Sexuality in plants, unveiled from genome evolution

Sexual polymorphism, a main strategy to maintain genetic diversity within a species, has long been a major focus in biology. Notwithstanding, in plants, evolution of sexual systems and mechanisms underlying these transitions have been little unveiled. We have elucidated the molecular mechanism of sex determination in persimmons (Diospyros spp.), where the Y-encoded smRNA gene OGI can repress the female-determining gene MeGI, and also in kiwifruits (Actinidia spp.), where the Y-encoded two sex determinants, Shy Girl and Friendly Boy, control gynoecium and androecium development, respectively. Although the molecular functions of these determinants are distinct, they have common evolutionary scenarios involving transitions of sexual systems. In persimmon, a recent genome triplication (hexaploidization) in cultivated persimmon (D. kaki) derived “flexible” sexuality via establishing epigenetic layers on the two sex determinants. On the other hand, an ancient Diospyros-specific paleo-genome duplication (paleo-tetraploidization) enabled neofunctionalization in the proto-MeGI, via positive selection, to establish a new function as a sex determinant. In kiwifruit, one of the two sex determinants, Shy Girl, was derived from neofunctionalization via Actinidia-specific duplication event. These findings exemplify how plant-specific numerous duplication events can drive flexible genetic material whose variation can be selected for development of new sexual systems

Recent advances in DNA microarrays.

The structure of the human genome is almost completely elucidated and the life sciences will now aim for a general and integrated study of gene expressions and the functional elucidation of proteins. In such a study, various new techniques have been developed, and DNA microarray technology is the most representative one. As for the DNA microarray techniques, several thousands to tens of thousands of gene segments are immobilized on a glass slide at high density, and cDNA probes prepared from specific cells or tissues are hybridized on the slides from which gene expression profiles are obtained at one sweep in a short time. The present development of this technique and its possible application to medicine-related fields are described.&#60;/P&#62;</p

Comparison of DNA methylation levels of repetitive loci during bovine development

<p> Abstract</p> <p>Background</p> <p>DNA methylation of cytosine residues in CpG dinucleotide controls gene expression and dramatically changes during development. Its pattern is disrupted in cloned animals suggesting incomplete reprogramming during somatic cell nuclear transfer (the first reprogramming). However, the second reprogramming occurs in the germ cells and epigenetic errors in somatic cells of cloned animals should be erased. To analyze the DNA methylation changes on the spermatogenesis of bulls, we measured DNA methylation levels of three repetitive elements in blastocysts, blood and sperm.</p> <p>Methods</p> <p>DNA from PBLs (peripheral blood leukocytes), sperm and individual IVF (<it>in vitro</it> fertilized) and parthenogenetic blastocysts was isolated and bisulfite converted. Three repetitive elements; Satellite I, Satellite II and <it>art2</it> sequences were amplified by PCR with specific pairs of primers. The PCR product was then cut by restriction enzymes and analyzed by agarose gel electrophoresis for determining the DNA methylation levels.</p> <p>Results</p> <p>Both Satellite I and Satellite II sequences were highly methylated in PBLs, whereas hypo-methylated in sperm and blastocysts. The <it>art2</it> sequence was half methylated both in PBLs and sperm but less methylated in blastocysts. There was no difference in DNA methylation levels between IVF and parthenogenetic blastocysts.</p> <p>Conclusions</p> <p>These results suggest that there is a dynamic change of DNA methylation during embryonic development and spermatogenesis in cattle. Satellite I and Satellite II regions are methylated during embryogenesis and then de-methylated during spermatogenesis. However, <it>art2</it> sequences are not de-methylated during spermatogenesis, suggesting that this region is not reprogrammed during germ cell development. These results show dynamic changes of DNA methylation levels during bovine embryogenesis, especially genome-wide reprogramming in germ cells.</p

Polyploidy before and after domestication of crop species

Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species

Extended collimator model for pencil-beam dose calculation in proton radiotherapy

We have developed a simple collimator model to improve the accuracy of penumbra behaviour in pencil-beam dose calculation for proton radiotherapy. In this model, transmission of particles through a three-dimensionally extended opening of a collimator is calculated in conjunction with phase-space distribution of the particles. Comparison of the dose distributions calculated using the new three-dimensional collimator model and the conventional twodimensional model to lateral dose profiles experimentally measured with collimated proton beams showed the superiority of the new model over the conventional one

Ongoing Rapid Evolution of a Post-Y Region Revealed by Chromosome-Scale Genome Assembly of a Hexaploid Monoecious Persimmon (Diospyros kaki)

