PLoS Genetics最新文献

{"title":"Whole-genome sequencing reveals a possible molecular basis of sex determination in the dioecious wild yam Dioscorea tokoro.","authors":"Aoi Kudoh, Satoshi Natsume, Yu Sugihara, Hiroaki Kato, Akira Abe, Kaori Oikawa, Motoki Shimizu, Kazue Itoh, Mai Tsujimura, Yoshitaka Takano, Toshiyuki Sakai, Hiroaki Adachi, Atsushi Ohta, Mina Ohtsu, Takuma Ishizaki, Toru Terachi, Hideki Innan, Ryohei Terauchi","doi":"10.1371/journal.pgen.1012123","DOIUrl":"10.1371/journal.pgen.1012123","url":null,"abstract":"<p><p>Dioecious plants, which have distinct male and female individuals, constitute ~5% of angiosperm species and have emerged frequently and independently from hermaphroditic ancestors. Although recent molecular studies of sex determination have started to reveal the diversity of the genetic systems underlying dioecy, research on the evolution of dioecy is limited, especially in monocots. Here, we explore the molecular basis of sex determination in the monocot Dioscorea tokoro, a dioecious wild yam endemic to East Asia. Chromosome-scale and haplotype-resolved genome assemblies and linkage analysis suggested that this plant has a male heterogametic sex-determination (XY) system, with sex-determination regions located on chromosome 3. Sequence comparison between the X- and Y-chromosomes and read coverage analysis revealed X- and Y-specific regions in putative pericentromeric chromosome regions. Within the Y-specific region, we propose two candidate genes that are likely involved in sex determination: BLH9, encoding a homeobox protein, and HSP90, encoding a molecular chaperone. BLH9 functions in a similar way as AtBLH9 in Arabidopsis thaliana. BLH9 could be involved in suppression of female organ development, whereas HSP90 might be required for pollen development. These results shed light on the complex evolution of dioecy in plants.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012123"},"PeriodicalIF":3.7,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13128126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147730483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Constitutively active RAS prolongs Cdc42 signalling, while MAPK signalling is attenuated during fission yeast mating.","authors":"Emma J Kelsall, Akatsuki Kimura, Ábel Vértesy, Kornelis R Straatman, Mishal Tariq, Raquel Gadea, Chandni Parmar, Gabriele Schreiber, Shubhchintan Randhawa, Takashi Y Ida, Cyril Dominguez, Edda Klipp, Kayoko Tanaka","doi":"10.1371/journal.pgen.1012117","DOIUrl":"10.1371/journal.pgen.1012117","url":null,"abstract":"<p><p>The small GTPase RAS is a signalling hub activating multiple pathways, which may respond differently to a constitutively active RAS mutation. We explored this issue in fission yeast, where RAS-mediated pheromone signalling (PS) activates two downstream pathways: the MAPKSpk1 and Cdc42 pathways. We observed that the yeast RAS mutation ras1.G17V, an equivalent of the mammalian ras.G12V oncogenic mutation, causes prolonged Cdc42 activation, whereas MAPKSpk1 activation was transient and attenuated. To explain this observation, we generated a PS framework by conducting genetic epistasis analysis of PS mutants and biochemical analysis of two Ras1 effectors, Cdc42-GEFScd1 and MAPKKKByr2, each of which triggers activation of the Cdc42 and MAPKSpk1 pathways, respectively. Cdc42-GEFScd1 and MAPKKKByr2 directly interacted with Ras1 in vitro in a competitive manner, and overexpression of the Ras binding domain of either Cdc42-GEFScd1 or MAPKKKByr2 in cells inhibited both downstream pathways, confirming that Ras1 signalling branches into the MAPKSpk1 and Cdc42 pathways. In conjunction with the genetic epistasis analysis, we developed the PS framework-based mathematical model to test which network structures can explain the transient MAPKSpk1 activation profile. Incorporating a negative-feedback circuit acting on pheromone production or sensing enabled the model to quantitatively reproduce MAPKSpk1 dynamics in the wild type and 20 additional PS mutants. The predicted PS negative-feedback was experimentally confirmed by deleting Sxa2, the carboxypeptidase that degrades one of the mating pheromones, which led to hyperactivation of both MAPKSpk1 and Cdc42. Our study provides a holistic understanding of the fission yeast pheromone signalling network, explaining how RAS signalling propagates differently through two downstream pathways. Our PS mathematical model may serve as a valuable reference framework for analysing other RAS signalling systems.