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 the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.[Supplemental material is available online at www.genome.org.]Early vertebrate genome evolution has long been in need of clarification, and it is now of particular interest because several distantly related vertebrate genomes were recently sequenced. The 2R hypothesis postulates that two rounds of whole-genome duplication (2R WGD) occurred at the base of the vertebrate lineage (Ohno 1970;Holland et al. 1994) because of the observation that invertebrates have one Hox gene cluster, whereas lobe-finned fishes and land vertebrates have four clusters. However, the 2R hypothesis has been quite controversial until recently (Skrabanek and
We performed threefold shotgun sequencing of the silkworm (Bombyx mori) genome to obtain a draft sequence and establish a basic resource for comprehensive genome analysis. By using the newly developed RAMEN assembler, the sequence data derived from whole-genome shotgun (WGS) sequencing were assembled into 49,345 scaffolds that span a total length of 514 Mb including gaps and 387 Mb without gaps. Because the genome size of the silkworm is estimated to be 530 Mb, almost 97% of the genome has been organized in scaffolds, of which 75% has been sequenced. By carrying out a BLAST search for 50 characteristic Bombyx genes and 11,202 non-redundant expressed sequence tags (ESTs) in a Bombyx EST database against the WGS sequence data, we evaluated the validity of the sequence for elucidating the majority of silkworm genes. Analysis of the WGS data revealed that the silkworm genome contains many repetitive sequences with an average length of <500 bp. These repetitive sequences appear to have been derived from truncated transposons, which are interspersed at 2.5- to 3-kb intervals throughout the genome. This pattern suggests that silkworm may have an active mechanism that promotes removal of transposons from the genome. We also found evidence for insertions of mitochondrial DNA fragments at 9 sites. A search for Bombyx orthologs to Drosophila genes controlling sex determination in the WGS data revealed 11 Bombyx genes and suggested that the sex-determining systems differ profoundly between the two species.
One of the most powerful techniques for attributing functions to genes in uni-and multicellular organisms is comprehensive analysis of mutant traits. In this study, systematic and quantitative analyses of mutant traits are achieved in the budding yeast Saccharomyces cerevisiae by investigating morphological phenotypes. Analysis of fluorescent microscopic images of triple-stained cells makes it possible to treat morphological variations as quantitative traits. Deletion of nearly half of the yeast genes not essential for growth affects these morphological traits. Similar morphological phenotypes are caused by deletions of functionally related genes, enabling a functional assignment of a locus to a specific cellular pathway. The high-dimensional phenotypic analysis of defined yeast mutant strains provides another step toward attributing gene function to all of the genes in the yeast genome.cell morphology ͉ functional genomics ͉ high-dimensional phenotyping ͉ phenome O ne of the ultimate goals of genetics is to reveal relationships between gene function and phenotypic traits. Comprehensive analysis of mutant traits is a very powerful technique for attributing functions to genes in uni-and multicellular organisms. In the budding yeast Saccharomyces cerevisiae, a complete set of mutants, each of which carries a precise deletion of one yeast ORF, has been systematically constructed (1). By using these mutant strains combined with microarray and robot technology, genome-wide analyses of various mutant traits, including general growth rate, fitness under a particular condition, and sensitivity to drugs, has been reported (reviewed in ref. 2).Cell morphology becomes an attractive target for comprehensive analysis, because more powerful methods for fluorescent microscopic imaging analysis in biological research have been emerging after development of high-resolution microscopes and specific fluorescent dyes. Yeast cell morphology reflects various cellular events, including progression through the cell cycle, establishment of cell polarity, and regulation of cell size control. Previous genome-wide studies of yeast morphology were focused on a specific morphology, such as cell size, cell shape, or bud site pattern (3-6), and therefore extracted limited information. Because morphological traits are often judged ''by eye,'' it has remained difficult to obtain quantitative and reproducible results.We recently developed an image-processing system that automatically processes digital cell images of each yeast cell (7,8) to obtain quantitative morphological data of yeast mutant cells. Mannoprotein (as a cell wall component marker), the actin cytoskeleton, and nuclear DNA are specifically stained simultaneously. Cells are then photographed, and fluorescence images are automatically processed. The obtained images of all yeast mutants and data-mining functions are available at our Saccharomyces cerevisiae Morphological Database (SCMD) web site (8,9).In this study, we employ high-dimensional and quantitative phenotyping of yeast muta...
The oncogenic mechanisms underlying acute lymphoblastic leukemia (ALL) in adolescents and young adults (AYA; 15-39 years old) remain largely elusive. Here we have searched for new oncogenes in AYA-ALL by performing RNA-seq analysis of Philadelphia chromosome (Ph)-negative AYA-ALL specimens (n = 73) with the use of a next-generation sequencer. Interestingly, insertion of D4Z4 repeats containing the DUX4 gene into the IGH locus was frequently identified in B cell AYA-ALL, leading to a high level of expression of DUX4 protein with an aberrant C terminus. A transplantation assay in mice demonstrated that expression of DUX4-IGH in pro-B cells was capable of generating B cell leukemia in vivo. DUX4 fusions were preferentially detected in the AYA generation. Our data thus show that DUX4 can become an oncogenic driver as a result of somatic chromosomal rearrangements and that AYA-ALL may be a clinical entity distinct from ALL at other ages.
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