Papers - NIIMURA Yoshihito
-
Identification of chemosensory receptor genes from vertebrate genomes. Reviewed
Niimura Y
Methods in molecular biology (Clifton, N.J.) 1068 95 - 105 2013
Language：English Publishing type：Research paper (scientific journal)
Chemical senses are essential for the survival of animals. In vertebrates, mainly three different types of receptors, olfactory receptors (ORs), vomeronasal receptors type 1 (V1Rs), and vomeronasal receptors type 2 (V2Rs), are responsible for the detection of chemicals in the environment. Mouse or rat genomes contain >1,000 OR genes, forming the largest multigene family in vertebrates, and have >100 V1R and V2R genes as well. Recent advancement in genome sequencing enabled us to computationally identify nearly complete repertories of OR, V1R, and V2R genes from various organisms, revealing that the numbers of these genes are highly variable among different organisms depending on each species' living environment. Here I would explain bioinformatic methods to identify the entire repertoires of OR, V1R, and V2R genes from vertebrate genome sequences.
-
Identification of olfactory receptor genes from mammalian genome sequences. Reviewed
Niimura Y
Methods in molecular biology (Clifton, N.J.) 1003 39 - 49 2013
Language：English Publishing type：Research paper (scientific journal) Publisher：Humana Press Inc.
Olfaction is essential for the survival of mammals. Diverse odorant molecules in the environment are detected by olfactory receptors (ORs) expressed in the olfactory epithelium of the nasal cavity. In general, mammalian genomes harbor ~1,000 OR genes, which form the largest multigene family in mammals. The recent advances in genome sequencing technology have enabled us to computationally identify nearly complete repertoires of OR genes from various organisms. Such studies have revealed that the numbers of OR genes are highly variable among organisms depending on their living environments. Because OR genes are intronless, it is possible to find all OR genes by conducting homology searches against the genome sequences using known OR genes as queries. However, some caution is necessary during the process of extracting intact coding sequences of OR genes and distinguishing among OR and non-OR genes. Presented here is a description of bioinformatics methods to identify the entire OR gene repertoires from mammalian genome sequences.
-
Olfactory receptor multigene family in vertebrates: from the viewpoint of evolutionary genomics. Reviewed
Niimura Y
Current genomics 13 ( 2 ) 103 - 14 2012.4
Language：English Publishing type：Research paper (scientific journal) Publisher：BENTHAM SCIENCE PUBL LTD
Olfaction is essential for the survival of animals. Diverse odor molecules in the environment are detected by the olfactory receptors (ORs) in the olfactory epithelium of the nasal cavity. There are ~400 and ~1,000 OR genes in the human and mouse genomes, respectively, forming the largest multigene family in mammals. The relationships between ORs and odorants are multiple-to-multiple, which allows for discriminating almost unlimited number of different odorants by a combination of ORs. However, the OR-ligand relationships are still largely unknown, and predicting the quality of odor from its molecular structure is unsuccessful.Extensive bioinformatic analyses using the whole genomes of various organisms revealed a great variation in number of OR genes among species, reflecting the diversity of their living environments. For example, higher primates equipped with a well-developed vision system and dolphins that are secondarily adapted to the aquatic life have considerably smaller numbers of OR genes than most of other mammals do. OR genes are characterized by extremely frequent gene duplications and losses. The OR gene repertories are also diverse among human individuals, explaining the diversity of odor perception such as the specific anosmia.OR genes are present in all vertebrates. The number of OR genes is smaller in teleost fishes than in mammals, while the diversity is higher in the former than the latter. Because the genome of amphioxus, the most basal chordate species, harbors vertebrate-like OR genes, the origin of OR genes can be traced back to the common ancestor of the phylum Chordata.
-
hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets. Reviewed
Johnson TA, Niimura Y, Tanaka H, Nakamura Y, Tsunoda T
Genome biology 12 ( 3 ) R21 2011
Language：English Publishing type：Research paper (scientific journal) Publisher：3
The analysis of contiguous homozygosity (runs of homozygous loci) in human genotyping datasets is critical in the search for causal disease variants in monogenic disorders, studies of population history and the identification of targets of natural selection. Here, we report methods for extracting homozygous segments from high-density genotyping datasets, quantifying their local genomic structure, identifying outstanding regions within the genome and visualizing results for comparative analysis between population samples.
