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Nature Communications Jun 2024Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear...
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
Topics: Polyploidy; Genome, Plant; Evolution, Molecular; Gene Duplication; Genomic Structural Variation; Mutation
PubMed: 38918389
DOI: 10.1038/s41467-024-49679-y -
Rice (New York, N.Y.) Jun 2024Great yield-enhancing prospects of autotetraploid rice was restricted by various polyploidy-induced reproductive dysfunction. To surmount these challenges, our group has...
Great yield-enhancing prospects of autotetraploid rice was restricted by various polyploidy-induced reproductive dysfunction. To surmount these challenges, our group has generated a series of valuable fertile tetraploid lines (denoted as neo-tetraploid rice) through 20-year efforts. With this context, a G-type lectin receptor-like kinase, OsNRFG6, was identified as a pivotal factor associated with reproductive regulation in neo-tetraploid rice. Nevertheless, it is still elusive about a comprehensive understanding of its precise functional roles and underlying molecular mechanisms during reproduction of neo-tetraploid rice. Here, we demonstrated that OsNRFG6 executed a constitutive expression pattern and encoded proteins localizing in perinucleus and endoplasmic reticulum. Subsequently, four independent mutant lines of OsNRFG6 within neo-tetraploid rice background were further identified, all displaying low seed-setting rate due to abortive embryo sacs and defective double fertilization. RNA-seq and RT-qPCR revealed a significant down-regulation of OsNRFG6 and female reproductive genes such as OsMEL1 and LOG in ovaries prior to and post-fertilization, attributing this effect to OsNRFG6 mutation. Furthermore, through yeast-two hybrids, bimolecular fluorescence complementation assays, and luciferase complementation imaging assays, it was determined that OsNRFG6 could interact with itself and two female reproductive proteins (LOG and OsDES1) to form protein complexes. These results elucidate the reproductive functions and molecular pathway governed by OsNRFG6 in regulating fertility of neo-tetraploid rice, offering insights into molecular understanding of fertility improvement in polyploid rice.
PubMed: 38916708
DOI: 10.1186/s12284-024-00720-0 -
Methods in Molecular Biology (Clifton,... 2024Solid tumors and tumor-derived cell lines commonly contain highly enlarged (giant) cancer cells that enter a state of transient dormancy (active sleep) after they are...
Solid tumors and tumor-derived cell lines commonly contain highly enlarged (giant) cancer cells that enter a state of transient dormancy (active sleep) after they are formed, but retain viability, secrete growth promoting factors, and exhibit the ability to generate rapidly proliferating progeny with stem cell-like properties. Giant cells with a highly enlarged nucleus or multiple nuclei are often called polyploid giant cancer cells (PGCCs). Although PGCCs constitute only a subset of cells within a solid tumor/tumor-derived cell line, their frequency can increase markedly following exposure to ionizing radiation or chemotherapeutic drugs. In this chapter we outline a simple and yet highly sensitive cell-based assay, called single-cell MTT, that we have optimized for determining the viability and metabolic activity of PGCCs before and after exposure to anticancer agents. The assay measures the ability of individual PGCCs to convert the MTT tetrazolium salt to its water insoluble formazan metabolite. In addition to evaluating PGCCs, this assay is also a powerful tool for determining the viability and metabolic activity of cancer cells undergoing premature senescence following treatment with anticancer agents, as well as for distinguishing dead cancer cells and dying cells (e.g., exhibiting features of apoptosis, ferroptosis, etc.) that have the potential to resume proliferation through a process called anastasis.
Topics: Humans; Polyploidy; Cell Survival; Giant Cells; Cell Line, Tumor; Single-Cell Analysis; Tetrazolium Salts; Neoplasms; Antineoplastic Agents; Cell Proliferation
PubMed: 38913317
DOI: 10.1007/978-1-0716-3946-7_17 -
Methods in Molecular Biology (Clifton,... 2024Polyploid giant cancer cells (PGCCs) play a fundamental role in tumor initiation, dormancy, drug resistance, and metastasis, although the detailed biology of PGCCs...