Plants have evolved sex chromosomes independently in many lineages, and loss of separate sexes can also occur. In this study, we assembled a monoecious recently hexaploidized persimmon (Diospyros kaki), in which the Y chromosome has lost the maleness-determining function. Comparative genomic analysis of D. kaki and its dioecious relatives uncovered the evolutionary process by which the nonfunctional Y chromosome (or Y-monoecy) was derived, which involved silencing of the sex-determining gene, OGI, approximately 2 million years ago. Analyses of the entire X and Y-monoecy chromosomes suggested that D. kaki's nonfunctional male-specific region of the Y chromosome (MSY), which we call a post-MSY, has conserved some characteristics of the original functional MSY. Specifically, comparing the functional MSY in Diospyros lotus and the nonfunctional "post-MSY" in D. kaki indicated that both have been rapidly rearranged, mainly via ongoing transposable element bursts, resembling structural changes often detected in Y-linked regions, some of which can enlarge the nonrecombining regions. The recent evolution of the post-MSY (and possibly also MSYs in dioecious Diospyros species) therefore probably reflects these regions' ancestral location in a pericentromeric region, rather than the presence of male-determining genes and/or genes controlling sexually dimorphic traits

Characterization of epstein-barr virus-infected mantle cell lymphoma lines.

It has been reported that Epstein-Barr virus (EBV) resides in resting B cells in vivo. However, an ideal in vitro system for studying EBV latent infection in vivo has not yet been established. In this study, a mantle cell lymphoma line, SP53, was successfully infected with a recombinant EBV containing a neomycin-resistant gene. The EBV-carrying SP53 cells were obtained by selection using G418. They expressed EBER-1, EBNAs, and LMP1; this expression pattern of the EBV genes was similar to that in a lymphoblastoid cell line (LCL). However, proliferation assay showed that the EBV-carrying SP53 cells have a doubling time of 73 h, compared with 57 h of SP53 cells. Transplantation of 10(8) SP53 cells to nude mice formed tumors in 4 of 10 mice inoculated, but the EBV-carrying SP53 cells did not. Unexpectedly, EBV infection reduced the proliferation and tumorigenicity of SP53 cells. However, the EBV-carrying SP53 cells showed higher resistance to apoptosis induced by serum starvation than did the SP53 cells. The inhibition of proliferation and the resistance to apoptosis induced in SP53 cells by EBV infection indicate that this cell line might to some extent provide a model of in vivo EBV reservoir cells.</p

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants

Most angiosperms bear hermaphroditic flowers, but a few species have evolved outcrossing strategies, such as dioecy, the presence of separate male and female individuals. We previously investigated the mechanisms underlying dioecy in diploid persimmon (D. lotus) and found that male flowers are specified by repression of the autosomal gene MeGI by its paralog, the Y-encoded pseudo-gene OGI. This mechanism is thought to be lineage-specific, but its evolutionary path remains unknown. Here, we developed a full draft of the diploid persimmon genome (D. lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. We also identified three paralogs, MeGI, OGI and newly identified Sister of MeGI (SiMeGI). Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. Transformation of tobacco plants with MeGI and SiMeGI revealed that MeGI specifically acquired a new function as a repressor of male organ development, while SiMeGI presumably maintained the original function. Later, a segmental duplication event spawned MeGI's regulator OGI on the Y-chromosome, completing the path leading to dioecy, and probably initiating the formation of the Y-chromosome. These findings exemplify how duplication events can provide flexible genetic material available to help respond to varying environments and provide interesting parallels for our understanding of the mechanisms underlying the transition into dieocy in plants. Author summary Plant sexuality has fascinated scientists for decades. Most plants can self-reproduce but not all. For example, a small subset of species have evolved a system called dioecy, with separate male and female individuals. Dioecy has evolved multiple times independently and, while we do not understand the molecular mechanisms underlying dioecy in many of these species yet, a picture is starting to emerge with recent progress in several dioecious species. Here, we focused on the evolutionary events leading to dioecy in persimmon. Our previous work had identified a pair of genes regulating sex in this species, called OGI and MeGI. We drafted the whole genome sequence of diploid persimmon to investigate their evolutionary history. We discovered a lineage-specific whole-genome duplication event, and observed that MeGI underwent adaptive evolution after this event. Transgenic analyses validated that MeGI newly acquired a male-suppressor function, while the other copy of this gene, SiMeGI, did not. The regulator of MeGI, OGI, resulted from a second smaller-scale segmental duplication event, finalizing the system. This study sheds light on the role of duplication as a mechanism that promote flexible genes functions, and how it can affect important biological functions, such as the establishment of a new sexual system