-
Difference in gene duplicability may explain the difference in overall structure of protein-protein interaction networks among eukaryotes. Reviewed
Hase T, Niimura Y, Tanaka H
BMC evolutionary biology 10 358 - 358 2010.11
Language：English Publishing type：Research paper (scientific journal) Publisher：BIOMED CENTRAL LTD
BACKGROUND: A protein-protein interaction network (PIN) was suggested to be a disassortative network, in which interactions between high- and low-degree nodes are favored while hub-hub interactions are suppressed. It was postulated that a disassortative structure minimizes unfavorable cross-talks between different hub-centric functional modules and was positively selected in evolution. However, by re-examining yeast PIN data, several researchers reported that the disassortative structure observed in a PIN might be an experimental artifact. Therefore, the existence of a disassortative structure and its possible evolutionary mechanism remains unclear. RESULTS: In this study, we investigated PINs from the yeast, worm, fly, human, and malaria parasite including four different yeast PIN datasets. The analyses showed that the yeast, worm, fly, and human PINs are disassortative while the malaria parasite PIN is not. By conducting simulation studies on the basis of a duplication-divergence model, we demonstrated that a preferential duplication of low- and high-degree nodes can generate disassortative and non-disassortative networks, respectively. From this observation, we hypothesized that the difference in degree dependence on gene duplications accounts for the difference in assortativity of PINs among species. Comparison of 55 proteomes in eukaryotes revealed that genes with lower degrees showed higher gene duplicabilities in the yeast, worm, and fly, while high-degree genes tend to have high duplicabilities in the malaria parasite, supporting the above hypothesis. CONCLUSIONS: These results suggest that disassortative structures observed in PINs are merely a byproduct of preferential duplications of low-degree genes, which might be caused by an organism's living environment.
-
Degeneration of olfactory receptor gene repertories in primates: no direct link to full trichromatic vision. Reviewed
Matsui A, Go Y, Niimura Y
Molecular biology and evolution 27 ( 5 ) 1192 - 200 2010.5
Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS
Odor molecules in the environment are detected by olfactory receptors (ORs), being encoded by a large multigene family in mammalian genomes. It is generally thought that primates are vision oriented and dependent weakly on olfaction. Previous studies suggested that Old World monkeys (OWMs) and hominoids lost many functional OR genes after the divergence from New World monkeys (NWMs) due to the acquisition of well-developed trichromatic vision. To examine this hypothesis, here we analyzed OR gene repertoires of five primate species including NWMs, OWMs, and hominoids for which high-coverage genome sequences are available, together with two prosimians and tree shrews with low-coverage genomes. The results showed no significant differences in the number of functional OR genes between NWMs (marmosets) and OWMs/hominoids. Two independent analyses, identification of orthologous genes among the five primates and estimation of the numbers of ancestral genes by the reconciled tree method, did not support a sudden loss of OR genes at the branch of the OWMs/hominoids ancestor but suggested a gradual loss in every lineage. Moreover, we found that humans retain larger numbers of ancestral OR genes that were in the common ancestor of NWMs/OWMs/hominoids than orangutans and macaques and that the OR gene repertoire in humans is more similar to that of marmosets than those of orangutans and macaques. These results suggest that the degeneration of OR genes in primates cannot simply be explained by the acquisition of trichromatic vision, and our sense of smell may not be inferior to other primate species.
-
Dynamic evolution of translation initiation mechanisms in prokaryotes. Reviewed
Nakagawa S, Niimura Y, Miura K, Gojobori T
Proceedings of the National Academy of Sciences of the United States of America 107 ( 14 ) 6382 - 7 2010.4
Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES
It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5' UTR of an mRNA and the anti-SD sequence in the 3' end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5' UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution.