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012117"},"PeriodicalIF":3.7,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108886/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147718715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Transcriptional repression of reaper by Stand still ensures female germline development in Drosophila.","authors":"","doi":"10.1371/journal.pgen.1012116","DOIUrl":"10.1371/journal.pgen.1012116","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1371/journal.pgen.1012041.].</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012116"},"PeriodicalIF":3.7,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13082591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Oocyte vitrification disrupts zygotic genome activation in embryos by impairing maternal spliceosome translation and Crxos splicing.","authors":"Jianpeng Qin, Ao Ning, Jian Han, Xiangyi Chen, Beijia Cao, Yujun Yao, Xiaoqing He, Bo Pan, Yaozong Wei, Kunlin Du, Shuqi Zou, Jiangfeng Ye, Guozhi Yu, Qiuxia Liang, Jie Qiao, Jie Yan, Guangbin Zhou","doi":"10.1371/journal.pgen.1012121","DOIUrl":"10.1371/journal.pgen.1012121","url":null,"abstract":"<p><p>Oocyte vitrification is indispensable in assisted reproduction, yet its link to compromised embryonic development remains mechanistically unresolved. Here, this study demonstrate through integrated transcriptome and translatome analysis that vitrification disrupts maternal mRNA translation-sparing global transcriptional output-in mouse oocytes. This translational perturbation prominently suppresses genes encoding spliceosome components, including Phf5a, leading to persistent and widespread alternative splicing defects in subsequent 2-cell embryos. Importantly, aberrant splicing specifically depletes the functional full-length transcript of the essential zygotic genome activation (ZGA) regulator Crxos (Egam1) while elevating a truncated, non-functional variant (Egam1ΔEXON3). Functional analyses confirm that loss of Crxos in 2‑cell embryos not only compromises developmental progression but also reduces global transcriptional activity, likely via impaired RNA Pol II recruitment and elongation at ZGA genes. Together, this work delineates a linear pathological cascade triggered by oocyte vitrification, comprising maternal translational suppression, spliceosome impairment, Crxos aberrant splicing, impaired ZGA, and developmental compromise, thereby offering a mechanistic basis for refining cryopreservation protocols in reproductive medicine.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012121"},"PeriodicalIF":3.7,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13095128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Worm orthologues of cytokinesis-associated proteins CIT and ASPM regulate neuronal microtubule dynamics and polarity in C. elegans.","authors":"Sunanda Sharma, Keerthana Ponniah, Ishanee Bandyopadhyay, Devyani Vadawale, Sandhya P Koushika, Anindya Ghosh-Roy","doi":"10.1371/journal.pgen.1012106","DOIUrl":"10.1371/journal.pgen.1012106","url":null,"abstract":"<p><p>The polarized architecture of neurons is intricately associated with the modulation of microtubule dynamics. Over the years, several microtubule-associated factors that regulate neuronal polarity have been identified. However, the precise details of how microtubule arrangement and stability are established in axons and dendrites are not clearly understood. To uncover the relevant factors involved in the biological pathways governing microtubule regulation in neurons, we conducted a suppressor screen using the neuronal ectopic extension phenotype caused by the loss of the kinesin-13 family microtubule depolymerizing protein KLP-7 in C. elegans. Interestingly, apart from eleven variants of α (mec-12) and β (mec-7) tubulins, we isolated a variant of cytokinesis-associated protein, W02B8.2/citk-1, the suggested kinase-less orthologue of mammalian citron-rho interacting kinase (CIT). Little is known about the role of CIT in microtubule regulation in post-mitotic neurons. In this study, we found that the kinase-less worm orthologues of CIT, citk-1 and citk-2, redundantly modulate microtubule stability in the axon-like anterior process and maintain the population of plus-end-out microtubules in the dendrite-like posterior process of the PLM mechanosensory neurons in a cell-autonomous manner. In the absence of citk-1 and citk-2, PLM neurons exhibit variable morphological defects, including neurite growth and synaptic branch defects. Moreover, we find that CITK-1/2 work in the same genetic pathway as ASPM-1 (the worm homolog of mammalian ASPM (abnormal spindle-like microcephaly-associated protein)) to modulate plus-end dynamics of microtubules in PLM neurons. Our findings suggest that the cytokinesis-associated CITK-1/2 and ASPM-1 have non-mitotic roles in regulation of microtubules in differentiated PLM neurons.