Masakazu Ishikawa, Hiroshi Shimizu, Masafumi Nozawa, Kazuho Ikeo, Takashi Gojobori
2016 Molecular Phylogenetics and Evolution  
doi:10.1016/j.ympev.2016.07.010 pmid:27404042 fatcat:m65f6scmizfhzf2nc7rgq2lqly

Effects of Cordycepin in Cordyceps militaris during Its Infection to Silkworm Larvae

Tatsuya Kato, Konomi Nishimura, Ahmad Suparmin, Kazuho Ikeo, Enoch Y. Park
2021 Microorganisms  
Cordyceps militaris produces cordycepin, a secondary metabolite that exhibits numerous bioactive properties. However, cordycepin pharmacology in vivo is not yet understood. In this study, the roles of cordycepin in C. militaris during its infection were investigated. After the injection of conidia, C. militaris NBRC100741 killed silkworm larvae more rapidly than NBRC103752. At 96 and 120 h, Cmcns genes (Cmcns1–4), which are part of the cordycepin biosynthesis gene cluster, were expressed in fat
more » ... bodies and cuticles. Thus, cordycepin may be produced in the infection of silkworm larvae. Further, cordycepin enhanced pathogenicity toward silkworm larvae of Metarhizium anisopliae and Beauveria bassiana, that are also entomopathogenic fungi and do not produce cordycepin. In addition, by RNA-seq analysis, the increased expression of the gene encoding a lipoprotein 30K-8 (Bmlp20, KWMTBOMO11934) and decreased expression of genes encoding cuticular proteins (KWMTBOMO13140, KWMTBOMO13167) and a serine protease inhibitor (serpin29, KWMTBOMO08927) were observed when cordycepin was injected into silkworm larvae. This result suggests that cordycepin may aid the in vivo growth of C. militaris in silkworm larvae by the influence of the expression of some genes in silkworm larvae.
doi:10.3390/microorganisms9040681 pmid:33806171 pmcid:PMC8065576 fatcat:lbmjstbkgzcsxltya3ahjkgo5m

Genome and Transcriptome Analysis of the Food-Yeast Candida utilis

Yasuyuki Tomita, Kazuho Ikeo, Hideyuki Tamakawa, Takashi Gojobori, Shigehito Ikushima, Conrad A. Nieduszynski
2012 PLoS ONE  
The industrially important food-yeast Candida utilis is a Crabtree effect-negative yeast used to produce valuable chemicals and recombinant proteins. In the present study, we conducted whole genome sequencing and phylogenetic analysis of C. utilis, which showed that this yeast diverged long before the formation of the CUG and Saccharomyces/Kluyveromyces clades. In addition, we performed comparative genome and transcriptome analyses using next-generation sequencing, which resulted in the
more » ... cation of genes important for characteristic phenotypes of C. utilis such as those involved in nitrate assimilation, in addition to the gene encoding the functional hexose transporter. We also found that an antisense transcript of the alcohol dehydrogenase gene, which in silico analysis did not predict to be a functional gene, was transcribed in the stationary-phase, suggesting a novel system of repression of ethanol production. These findings should facilitate the development of more sophisticated systems for the production of useful reagents using C. utilis.
doi:10.1371/journal.pone.0037226 pmid:22629373 pmcid:PMC3356342 fatcat:ugmzst7rorehrmrntstjyvz5qy
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