Oxford University Press (OUP) Acta Medica Okayama 1040-4651 37 7 2025 Pancentromere analysis of Allium species reveals diverse centromere positions in onion and gigantic centromeres in garlic koaf142 EN Kiyotaka Nagaki Institute of Plant Science and Resources, Okayama University Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Keisuke Tanaka NODAI Genome Research Center, Tokyo University of Agriculture Hisato Kobayashi NODAI Genome Research Center, Tokyo University of Agriculture In eukaryotes, centromeres interact with the kinetochore for distribution of genetic information in cell division, yet their sequence and size are diverse among species. However, their position on chromosomes is considered to be conserved within a species. In this study, we analyzed the centromeres of 3 Allium species, namely, Welsh onion (Allium fistulosum), onion (Allium cepa), and garlic (Allium sativum) via pancentromere analysis and repetitive sequence analysis of centromeres and their neighborhoods and revealed their mobility, sequence organization, and size. Among the 3 species, Welsh onion and garlic had stable centromeres, but the onion centromere appeared to be polymorphic and frequently differed in position by up to 28.0 Mb among cultivars and between multiple individuals of the same cultivar. This mobility was stabilized by hybridization with Welsh onions. Furthermore, these 3 species have very different centromere sequence organization, including differences in the existence and maturity of centromeric satellites, and differences in centromere size, with Welsh onion having a centromere of 1.9 Mb, and garlic having a centromere of ∼10.6 Mb, the largest of any organism with monocentric chromosomes analyzed to date. Our pancentromere analysis of these Allium species reveals the variation in sequence organization, size, and position of this important chromosomal region. No potential conflict of interest relevant to this article was reported.

Oxford University Press (OUP) Acta Medica Okayama 0032-0781 64 11 2023 Transcriptomic Interpretation on Explainable AI-Guided Intuition Uncovers Premonitory Reactions of Disordering Fate in Persimmon Fruit 1323 1330 EN Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Eriko Kuwada Graduate School of Environmental and Life Science, Okayama University Maria Suzuki Graduate School of Environmental and Life Science, Okayama University Tetsuya Suzuki Gifu Prefectural Agricultural Technology Center Takeshi Niikawa Gifu Prefectural Agricultural Technology Center Seiichi Uchida Faculty of Information Science and Electrical Engineering, Kyusyu University Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Deep neural network (DNN) techniques, as an advanced machine learning framework, have allowed various image diagnoses in plants, which often achieve better prediction performance than human experts in each specific field. Notwithstanding, in plant biology, the application of DNNs is still mostly limited to rapid and effective phenotyping. The recent development of explainable CNN frameworks has allowed visualization of the features in the prediction by a convolutional neural network (CNN), which potentially contributes to the understanding of physiological mechanisms in objective phenotypes. In this study, we propose an integration of explainable CNN and transcriptomic approach to make a physiological interpretation of a fruit internal disorder in persimmon, rapid over-softening. We constructed CNN models to accurately predict the fate to be rapid softening in persimmon cv. Soshu, only with photo images. The explainable CNNs, such as Gradient-weighted Class Activation Mapping (Grad-Class Activation Mapping (CAM)) and guided Grad-CAM, visualized specific featured regions relevant to the prediction of rapid softening, which would correspond to the premonitory symptoms in a fruit. Transcriptomic analyses to compare the featured regions of the predicted rapid-softening and control fruits suggested that rapid softening is triggered by precocious ethylene signal–dependent cell wall modification, despite exhibiting no direct phenotypic changes. Further transcriptomic comparison between the featured and non-featured regions in the predicted rapid-softening fruit suggested that premonitory symptoms reflected hypoxia and the related stress signals finally to induce ethylene signals. These results would provide a good example for the collaboration of image analysis and omics approaches in plant physiology, which uncovered a novel aspect of fruit premonitory reactions in the rapid-softening fate. No potential conflict of interest relevant to this article was reported.

Oxford University Press Acta Medica Okayama 1340-2838 30 5 2023 Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon dsad015 EN Ayano Horiuchi Graduate School of Environmental and Life Science, Okayama University Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Kenta Shirasawa Kazusa DNA Research Institute Noriyuki Onoue Institute of Fruit Tree and Tea Science, NARO Ryusuke Matsuzaki Institute of Fruit Tree and Tea Science, NARO Ryutaro Tao Graduate School of Agriculture, Kyoto University Yasutaka Kubo Graduate School of Environmental and Life Science, Okayama University Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties in applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characteristics, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events. No potential conflict of interest relevant to this article was reported.