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012106"},"PeriodicalIF":3.7,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ZmSKIP enhances drought tolerance by reducing stomatal aperture in maize.","authors":"Yao Wang, Yujiao Zhou, Qimeng Li, Yanyan Zhang, Li Yang, Qiao Zhou, Wen Xu, Tianhong Liu, Yaxi Liu, Fengkai Wu, Guangchao Sun, Wei Guo, Yanli Lu, Jie Xu","doi":"10.1371/journal.pgen.1012077","DOIUrl":"10.1371/journal.pgen.1012077","url":null,"abstract":"<p><p>SKI-INTERACTING PROTEINS (SKIPs), primarily known as splicing factors, control gene expression at the post-transcriptional level in stress responses in plants. However, little is known about SKIPs in regulating plant drought stress at the transcriptional level, particularly in maize (Zea mays L.). Here, we discover that ZmSKIP enhances drought tolerance in maize. ZmSKIP transgenic plants were generated to study how ZmSKIP positively regulates drought tolerance. Overexpression of ZmSKIP promoted stomatal closure and reduced water loss, whereas the opposite effect was observed in skip-aa mutants. ZmSKIP directly binds to the \"TAATA\" motif in the promoter of B-cell lymphoma 2-associated athanogene 8 (ZmBAG8). bag8 mutants exhibit the decreased water loss and reduced stomatal aperture phenotype under drought stress. Additionally, ZmSKIP can be recruited by ZmBAG8 in stress granules (SGs) to decrease its protein abundance in the nucleus. Increased ZmBAG8 expression leads to larger stomatal aperture and normal plant growth. Under drought stress, the interaction between ZmSKIP and ZmBAG8 was abolished, while ZmSnRK2.3 phosphorylates ZmSKIP at Ser236 and Ser244 to enhances drought tolerance by strengthening the ability of ZmSKIP to suppress ZmBAG8 expression. Thus, our findings demonstrate that ZmSnRK2.3-mediated phosphorylation of ZmSKIP reduces ZmBAG8 expression and stomatal aperture, thereby enhancing drought tolerance in maize.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012077"},"PeriodicalIF":3.7,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13075797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147678021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chronic replication stress-mediated genomic instability disrupts placenta development in mice.","authors":"Mumingjiang Munisha, Rui Huang, Jordan Khan, John C Schimenti","doi":"10.1371/journal.pgen.1012111","DOIUrl":"10.1371/journal.pgen.1012111","url":null,"abstract":"<p><p>Abnormal placentation drives many pregnancy-related pathologies and poor fetal outcomes, but the underlying molecular causes are understudied. Here, we show that persistent replication stress due to mutations in the MCM2-7 replicative helicase disrupts placentation and reduces embryo viability in mice. MCM-deficient embryos exhibited normal morphology, but their placentae had a drastically diminished junctional zone (JZ). Whereas cell proliferation in the labyrinth zone (LZ) remained unaffected, it was reduced in the JZ during development. MCM2-7 deficient trophoblast stem cells (TSCs) failed to maintain stemness, suggesting that replication stress affects the initial trophoblast progenitor pool in a manner that preferentially impacts the developing JZ. In contrast, pluripotency of mouse embryonic stem cells (ESCs) with MCM2-7 deficiency were not affected. Developing female mice deficient for FANCM, a protein involved in replication-associated DNA repair, also had placentae with a diminished JZ. These findings indicate that replication stress-induced genomic instability compromises embryo outcomes by impairing placentation.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012111"},"PeriodicalIF":3.7,"publicationDate":"2026-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13099090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147678056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: An essential gene screening identifies yeast Mot1 as a suppressor of R-loops and genome instability.","authors":"María E Soler-Oliva, Rocío A Domínguez-Sierra, Hélène Gaillard, Andrés Aguilera","doi":"10.1371/journal.pgen.1012108","DOIUrl":"10.1371/journal.pgen.1012108","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1371/journal.pgen.1012040.].