-
Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents. Reviewed
Niimura Y
Human genomics 4 ( 2 ) 107 - 18 2009.12
Language：English Publishing type：Research paper (scientific journal)
-
On the origin and evolution of vertebrate olfactory receptor genes: comparative genome analysis among 23 chordate species. Reviewed
Niimura Y
Genome biology and evolution 1 34 - 44 2009.4
Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS
Olfaction is a primitive sense in organisms. Both vertebrates and insects have receptors for detecting odor molecules in the environment, but the evolutionary origins of these genes are different. Among studied vertebrates, mammals have approximately 1,000 olfactory receptor (OR) genes, whereas teleost fishes have much smaller (approximately 100) numbers of OR genes. To investigate the origin and evolution of vertebrate OR genes, I attempted to determine near-complete OR gene repertoires by searching whole-genome sequences of 14 nonmammalian chordates, including cephalochordates (amphioxus), urochordates (ascidian and larvacean), and vertebrates (sea lamprey, elephant shark, five teleost fishes, frog, lizard, and chicken), followed by a large-scale phylogenetic analysis in conjunction with mammalian OR genes identified from nine species. This analysis showed that the amphioxus has >30 vertebrate-type OR genes though it lacks distinctive olfactory organs, whereas all OR genes appear to have been lost in the urochordate lineage. Some groups of genes (theta, kappa, and lambda) that are phylogenetically nested within vertebrate OR genes showed few gene gains and losses, which is in sharp contrast to the evolutionary pattern of OR genes, suggesting that they are actually non-OR genes. Moreover, the analysis demonstrated a great difference in OR gene repertoires between aquatic and terrestrial vertebrates, reflecting the necessity for the detection of water-soluble and airborne odorants, respectively. However, a minor group (beta) of genes that are atypically present in both aquatic and terrestrial vertebrates was also found. These findings should provide a critical foundation for further physiological, behavioral, and evolutionary studies of olfaction in various organisms.
DOI： 10.1093/gbe/evp003
-
The evolution of animal chemosensory receptor gene repertoires: roles of chance and necessity. Reviewed
Nei M, Niimura Y, Nozawa M
Nature reviews. Genetics 9 ( 12 ) 951 - 63 2008.12
Language：English Publishing type：Research paper (scientific journal) Publisher：NATURE PUBLISHING GROUP
Chemosensory receptors are essential for the survival of organisms that range from bacteria to mammals. Recent studies have shown that the numbers of functional chemosensory receptor genes and pseudogenes vary enormously among the genomes of different animal species. Although much of the variation can be explained by the adaptation of organisms to different environments, it has become clear that a substantial portion is generated by genomic drift, a random process of gene duplication and deletion. Genomic drift also generates a substantial amount of copy-number variation in chemosensory receptor genes within species. It seems that mutation by gene duplication and inactivation has important roles in both the adaptive and non-adaptive evolution of chemosensation.
DOI： 10.1038/nrg2480
-
Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees. Reviewed
Go Y, Niimura Y
Molecular biology and evolution 25 ( 9 ) 1897 - 907 2008.9
Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS
Animals recognize their external world through the detection of tens of thousands of chemical odorants. Olfactory receptor (OR) genes encode proteins for detecting odorant molecules and form the largest multigene family in mammals. It is known that humans have fewer OR genes and a higher fraction of OR pseudogenes than mice or dogs. To investigate whether these features are human specific or common to all higher primates, we identified nearly complete sets of OR genes from the chimpanzee and macaque genomes and compared them with the human OR genes. In contrast to previous studies, here we show that the number of OR genes ( approximately 810) and the fraction of pseudogenes (51%) in chimpanzees are very similar to those in humans, though macaques have considerably fewer OR genes. The pseudogenization rates and the numbers of genes affected by positive selection are also similar between humans and chimpanzees. Moreover, the most recent common ancestor between humans and chimpanzees had a larger number of functional OR genes (>500) and a lower fraction of pseudogenes (41%) than its descendents, suggesting that the OR gene repertoires are in a phase of deterioration in both lineages. Interestingly, despite the close evolutionary relationship between the 2 species, approximately 25% of their functional gene repertoires are species specific due to massive gene losses. These findings suggest that the tempo of evolution of OR genes is similar between humans and chimpanzees, but the OR gene repertoires are quite different between them. This difference might be responsible for the species-specific ability of odor perception.
-
Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network. Reviewed
Hase T, Niimura Y, Kaminuma T, Tanaka H
PloS one 3 ( 2 ) e1667 2008.2
Language：English Publishing type：Research paper (scientific journal) Publisher：PUBLIC LIBRARY SCIENCE
Protein-protein interaction networks (PINs) are scale-free networks with a small-world property. In a small-world network, the average cluster coefficient (<C>) is much higher than in a random network, but the average shortest path length (<L>) is similar between the two networks. To understand the evolutionary mechanisms shaping the structure of PINs, simulation studies using various network growth models have been performed. It has been reported that the heterodimerization (HD) model, in which a new link is added between duplicated nodes with a uniform probability, could reproduce scale-freeness and a high <C>. In this paper, however, we show that the HD model is unsatisfactory, because (i) to reproduce the high <C> in the yeast PIN, a much larger number (n(HI)) of HD links (links between duplicated nodes) are required than the estimated number of n(HI) in the yeast PIN and (ii) the spatial distribution of triangles in the yeast PIN is highly skewed but the HD model cannot reproduce the skewed distribution. To resolve these discrepancies, we here propose a new model named the non-uniform heterodimerization (NHD) model. In this model, an HD link is preferentially attached between duplicated nodes when they share many common neighbors. Simulation studies demonstrated that the NHD model can successfully reproduce the high <C>, the low n(HI), and the skewed distribution of triangles in the yeast PIN. These results suggest that the survival rate of HD links is not uniform in the evolution of PINs, and that an HD link between high-degree nodes tends to be evolutionarily conservative. The non-uniform survival rate of HD links can be explained by assuming a low mutation rate for a high-degree node, and thus this model appears to be biologically plausible.