Oxford University Press Acta Medica Okayama 0737-4038 40 7 2023 Ongoing Rapid Evolution of a Post-Y Region Revealed by Chromosome-Scale Genome Assembly of a Hexaploid Monoecious Persimmon (Diospyros kaki) msad151 EN Ayano Horiuchi Graduate School of Environmental and Life Science, Okayama University Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Kenta Shirasawa Department of Frontier Research and Development, Kazusa DNA Research Institute Noriyuki Onoue Institute of Fruit Tree and Tea Science, NARO Naoko Fujita Graduate School of Environmental and Life Science, Okayama University Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Takashi Akagi Graduate School of Environmental and Life Science, Okayama University 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. No potential conflict of interest relevant to this article was reported.

Elsevier Acta Medica Okayama 13695266 69 2022 Polyploidy before and after domestication of crop species 102255 EN Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Katharina Jung Department of Evolutionary Biology and Environmental Studies, University of Zurich Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Kentaro K. Shimizu Department of Evolutionary Biology and Environmental Studies, University of Zurich 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. No potential conflict of interest relevant to this article was reported.

Wiley Acta Medica Okayama 1526-9914 23 2022 Validation of pencil beam scanning proton therapy with multi-leaf collimator calculated by a commercial Monte Carlo dose engine e13817 EN Yuki Tominaga Division of Radiological Technology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University Yusuke Sakurai Department of Radiotherapy, Medical Co. Hakuhokai, Osaka Proton Therapy Clinic Junya Miyata Division of Radiological Technology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University Shuichi Harada Hyogo Ion Beam Medical Support Takashi Akagi Hyogo Ion Beam Medical Support Masataka Oita Division of Radiological Technology, Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University This study aimed to evaluate the clinical beam commissioning results and lateral penumbra characteristics of our new pencil beam scanning (PBS) proton therapy using a multi-leaf collimator (MLC) calculated by use of a commercial Monte Carlo dose engine. Eighteen collimated uniform dose plans for cubic targets were optimized by the RayStation 9A treatment planning system (TPS), varying scan area, modulation widths, measurement depths, and collimator angles. To test the patient-specific measurements, we also created and verified five clinically realistic PBS plans with the MLC, such as the liver, prostate, base-of-skull, C-shape, and head-and-neck. The verification measurements consist of the depth dose (DD), lateral profile (LP), and absolute dose (AD). We compared the LPs and ADs between the calculation and measurements. For the cubic plans, the gamma index pass rates (gamma-passing) were on average 96.5% +/- 4.0% at 3%/3 mm for the DD and 95.2% +/- 7.6% at 2%/2 mm for the LP. In several LP measurements less than 75 mm depths, the gamma-passing deteriorated (increased the measured doses) by less than 90% with the scattering such as the MLC edge and range shifter. The deteriorated gamma-passing was satisfied by more than 90% at 2%/2 mm using uncollimated beams instead of collimated beams except for three planes. The AD differences and the lateral penumbra width (80%-20% distance) were within +/- 1.9% and +/- 1.1 mm, respectively. For the clinical plan measurements, the gamma-passing of LP at 2%/2 mm and the AD differences were 97.7% +/- 4.2% on average and within +/- 1.8%, respectively. The measurements were in good agreement with the calculations of both the cubic and clinical plans inserted in the MLC except for LPs less than 75 mm regions of some cubic and clinical plans. The calculation errors in collimated beams can be mitigated by substituting uncollimated beams. No potential conflict of interest relevant to this article was reported.