</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012108"},"PeriodicalIF":3.7,"publicationDate":"2026-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13068210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147655199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of a congenic strain for the oyster mushroom reveals the structure and evolution of mating-type loci.","authors":"Yi-Yun Lee, Guillermo Vidal-Diez de Ulzurrun, Rebecca J Tay, Yen-Ping Hsueh","doi":"10.1371/journal.pgen.1011966","DOIUrl":"10.1371/journal.pgen.1011966","url":null,"abstract":"<p><p>Pleurotus ostreatus, a widely cultivated edible oyster mushroom, is an ecologically versatile species with applications in biotechnology, agriculture, and food production. It functions as a decomposer and in nutrient-limited conditions it enhances its survival by using a potent toxin to prey on nematodes. Its adaptability is further regulated by sexual reproduction, which follows a tetrapolar mating system governed by two unlinked, multiallelic loci, matA and matB. The two mating-compatible monokaryotic strains PC9 and PC15, derived from the parental dikaryon strain N001, exhibit significant physiological differences. PC9 grows robustly in laboratory conditions, whereas PC15 grows more slowly, making PC9 the preferred strain for research. To advance P. ostreatus as a genetic model, we characterized the mating-type (MAT) loci of both monokaryon strains and developed a congenic strain. We analyzed the MAT loci in multiple P. ostreatus strains, and identified 11 A and 12 B alleles among twelve haplotypes, confirming their multiallelic nature. Using 10 rounds of backcrossing, we introgressed the matA and matB loci from PC15 into the PC9 genetic background to generate the congenic strain PC9.15. After sequencing and assembling a high-quality and contiguous genome for PC9.15, we confirmed that the genomes of PC9.15 and PC9 are 99% similar, with the only major difference placed at the matA and matB loci.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1011966"},"PeriodicalIF":3.7,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13108863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147640353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactate and histone H3K18 lactylation are associated with metabolic control of gene expression in the retina.","authors":"Mohita Gaur, Matthew J Brooks, Xulong Liang, Ke Jiang, Anjani Kumari, Milton A English, Paolo Cifani, Maria C Panepinto, Jacob Nellissery, Robert N Fariss, Laura Campello, Claire Marchal, Anand Swaroop","doi":"10.1371/journal.pgen.1012100","DOIUrl":"10.1371/journal.pgen.1012100","url":null,"abstract":"<p><p>High aerobic glycolysis in retinal photoreceptors, as in cancer cells, is implicated in mitigating energy and metabolic demands. Lactate, a product of glycolysis, can exert epigenetic regulation through histone lactylation in cancer. Here, we show that enhanced ATP production during mouse retinal development is achieved primarily through increase in glycolysis. Histone lactylation, especially H3K18La, parallels increased glycolysis and lactate levels in the developing retina. Multi-omics analyses, combined with confocal imaging, reveal the localization of H3K18La near H3K27Ac in the euchromatin at promoters of active retinal genes. In mouse retinal explants, glucose metabolism is associated with lactate levels as well as H3K18La and consequently gene expression. However, inhibition of glycolysis with 2-deoxyglucose (2-DG) reduces global H3K18La and H3K27Ac marks with somewhat distinct transcriptional changes. Evaluation of accessible chromatin at H3K18La-marked promoters uncovers an enrichment of GC-rich motifs for transcription factors of SP, KMT and KLF families, among others, indicating the specificity of H3K18La-mediated gene regulation. Our results indicate glycolysis/lactate/H3K18La as a potential axis for transcriptional response to changing metabolic conditions in the retina, especially photoreceptors.</p>","PeriodicalId":49007,"journal":{"name":"PLoS Genetics","volume":"22 4","pages":"e1012100"},"PeriodicalIF":3.7,"publicationDate":"2026-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13095125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147640324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}