Yuji Kohara
A5020422862- Genetics, Aging, and Longevity in Model Organisms
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Developmental Biology and Gene Regulation
- Marine Ecology and Invasive Species
- Protist diversity and phylogeny
- CRISPR and Genetic Engineering
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Reproductive Biology and Fertility
- Animal Genetics and Reproduction
- Microbial Community Ecology and Physiology
- Circadian rhythm and melatonin
- Bacteriophages and microbial interactions
- DNA Repair Mechanisms
- Wheat and Barley Genetics and Pathology
- Genetic diversity and population structure
- Spaceflight effects on biology
- Genomics and Chromatin Dynamics
- Identification and Quantification in Food
- Polar Research and Ecology
- Mitochondrial Function and Pathology
- Nematode management and characterization studies
- RNA Research and Splicing
National Institute of Genetics
2011-2023
The Graduate University for Advanced Studies, SOKENDAI
2004-2017
Research Organization of Information and Systems
2004-2017
Second Genome (United States)
2016
The University of Tokyo
2001-2011
National Institute for Basic Biology
1999-2009
National Institute for Environmental Studies
2009
University of Miyazaki
2009
Stanford University
2008
Niigata University
2007
We report the draft genome sequence of model moss Physcomitrella patens and compare its features with those flowering plants, from which it is separated by more than 400 million years, unicellular aquatic algae. This comparison reveals genomic changes concomitant evolutionary movement to land, including a general increase in gene family complexity; loss genes associated environments (e.g., flagellar arms); acquisition for tolerating terrestrial stresses variation temperature water...
The first chordates appear in the fossil record at time of Cambrian explosion, nearly 550 million years ago. modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate origins chordate and vertebrates, we generated draft protein-coding portion genome most studied ascidian, Ciona intestinalis . contains ∼16,000 genes, similar number other invertebrates, but only half that found vertebrates. Vertebrate gene families are typically simplified form ,...
Lancelets (‘amphioxus’) are the modern survivors of an ancient chordate lineage, with a fossil record dating back to Cambrian period. Here we describe structure and gene content highly polymorphic ∼520-megabase genome Florida lancelet Branchiostoma floridae, analyse it in context evolution. Whole-genome comparisons illuminate murky relationships among three groups (tunicates, lancelets vertebrates), allow not only reconstruction complement last common ancestor but also partial its genomic...
The medaka fish (Oryzias latipes) is a popular pet in Japan and more recently laboratory model organism for developmental genetics evolutionary biology. Now the medaka's genome has been sequenced analysed by large Japanese consortium. Cichlids stickleback, which are emerging systems understanding genetic basis of vertebrate speciation, evolutionarily closer to than zebrafish, so sequence will yield valuable insights into 400 million years evolution. long organism; it now its Teleosts...
The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical physiological adaptations to land, a life cycle with alternation between multicellular haploid diploid generations that facilitated efficient dispersal desiccation tolerant spores, in plant. We analyzed genome liverwort Marchantia polymorpha, member basal plant...
Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support lives photosynthetic eukaryotes, including higher plants1,2. Here we report 16,520,305-base-pair sequence 20 chromosomes red alga Cyanidioschyzon merolae 10D as first complete algal genome. We identified 5,331 in total, which at least 86.3% were expressed. Unique characteristics this genomic structure include: a lack introns all but 26 genes; only three copies ribosomal...
Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of Bruijn graph structure predominantly used. To address increasing demand for sequencing nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical methods are used overcome such problems. However, these costly and time consuming, forfeiting...
DNA methylation is an important epigenetic modification regulating various biological phenomena, including genomic imprinting and transposon silencing. It known that of the differentially methylated regions (DMRs) associated with paternally imprinted genes some repetitive elements occurs during male germ cell development in mouse. We have performed a detailed analysis DMRs (H19, Dlk1/Gtl2 Rasgrf1), interspersed repeats [SineB1, intracisternal A particle (IAP) Line1] satellite (major minor)...
Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as two rounds whole-genome duplications (2R WGD) affected evolutionary complexity novelty in vertebrates. Reconstructing ancestral highly nontrivial because difficulty identifying traces originating from 2R WGD. To resolve this problem, we developed a novel method capable pinning down remains WGD human medaka fish using invertebrate...
Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one most stress-tolerant species. Precise gene repertoire analyses reveal presence proportion (1.2% or less) putative foreign genes, loss pathways that promote stress damage, expansion families...
The whole genome of Jatropha curcas was sequenced, using a combination the conventional Sanger method and new-generation multiplex sequencing methods. Total length non-redundant sequences thus obtained 285 858 490 bp consisting 120 586 contigs 29 831 singlets. They accounted for ∼95% gene-containing regions with average G + C content 34.3%. A total 40 929 complete partial structures protein encoding genes have been deduced. Comparison other plant species indicated that 1529 (4%) putative...
Three-prime untranslated regions (3'UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3' rapid amplification complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined approximately 26,000 distinct 3'UTRs in Caenorhabditis elegans for 85% the 18,328 experimentally supported protein-coding genes revised 40% gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed...
The mosses and flowering plants diverged >400 million years ago. have haploid-dominant life cycles, whereas the are diploid-dominant. common ancestors of land been inferred to be haploid-dominant, suggesting that genes used in diploid body were recruited from haploid during evolution plants. To assess this evolutionary hypothesis, we constructed an EST library moss Physcomitrella patens , compared transcriptome genome Arabidopsis thaliana . We full-length enriched cDNA libraries...
The development of the nervous system requires coordinated activity a variety regulatory factors that define individual properties specific neuronal subtypes. We report cascade composed three homeodomain proteins act to interneuron class in nematode C. elegans. describe set differentiation markers characteristic for AIY and show ceh-10 paired-type ttx-3 LIM-type homeobox genes function regulate all known subtype-specific features interneurons. In contrast, acquisition several pan-neuronal is...