Frontiers Media SA Acta Medica Okayama 1664-462X 13 2022 Examining the Role of Low Temperature in Satsuma Mandarin Fruit Peel Degreening via Comparative Physiological and Transcriptomic Analysis 918226 EN Oscar W. Mitalo Graduate School of Environmental and Life Science, Okayama University William O. Asiche Department of Research and Development, Del Monte Kenya Ltd Seung W. Kang Graduate School of Life and Environmental Sciences, University of Tsukuba Hiroshi Ezura Graduate School of Life and Environmental Sciences, University of Tsukuba Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Yasutaka Kubo Graduate School of Environmental and Life Science, Okayama University Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Peel degreening is the most conspicuous aspect of fruit ripening in many citrus fruits because of its importance for marketability. In this study, peel degreening in response to propylene (an ethylene analog) and at varying storage temperatures was characterized in Satsuma mandarin (Citrus unshiu Marc.) fruit. Propylene treatment triggered rapid peel degreening (within 4-6 days), indicated by an increase in the citrus color index (CCI) and chlorophyll loss. Peel degreening was also observed in fruit at 10 degrees C and 15 degrees C after 28-42 days, with gradual CCI increase and chlorophyll reduction. However, fruit at 5 degrees C, 20 degrees C, and 25 degrees C remained green, and no substantial changes in peel CCI and chlorophyll content were recorded during the 42-day storage duration. The transcriptomes of peels of fruit treated with propylene for 4 days and those stored at varying temperatures for 28 days were then analyzed by RNA-Seq. We identified three categories of differentially expressed genes that were regulated by (i) propylene (and by analogy, ethylene) alone, (ii) low temperature (5 degrees C, 10 degrees C, or 15 degrees C vs. 25 degrees C) alone, and (iii) either propylene or low temperature. Gene-encoding proteins associated with chlorophyll degradation (such as CuSGR1, CuNOL, CuACD2, CuCAB2, and CuLHCB2) and a transcription factor (CuERF114) were differentially expressed by propylene or low temperature. To further examine temperature-induced pathways, we also monitored gene expression during on-tree fruit maturation vs. postharvest. The onset of on-tree peel degreening coincided with autumnal drops in field temperatures, and it was accompanied by differential expression of low temperature-regulated genes. On the contrary, genes that were exclusively regulated by propylene (such as CuCOPT1 and CuPOX-A2) displayed insignificant expression changes during on-tree peel degreening. These findings indicate that low temperatures could be involved in the fruit ripening-related peel degreening independently of ethylene. No potential conflict of interest relevant to this article was reported.

Japanese Society for Horticultural Science Acta Medica Okayama 2189-0102 91 3 2022 Deep Learning Predicts Rapid Over-softening and Shelf Life in Persimmon Fruits EN Maria Suzuki Graduate School of Environmental and Life Science, Okayama University Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Hideaki Asakuma Fukuoka Agriculture and Forestry Research Center Kouki Takeshita Department of Advanced Information Technology, Kyushu University Kohei Baba Department of Advanced Information Technology, Kyushu University Yasutaka Kubo Graduate School of Environmental and Life Science, Okayama University Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Seiichi Uchida Department of Advanced Information Technology, Kyushu University Takashi Akagi Graduate School of Environmental and Life Science, Okayama University In contrast to the progress in the research on physiological disorders relating to shelf life in fruit crops, it has been difficult to non-destructively predict their occurrence. Recent high-tech instruments have gradually enabled non-destructive predictions for various disorders in some crops, while there are still issues in terms of efficiency and costs. Here, we propose application of a deep neural network (or simply deep learning) to simple RGB images to predict a severe fruit disorder in persimmon, rapid over-softening. With 1,080 RGB images of ‘Soshu’ persimmon fruits, three convolutional neural networks (CNN) were examined to predict rapid over-softened fruits with a binary classification and the date to fruit softening. All of the examined CNN models worked successfully for binary classification of the rapid over-softened fruits and the controls with > 80% accuracy using multiple criteria. Furthermore, the prediction values (or confidence) in the binary classification were correlated to the date to fruit softening. Although the features for classification by deep learning have been thought to be in a black box by conventional standards, recent feature visualization methods (or “explainable” deep learning) has allowed identification of the relevant regions in the original images. We applied Grad-CAM, Guided backpropagation, and layer-wise relevance propagation (LRP), to find early symptoms for CNNs classification of rapid over-softened fruits. The focus on the relevant regions tended to be on color unevenness on the surface of the fruit, especially in the peripheral regions. These results suggest that deep learning frameworks could potentially provide new insights into early physiological symptoms of which researchers are unaware. No potential conflict of interest relevant to this article was reported.

