Transforming Biobanking with AI: Perspectives from Leading Experts.
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Journal Article↗
Biomedical subjects
Soichi Ogishima
Publications and source records attributed to Soichi Ogishima.
Missing link in the evolution of Hox clusters.
Hox cluster has key roles in regulating the patterning of the antero-posterior axis in a metazoan embryo. It consists of the anterior, central and posterior genes; the central genes have been identified only in bilaterians, but not in cnidarians, and are responsible for archiving morphological complexity in bilaterian development. However, their evolutionary history has not been revealed, that is, there has been a "missing link". Here we show the evolutionary history of Hox clusters of 18 bilaterians and 2 cnidarians by using a new method, "motif-based reconstruction", examining the gain/loss processes of evolutionarily conserved sequences, "motifs", outside the homeodomain. We successfully identified the missing link in the evolution of Hox clusters between the cnidarian-bilaterian ancestor and the bilaterians as the ancestor of the central genes, which we call the proto-central gene. Exploring the correspondent gene with the proto-central gene, we found that one of the acoela Hox genes has the same motif repertory as that of the proto-central gene. This interesting finding suggests that the acoela Hox cluster corresponds with the missing link in the evolution of the Hox cluster between the cnidarian-bilaterian ancestor and the bilaterians. Our findings suggested that motif gains/diversifications led to the explosive diversity of the bilaterian body plan.
Amino Acid Motifs↗
Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method.
A new method for reconstructing phylogenetic relationships of within-host (patient) viral evolution from noncontemporaneous samples is presented. This method has two important features: noncontemporaneous viral samples can be dealt with by a simple computing algorithm, and both neutral and adaptive evolution patterns occurring during the process of viral evolution can be estimated. In our previous study, we proposed a preliminary formulation of this algorithm that was based on the maximum likelihood method. However, that preliminary formulation was difficult to use because the calculation of the likelihood required an extremely large amount of time and the number of possible tree topologies increased exponentially according to the increase in the number of viral variants. In this paper, we propose another new algorithm, referred to as a distance-based sequential-linking algorithm, in which the neighbor-joining method is employed for reconstruction of the longitudinal phylogenetic tree from serial viral samples. This algorithm is applied to a longitudinal data set of the env gene (V3 region) of human immunodeficiency virus type 1 (HIV-1) obtained over 7 years after the infection of a single patient. The results suggest that this method can successfully reconstruct a longitudinal phylogenetic tree from noncontemporaneous viral samples within a reasonable calculation time. This revised method proved to be a useful tool for estimating the dynamic process of within-host viral evolution.
Evolution, Molecular↗
Standardized phylogenetic tree: a reference to discover functional evolution.
Functional evolution is often driven by positive natural selection. Although it is thought to be rare in evolution at the molecular level, its effects may be observed as the accelerated evolutionary rates. Therefore one of the effective ways to identify functional evolution is to identify accelerated evolution. Many methods have been developed to test the statistical significance of the accelerated evolutionary rate by comparison with the appropriate reference rate. The rates of synonymous substitution are one of the most useful and popular references, especially for large-scale analyses. On the other hand, these rates are applicable only to a limited evolutionary time period because they saturate quickly--i.e., multiple substitutions happen frequently because of the lower functional constraint. The relative rate test is an alternative method. This technique has an advantage in terms of the saturation effect but is not sufficiently powerful when the evolutionary rate differs considerably among phylogenetic lineages. For the aim to provide a universal reference tree, we propose a method to construct a standardized tree which serves as the reference for accelerated evolutionary rate. The method is based upon multiple molecular phylogenies of single genes with the aim of providing higher reliability. The tree has averaged and normalized branch lengths with standard deviations for statistical neutrality limits. The standard deviation also suggests the reliability level of the branch order. The resulting tree serves as a reference tree for the reliability level of the branch order and the test of evolutionary rate acceleration even when some of the species lineages show an accelerated evolutionary rate for most of their genes due to bottlenecking and other effects.
Animals↗