Polyploid giant cancer cells (PGCCs) play a fundamental role in tumor initiation, dormancy, drug resistance, and metastasis, although the detailed biology of PGCCs remains poorly understood. The lack of literature on establishing a reproducible in vitro system for generating PGCCs is the leading technological obstacle to studying the biology of PGCCs. Here we provide a detailed protocol for generating stable PGCCs from Hey cancer cells and studying the PGCCs' embryonic stemness. This protocol includes (1) generating PGCCs of high purity in 2D culture by exposing Hey cells to paclitaxel, monitoring the cell cycle and amitotic budding of daughter cells from PGCCs, and collecting and studying the daughter cells; (2) inducing PGCCs to form spheroids expressing embryonic stemness markers and observing the spheroids' cleavage and blastocyst-like structure; and (3) inducing redifferentiation of PGCCs into different lineages of differentiated cells.
Topics: Humans; Polyploidy; Ovarian Neoplasms; Female; Cell Line, Tumor; Cell Differentiation; Giant Cells; Cell Culture Techniques; Neoplastic Stem Cells; Spheroids, Cellular; Paclitaxel; Cell Cycle
PubMed: 38913316
DOI: 10.1007/978-1-0716-3946-7_16 -
Scientific Data Jun 2024Synthetic hexaploid wheats (SHWs) are effective genetic resources for transferring agronomically important genes from wild relatives to common wheat (Triticum aestivum...
Synthetic hexaploid wheats (SHWs) are effective genetic resources for transferring agronomically important genes from wild relatives to common wheat (Triticum aestivum L.). Dozens of reference-quality pseudomolecule assemblies of hexaploid wheat have been generated, but none is reported for SHW-derived cultivars. Here, we generated a chromosome-scale assembly for the SHW-derived cultivar 'Chuanmai 104' based on PacBio HiFi reads and chromosome conformation capture sequencing. The total assembly size was 14.81 Gb with a contig N50 length of 58.25 Mb. A BUSCO analysis yielded a completeness score of 99.30%. In total, repetitive elements comprised 81.36% of the genome and 122,554 high-confidence protein-coding gene models were predicted. In summary, the first chromosome-level assembly for a SHW-derived cultivar presents a promising outlook for the study and utilization of SHWs in wheat improvement, which is essential to meet the global food demand.
Topics: Triticum; Chromosomes, Plant; Genome, Plant; Polyploidy
PubMed: 38909086
DOI: 10.1038/s41597-024-03527-2 -
Oncology Reports Aug 2024Monopolar spindle 1 kinase (Mps1, also known as TTK protein kinase) inhibitors exert marked anticancer effects against triple‑negative breast cancer (TNBC) by causing...
Monopolar spindle 1 kinase (Mps1, also known as TTK protein kinase) inhibitors exert marked anticancer effects against triple‑negative breast cancer (TNBC) by causing genomic instability and cell death. As aneuploid cells are vulnerable to compounds that induce energy stress through adenosine monophosphate‑activated protein kinase (AMPK) activation, the synergistic effect of Mps1/TTK inhibition and AMPK activation was investigated in the present study. The combined effects of CFI‑402257, an Mps1/TTK inhibitor, and AICAR, an AMPK agonist, were evaluated in terms of cytotoxicity, cell‑cycle distribution, and xenograft models. Additional molecular mechanistic studies were conducted to elucidate the mechanisms underlying apoptosis and autophagic cell death. The combination of CFI‑402257 and AICAR showed selective cytotoxicity in a TNBC cell line. The formation of polyploid cells was attenuated, and apoptosis was increased by the combination treatment, which also induced autophagy through dual inhibition of the PI3K/Akt/mTOR and mitogen‑activated protein kinase (MAPK) signaling pathways. Additionally, the combination therapy showed strongly improved efficacy in comparison with CFI‑402257 and AICAR monotherapy in the MDA‑MB‑231 xenograft model. The present study suggested that the combination of CFI‑402257 and AICAR is a promising therapeutic strategy for TNBC.