Frontiers Media Acta Medica Okayama 1664-462X 11 2020 Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon 567249 EN Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Naoko Fujita Graduate School of Environmental and Life Science, Okayama University Ho-Wen Yang Department of Crop Sciences, University of Illinois at Urbana-Champaign Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Yasutaka Kubo Graduate School of Environmental and Life Science, Okayama University Ryutaro Tao Graduate School of Agriculture, Kyoto University Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Sex expression in plants is often flexible and contributes to the maintenance of genetic diversity within a species. In diploid persimmons (the genus Diospyros), the sexuality is controlled by the Y chromosome-encoded small-RNA gene, OGI, and its autosomal counterpart, MeGI. Hexaploid Oriental persimmon (Diospyros kaki) evolved more flexible sex expression, where genetically male individuals carrying OGI can produce both male and female flowers (monoecy). This is due to (semi-)inactivation of OGI by the Kali-SINE retrotransposon insertion on the promoter region and the resultant DNA methylations. Instead, flower sex determination in Oriental persimmon is also dependent on DNA methylation states of MeGI. Here, we focused on a cultivar, Kumemaru, which shows stable male flower production. Our results demonstrated that cv. Kumemaru carries OGI with Kali-SINE, which was highly methylated as well as in other monoecious cultivars; nevertheless, OGI gene could have a basal expression level. Transcriptomic analysis between cv. Kumemaru and 14 cultivars that predominantly produce female flowers showed differentially expressed genes (DEGs) specific to cv. Kumemaru, which is mainly involved in stress responses. Co-expression gene networks focusing on the DEGs also suggested the involvement of stress signals, mainly via gibberellin (GA), salicylic acid (SA), and especially jasmonic acid (JA) signal pathways. We also identified potential regulators of this co-expression module, represented by the TCP4 transcription factor. Furthermore, we attempted to identify cv. Kumemaru-specific transcript polymorphisms potentially contributing to derepressed OGI expression by cataloging subsequences (k-mers) in the transcriptomic reads from cv. Kumemaru and the other 14 female cultivars. Overall, although the direct genetic factor to activate OGI remains to be solved, our results implied the involvement of stress signals in the release of silenced OGI and the resultant continuous male production. No potential conflict of interest relevant to this article was reported.

OXFORD UNIV PRESS Acta Medica Okayama 1340-2838 27 3 2020 Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon dsaa012 EN Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Eiji Yamamoto Kazusa DNA Research Institute Kenta Shirasawa Kazusa DNA Research Institute Noriyuki Onoue Institute of Fruit Tree and Tea Science, NARO Atsushi Kono Institute of Fruit Tree and Tea Science, NARO Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Yasutaka Kubo Graduate School of Environmental and Life Science, Okayama University Ryutaro Tao Graduate School of Agriculture, Kyoto University Isabelle M. Henry Department of Plant Biology and Genome Center, University of California Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F-1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression. No potential conflict of interest relevant to this article was reported.

Oxford University Press Acta Medica Okayama 0022-0957 71 16 2020 Low temperature modulates natural peel degreening in lemon fruit independently of endogenous ethylene 4778 4796 EN Oscar W. Mitalo Graduate School of Environmental and Life Science, Okayama University Takumi Otsuki Graduate School of Environmental and Life Science, Okayama University Rui Okada Graduate School of Environmental and Life Science, Okayama University Saeka Obitsu Graduate School of Environmental and Life Science, Okayama University Kanae Masuda Graduate School of Environmental and Life Science, Okayama University Yuko Hojo Institute of Plant Science and Resources, Okayama University Takakazu Matsuura Institute of Plant Science and Resources, Okayama University Izumi C. Mori Institute of Plant Science and Resources, Okayama University Daigo Abe National Agriculture and Food Research Organization, Shikoku Research Station William O. Asiche Department of Research and Development, Del Monte Kenya Ltd Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Yasutaka Kubo Graduate School of Environmental and Life Science, Okayama University Koichiro Ushijima Graduate School of Environmental and Life Science, Okayama University Peel degreening is an important aspect of fruit ripening in many citrus fruit, and previous studies have shown that it can be advanced by ethylene treatment or by low-temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To determine how natural peel degreening is regulated in lemon fruit (Citrus limon), we studied transcriptome and physiochemical changes in the flavedo in response to ethylene treatment and low temperatures. Treatment with ethylene induced rapid peel degreening, which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25 degrees C, moderately low storage temperatures of 5-20 degrees C also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. Peel degreening of fruit on trees occurred in association with drops in ambient temperature, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit. No potential conflict of interest relevant to this article was reported.

Public Library of Science Acta Medica Okayama 1553-7404 16 2 2020 The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants e1008566 EN Takashi Akagi Graduate School of Environmental and Life Science, Okayama University Kenta Shirasawa Kazusa DNA Research Institute Hideki Nagasaki Kazusa DNA Research Institute Hideki Hirakawa Kazusa DNA Research Institute Ryutaro Tao Graduate School of Agriculture, Kyoto University Luca Comai Genome Center and Department of Plant Biology, University of California Davis Isabelle M. Henry Genome Center and Department of Plant Biology, University of California Davis 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. No potential conflict of interest relevant to this article was reported.

岡山大学農学部 Acta Medica Okayama 2186-7755 109 2020 ゲノム進化が紐解く植物の性決定 37 40 EN Takashi Akagi 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. No potential conflict of interest relevant to this article was reported.