-
Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Reviewed
Nakagawa S, Niimura Y, Gojobori T, Tanaka H, Miura K
Nucleic acids research 36 ( 3 ) 861 - 71 2008.2
Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS
Understanding regulatory mechanisms of protein synthesis in eukaryotes is essential for the accurate annotation of genome sequences. Kozak reported that the nucleotide sequence GCCGCC(A/G)CCAUGG (AUG is the initiation codon) was frequently observed in vertebrate genes and that this 'consensus' sequence enhanced translation initiation. However, later studies using invertebrate, fungal and plant genes reported different 'consensus' sequences. In this study, we conducted extensive comparative analyses of nucleotide sequences around the initiation codon by using genomic data from 47 eukaryote species including animals, fungi, plants and protists. The analyses revealed that preferred nucleotide sequences are quite diverse among different species, but differences between patterns of nucleotide bias roughly reflect the evolutionary relationships of the species. We also found strong biases of A/G at position -3, A/C at position -2 and C at position +5 that were commonly observed in all species examined. Genes with higher expression levels showed stronger signals, suggesting that these nucleotides are responsible for the regulation of translation initiation. The diversity of preferred nucleotide sequences around the initiation codon might be explained by differences in relative contributions from two distinct patterns, GCCGCCAUG and AAAAAAAUG, which implies the presence of multiple molecular mechanisms for controlling translation initiation.
DOI： 10.1093/nar/gkm1102
-
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Reviewed
Genome Information Integration Project And H-Invitational 2., Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T
Nucleic acids research 36 ( Database issue ) D793 - 9 2008.1
Language：English Publishing type：Research paper (scientific journal) Publisher：OXFORD UNIV PRESS
Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.
DOI： 10.1093/nar/gkm999
-
Extensive gains and losses of olfactory receptor genes in mammalian evolution. Reviewed
Niimura Y, Nei M
PloS one 2 ( 8 ) e708 2007.8
Language：English Publishing type：Research paper (scientific journal) Publisher：PUBLIC LIBRARY SCIENCE
Odor perception in mammals is mediated by a large multigene family of olfactory receptor (OR) genes. The number of OR genes varies extensively among different species of mammals, and most species have a substantial number of pseudogenes. To gain some insight into the evolutionary dynamics of mammalian OR genes, we identified the entire set of OR genes in platypuses, opossums, cows, dogs, rats, and macaques and studied the evolutionary change of the genes together with those of humans and mice. We found that platypuses and primates have <400 functional OR genes while the other species have 800-1,200 functional OR genes. We then estimated the numbers of gains and losses of OR genes for each branch of the phylogenetic tree of mammals. This analysis showed that (i) gene expansion occurred in the placental lineage each time after it diverged from monotremes and from marsupials and (ii) hundreds of gains and losses of OR genes have occurred in an order-specific manner, making the gene repertoires highly variable among different orders. It appears that the number of OR genes is determined primarily by the functional requirement for each species, but once the number reaches the required level, it fluctuates by random duplication and deletion of genes. This fluctuation seems to have been aided by the stochastic nature of OR gene expression.
-
Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. Reviewed
Niimura Y, Nei M
Journal of human genetics 51 ( 6 ) 505 - 517 2006
Language：English Publishing type：Research paper (scientific journal) Publisher：SPRINGER TOKYO
The numbers of functional olfactory receptor (OR) genes in humans and mice are about 400 and 1,000 respectively. In both humans and mice, these genes exist as genomic clusters and are scattered over almost all chromosomes. The difference in the number of genes between the two species is apparently caused by massive inactivation of OR genes in the human lineage and a substantial increase of OR genes in the mouse lineage after the human-mouse divergence. Compared with mammals, fishes have a much smaller number of OR genes. However, the OR gene family in fishes is much more divergent than that in mammals. Fishes have many different groups of genes that are absent in mammals, suggesting that the mammalian OR gene family is characterized by the loss of many group genes that existed in the ancestor of vertebrates and the subsequent expansion of specific groups of genes. Therefore, this gene family apparently changed dynamically depending on the evolutionary lineage and evolved under the birth-and-death model of evolution. Study of the evolutionary changes of two gene families for vomeronasal receptors and two gene families for taste receptors, which are structurally similar, but remotely related to OR genes, showed that some of the gene families evolved in the same fashion as the OR gene family. It appears that the number and types of genes in chemosensory receptor gene families have evolved in response to environmental needs, but they are also affected by fortuitous factors.