Topics: Triple Negative Breast Neoplasms; Humans; Female; Animals; Mice; Aminoimidazole Carboxamide; AMP-Activated Protein Kinases; Xenograft Model Antitumor Assays; Cell Line, Tumor; Ribonucleotides; Protein Serine-Threonine Kinases; Cell Cycle Proteins; Apoptosis; Autophagy; Protein-Tyrosine Kinases; Protein Kinase Inhibitors; Cell Proliferation; Signal Transduction; Drug Synergism; Biphenyl Compounds; Pyrones; Thiophenes
PubMed: 38904203
DOI: 10.3892/or.2024.8760 -
BMC Genomics Jun 2024Wheat grain endosperm is mainly composed of proteins and starch. The contents and the overall composition of seed storage proteins (SSP) markedly affect the processing...
Multi-omic analysis reveals the effects of interspecific hybridization on the synthesis of seed reserve polymers in a Triticum turgidum ssp. durum × Aegilops sharonensis amphidiploid.
BACKGROUND
Wheat grain endosperm is mainly composed of proteins and starch. The contents and the overall composition of seed storage proteins (SSP) markedly affect the processing quality of wheat flour. Polyploidization results in duplicated chromosomes, and the genomes are often unstable and may result in a large number of gene losses and gene rearrangements. However, the instability of the genome itself, as well as the large number of duplicated genes generated during polyploidy, is an important driving force for genetic innovation. In this study, we compared the differences in starch and SSP, and analyzed the transcriptome and metabolome among Aegilops sharonensis (R7), durum wheat (Z636) and amphidiploid (Z636×R7) to reveal the effects of polyploidization on the synthesis of seed reserve polymers.
RESULTS
The total starch and amylose content of Z636×R7 was significantly higher than R7 and lower than Z636. The gliadin and glutenin contents of Z636×R7 were higher than those in Z636 and R7. Through transcriptome analysis, there were 21,037, 2197, 15,090 differentially expressed genes (DEGs) in the three comparison groups of R7 vs Z636, Z636 vs Z636×R7, and Z636×R7 vs R7, respectively, which were mainly enriched in carbon metabolism and amino acid biosynthesis pathways. Transcriptome data and qRT-PCR were combined to analyze the expression levels of genes related to storage polymers. It was found that the expression levels of some starch synthase genes, namely AGP-L, AGP-S and GBSSI in Z636×R7 were higher than in R7 and among the 17 DEGs related to storage proteins, the expression levels of 14 genes in R7 were lower than those in Z636 and Z636×R7. According to the classification analysis of all differential metabolites, most belonged to carboxylic acids and derivatives, and fatty acyls were enriched in the biosynthesis of unsaturated fatty acids, niacin and nicotinamide metabolism, one-carbon pool by folate, etc. CONCLUSION: After allopolyploidization, the expression of genes related to starch synthesis was down-regulated in Z636×R7, and the process of starch synthesis was inhibited, resulting in delayed starch accumulation and prolongation of the seed development process. Therefore, at the same development time point, the starch accumulation of Z636×R7 lagged behind that of Z636. In this study, the expression of the GSe2 gene in Z636×R7 was higher than that of the two parents, which was beneficial to protein synthesis, and increased the protein content. These results eventually led to changes in the synthesis of seed reserve polymers. The current study provided a basis for a greater in-depth understanding of the mechanism of wheat allopolyploid formation and its stable preservation, and also promoted the effective exploitation of high-value alleles.
Topics: Triticum; Aegilops; Seeds; Hybridization, Genetic; Polyploidy; Starch; Transcriptome; Gene Expression Profiling; Gene Expression Regulation, Plant; Proteomics; Multiomics
PubMed: 38902625
DOI: 10.1186/s12864-024-10352-9 -
BMC Genomics Jun 2024Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance,...
Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation.
Topics: Crops, Agricultural; Genome, Plant; Proteomics; Molecular Sequence Annotation; Genomics; Plant Proteins
PubMed: 38898442
DOI: 10.1186/s12864-024-10521-w -
Science Advances Jun 2024Platelet-producing megakaryocytes (MKs) primarily reside in the bone marrow, where they duplicate their DNA content with each cell cycle resulting in polyploid cells...
Platelet-producing megakaryocytes (MKs) primarily reside in the bone marrow, where they duplicate their DNA content with each cell cycle resulting in polyploid cells with an intricate demarcation membrane system. While key elements of the cytoskeletal reorganizations during proplatelet formation have been identified, what initiates the release of platelets into vessel sinusoids remains largely elusive. Using a cell cycle indicator, we observed a unique phenomenon, during which amplified centrosomes in MKs underwent clustering following mitosis, closely followed by proplatelet formation, which exclusively occurred in G of interphase. Forced cell cycle arrest in G increased proplatelet formation not only in vitro but also in vivo following short-term starvation of mice. We identified that inhibition of the centrosomal protein kinesin family member C1 (KIFC1) impaired clustering and subsequent proplatelet formation, while KIFC1-deficient mice exhibited reduced platelet counts. In summary, we identified KIFC1- and cell cycle-mediated centrosome clustering as an important initiator of proplatelet formation from MKs.
Topics: Centrosome; Animals; Megakaryocytes; Mice; Cell Cycle; Blood Platelets; Kinesins; Mice, Knockout; Humans; Mitosis
PubMed: 38896608
DOI: 10.1126/sciadv.adl6153 -
Biology of the Cell Jun 2024The Endosomal Sorting Complex Required for Transport (ESCRT) is a highly conserved cellular machinery essential for many cellular functions, including transmembrane...
BACKGROUND
The Endosomal Sorting Complex Required for Transport (ESCRT) is a highly conserved cellular machinery essential for many cellular functions, including transmembrane protein sorting, endosomal trafficking, and membrane scission. CHMP4B is a key component of ESCRT-III subcomplex and has been thoroughly studied in the meroistic ovaries of Drosophila melanogaster showing its relevance in maintaining this reproductive organ during the life of the fly. However, the role of the CHMP4B in the most basal panoistic ovaries remains elusive.
RESULTS
Using RNAi, we examined the function of CHMP4B in the ovary of Blattella germanica in two different physiological stages: in last instar nymphs, with proliferative follicular cells, and in vitellogenic adults when follicular cells enter in polyploidy and endoreplication. In Chmp4b-depleted specimens, the actin fibers change their distribution, appearing accumulated in the basal pole of the follicular cells, resulting in an excess of actin bundles that surround the basal ovarian follicle and modifying their shape. Depletion of Chmp4b also determines an actin accumulation in follicular cell membranes, resulting in different cell morphologies and sizes. In the end, these changes disrupt the opening of intercellular spaces between the follicular cells (patency) impeding the incorporation of yolk proteins to the growing oocyte and resulting in female sterility. In addition, the nuclei of follicular cells appeared unusually elongated, suggesting an incomplete karyokinesis.
CONCLUSIONS
These results proved CHMP4B essential in preserving the proper expression of cytoskeleton proteins vital for basal ovarian follicle growth and maturation and for yolk protein incorporation. Moreover, the correct distribution of actin fibers in the basal ovarian follicle emerged as a critical factor for the successful completion of ovulation and oviposition.
SIGNIFICANCE
The overall results, obtained in two different proliferative stages, suggest that the requirement of CHMP4B in B. germanica follicular epithelium is not related to the proliferative stage of the tissue.
PubMed: 38895958
DOI: 10.1111/boc.202400010