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Norihiro Okada

Publications and source records attributed to Norihiro Okada.

62 records · Page 4Linked to original sources
PubMed2002

Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data.

The family Vespertilionidae comprises the largest number of species in the order Chiroptera, and its members are distributed over most of the world. We collected sequences of the mitochondrial NDI (NADH dehydrogenase subunit 1) gene from 38 species as well as 20 sequences of exon28 of the vWF (von Willebrand Factor) gene and analyzed phylogenetic relationships in Vespertilionidae using maximum-likelihood analyses and SINE (short interspersed elements) insertions. Our data strongly suggest the following: (1) Murininae and Myotis, each of which is classified into different subfamilies, are monophyletic; (2) the monophyly of Murininae, Myotis, Pipistrellini, and Plecotini is supported by our analyses of the NDI and nuclear vWF as well as data from SINE insertions, while Miniopterinae was not included in this group; and (3) Rhinolophoidea (microchiroptera) is separated from all the other microchiropteran species. Our study represents the most comprehensive phylogenetic model of Vespertilionidae to date.

Animals↗
PubMed2002

Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins.

We characterized two novel 7SL RNA-derived short interspersed nuclear element (SINE) families (Tu types I and II) and a novel tRNA-derived SINE family (Tu type III) from the tree shrew (Tupaia belangeri). Tu type I contains a monomer unit of a 7SL RNA-derived Alu-like sequence and a tRNA-derived region that includes internal RNA polymerase III promoters. Tu type II has a similar hybrid structure, although the monomer unit of the 7SL RNA-derived sequence is replaced by a dimer. Along with the primate Alu, the galago Alu type II, and the rodent B1, these two families represent the fourth and fifth 7SL RNA-derived SINE families to be identified. Furthermore, comparison of the Alu domains of Tu types I and II with those of other 7SL RNA-derived SINEs reveals that the nucleotides responsible for stabilization of the Alu domain have been conserved during evolution, providing the possibility that these conserved nucleotides play an indispensable role in retropositional activity. Evolutionary relationships among these 7SL RNA-derived SINE families, as well as phylogenetic relationships of their host species, are discussed.

Alu Elements↗
PubMed2002

Combining multiple data sets in a likelihood analysis: which models are the best?

Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecular data sets. Here, we compare several models for combining different genes for the purpose of evaluating the likelihood of tree topologies. Three methods of branch length estimation were studied: assuming all genes have the same branch lengths (concatenate model), assuming that branch lengths are proportional among genes (proportional model), or assuming that each gene has a separate set of branch lengths (separate model). We also compared three models of among-site rate variation: the homogenous model, a model that assumes one gamma parameter for all genes, and a model that assumes one gamma parameter for each gene. On the basis of two nuclear and one mitochondrial amino acid data sets, our results suggest that, depending on the data set chosen, either the separate model or the proportional model represents the most appropriate method for branch length analysis. For all the data sets examined, one gamma parameter for each gene represents the best model for among-site rate variation. Using these models we analyzed alternative mammalian tree topologies, and we describe the effect of the assumed model on the maximum likelihood tree. We show that the choice of the model has an impact on the best phylogeny obtained.

Animals↗
PubMed2002

Mosaic structure and retropositional dynamics during evolution of subfamilies of short interspersed elements in African cichlids.

The African cichlid (AFC) family of short interspersed elements (SINEs) is found in the genomes of cichlid fish. The alignment of the sequences of 70 members of this family, isolated from such fish in Africa, revealed the presence of correlated changes in specific nucleotides (diagnostic nucleotides) that allowed us to categorize the various members into six subfamilies, which were designated Af1 through Af6. Dividing the SINE consensus sequence into a 5'-head and 3'-tail region, these subfamilies were defined by various combinations of four types of head region (A-D) and three types of tail region [X, Y, and (YX)], with each region of each type including unique diagnostic nucleotides. The observed structures of the subfamilies Af1 through Af6 were AX, AY, CY, A(YX), BY, and DX, respectively. The formation of such structures might have involved the shuffling of head or tail regions among preexisting and existing (or both) subfamilies of the AFC family (and, probably, even another SINE family or a pseudogene for a tRNA in the case of the Af6 subfamily) by recombination at the so-called core region during the course of evolution. By plotting the timing of the retroposition of individual members of each subfamily on a phylogenetic tree of AFCs, we found that the Af3 and Af6 subfamilies became active only recently in the evolutionary history of these fish. The integrity of the 3'-tails of SINEs, which are, apparently, recognized by reverse transcriptase, has been reported to be indispensable for retention of retropositional activity. Therefore, we postulate that recombination might have been involved in the apparent recent activation of the retroposition of the Af3 and Af6 subfamilies via introduction of active tails (types Y and X, respectively) into potential ancestral sequences that might have had inactive tails. If this hypothesis is correct, shuffling of tail regions among subfamilies by recombination at the core region might have played a role in the recycling of dead copies of AFC SINEs.

Animals↗
PubMed2002

V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5'-end tRNA-related region and followed by a potentially recombinogenic (TG)(n) tract, with a 3' tail derived from the 3' untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be approximately 550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3' tails of V-SINEs differ from one another, it is possible that the original 3' tail might have been replaced, via recombination, by the 3' tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates.

Amino Acid Sequence↗