-
Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Reviewed
Niimura Y, Nei M
Proceedings of the National Academy of Sciences of the United States of America 102 ( 17 ) 6039 - 44 2005.4
Language：English Publishing type：Research paper (scientific journal) Publisher：NATL ACAD SCIENCES
Olfaction, which is an important physiological function for the survival of mammals, is controlled by a large multigene family of olfactory receptor (OR) genes. Fishes also have this gene family, but the number of genes is known to be substantially smaller than in mammals. To understand the evolutionary dynamics of OR genes, we conducted a phylogenetic analysis of all functional genes identified from the genome sequences of zebrafish, pufferfish, frogs, chickens, humans, and mice. The results suggested that the most recent common ancestor between fishes and tetrapods had at least nine ancestral OR genes, and all OR genes identified were classified into nine groups, each of which originated from one ancestral gene. Eight of the nine group genes are still observed in current fish species, whereas only two group genes were found from mammalian genomes, showing that the OR gene family in fishes is much more diverse than in mammals. In mammals, however, one group of genes, gamma, expanded enormously, containing approximately 90% of the entire gene family. Interestingly, the gene groups observed in mammals or birds are nearly absent in fishes. The OR gene repertoire in frogs is as diverse as that in fishes, but the expansion of group gamma genes also occurred, indicating that the frog OR gene family has both mammal- and fish-like characters. All of these observations can be explained by the environmental change that organisms have experienced from the time of the common ancestor of all vertebrates to the present.
-
Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Reviewed
Niimura Y, Nei M
Gene 346 13 - 21 2005.2
Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV
Olfactory receptor (OR) genes form the largest multigene family in mammalian genomes. Humans have approximately 800 OR genes, but >50% of them are pseudogenes. By contrast, mice have approximately 1400 OR genes and pseudogenes are approximately 25%. To understand the evolutionary processes that shaped the difference of OR gene families between humans and mice, we studied the genomic locations of all human and mouse OR genes and conducted a detailed phylogenetic analysis using functional genes and pseudogenes. We identified 40 phylogenetic clades with high bootstrap supports, most of which contain both human and mouse genes. Interestingly, a particular clade contains approximately 100 pseudogenes in humans, whereas the numbers of pseudogenes are <20 for most of the mouse clades. We also found that the organization of OR genomic clusters is well conserved between humans and mice in many chromosomal locations. Despite the difference in the numbers of genes, the numbers of large genomic clusters are nearly the same for humans and mice. These observations suggest that the greater OR gene repertoire in mice has been generated mainly by tandem gene duplication within each genomic cluster.
-
Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages. Reviewed
Niimura Y, Nei M
Gene 346 23 - 8 2005.2
Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV
The numbers of functional olfactory receptor (OR) genes are quite variable among mammalian species. Previously we have reported that humans have 388 functional OR genes and 414 pseudogenes, while mice have 1037 functional genes and 354 pseudogenes. These observations suggest either that humans lost many functional OR genes after the human-mouse divergence (HMD) or that mice gained many functional genes. To distinguish between these two hypotheses, we devised a new method of inferring the number of functional OR genes in the most recent common ancestor (MRCA) of humans and mice. An application of this method suggested that the MRCA had approximately 750 functional OR genes and that mice acquired approximately 350 new OR genes after the HMD whereas approximately 430 OR genes in the MRCA have become pseudogenes or eliminated in the human lineage. Therefore, the two evolutionary hypotheses mentioned above are not mutually exclusive and both are nearly equally responsible for the difference in the number of OR genes between humans and mice.
-
The map-based sequence of the rice genome Reviewed
International Rice, Genome Sequencing Project, Iwama, H, Gojobori, T, Itoh, T, Niimura, Y
Nature 436 793 - 800 2005
Language：English Publishing type：Research paper (scientific journal)
国立遺伝学研究所以外の共著者あり
DOI： 10.1038/nature03895