Wheat, a highly versatile staple crop cultivated extensively for its grains on a global scale, is poised to experience increased demand to sustain the burgeoning population, owing to its superior nutritional potential. Modern wheat, a hexaploid species, has evolved through the introgression of numerous preceding ploidies, including Einkorn, Emmer, Aegilops, and others, each possessing distinct qualitative and quantitative traits. Scientometric and topical analyses serve as effective tools to quantitatively evaluate scientific research by measuring the knowledge expressed in scientific publications and keywords. Thus, comprehending the research status regarding wheat domestication events within primary, secondary, and tertiary gene pools is paramount for enhancing wheat production. In this study, we analyze data retrieved from PubMed to elucidate the research status and identify bottlenecks across different ploidy of genomic pools of wheat. The publication trends on wheat have experienced exponential growth over the past three decades, with China emerging as a leading center for publications. In contrast to the publication frequency observed in hexaploid common wheat, scholarly output concerning Einkorn and Aegilops is approximately tenfold lesser, with emmer trailing behind at three times fewer publications. This discrepancy underscores the prioritization of expedited research initiatives targeting these species, aimed at elucidating latent biological characteristics and optimizing their breeding capabilities. Keywords such as \"stress,\" \"GWAS,\" and \"gene\" are prominent, reflecting the challenges posed by climatic factors on wheat production and their mitigation through molecular breeding and gene manipulation. Notably, the keyword \"einkorn\" highlights its potential as a donor for fine-tuning traits related to wheat adaptation processes and quality, crucial for modern wheat\'s survivability under adverse climates. Conversely, higher publication rates on emmer are primarily associated with Italy, possibly due to its favorable Mediterranean climate for tetraploid wheat. Keywords like \"Pasta\" and \"Ochratoxin, DON\" are prevalent, with the former being derived from durum wheat and the latter being reported in higher amounts in durum compared to other wheat species, rendering it less suitable for consumption. Enriched keywords such as \"genome\" and \"resistance\" underscore the critical characteristics of Aegilops. Other significant keywords like \"Aceria tosichella\" possibly indicate multiple stages of resistance conferred by Aegilops, while the presence of the grain softness protein \"puroindoline\" enhances its acceptability for donation by Aegilops. Spelt, a close relative of common wheat, exhibits a research trend with thousands of annual publications and enriched keywords such as \"stress\" and \"yield\" reflect the current scientific emphasis on wheat research. Furthermore, hierarchical keywords like \"bio-control\" and \"celiac disease\" merit consideration for future research on hexaploid wheat.

BACKGROUND: Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies.
RESULTS: We introduce Polyphest (POLYploid PHylogeny ESTimation), a new method for efficiently and accurately inferring species phylogenies in the presence of both polyploidy and ILS. Polyphest bypasses the need for extensive network space searches by first generating a multilabeled tree based on gene trees, which is then converted into a (uniquely labeled) species phylogeny. We compare the performance of Polyphest to that of two polyploid phylogeny estimation methods, one of which does not account for ILS, namely PADRE, and another that accounts for ILS, namely MPAllopp. Polyphest is more accurate than PADRE and achieves comparable accuracy to MPAllopp, while being significantly faster. We also demonstrate the application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes.
METHODS: Polyphest is available at https://github.com/NakhlehLab/Polyphest.

BACKGROUND: The endocycle can generate cells referred to as \'polyploid\'. Fizzy-related protein (Fzr) plays an important role in driving the mitosis-to-endocycle transition. The brown planthopper (BPH), Nilaparvata lugens (Stål), a serious insect pest, feeds exclusively on rice. However, polyploidy and its regulatory mechanisms are poorly understood in BPH.
RESULTS: Here, we found that the ploidy levels of follicles H (FH) and accessory gland (AG) significantly increased with BPH age when examining the polyploidy of FH and AG of salivary glands. Fzr was identified as an important regulator for polyploidy in BPH salivary gland. Knockdown of Fzr resulted in a decrease in cell size and DNA content in nymph salivary glands. Fzr knockdown transcriptionally upregulated cyclin-dependent kinase 1 (CDK1), CDK2, cyclin A (CycA) and CycB, and downregulated CycD, CycE, Myc and mini-chromosome maintenance protein 2-7 (MCM2-7). Phenotypically, Fzr knockdown significantly suppressed salivary protein production, feeding and survival in BPH nymphs.
CONCLUSIONS: Our results show that BPH salivary glands exhibit obvious polyploidy, and Fzr positively regulates the endocycle in nymph salivary gland. These findings provide clues for the study of the regulatory mechanisms of insect polyploidy. © 2024 Society of Chemical Industry.

Poales, as one of the largest orders of angiosperm, holds crucial economic and ecological importance. Nevertheless, achieving a consensus topology has been challenging in previous studies due to limited molecular data and sparse taxon sampling. The uneven distribution of species diversity among families and the factors leading to elevated species richness in certain lineages have also been subjects of ongoing discussion and investigation. In this study, we conducted a comprehensive sampling, including representatives from all 14 families and 85 taxa of Poales, along with five additional outgroups. To reconstruct the phylogeny of Poales, we employed a combination of coalescent and concatenation methods on three nuclear gene sets (1093, 491, 143) and one plastid gene set (53), which were inferenced from genomic data. We also conducted phylogenetic hypothesis analyses to evaluate two major conflicting nodes detected in phylogenetic analyses. As a result, we successfully resolved the backbone of Poales and provided a timeline for its evolutionary history. We recovered the sister relationship between Typhaceae and Bromeliaceae as the earliest diverging families within Poales. The clade consisting of Ecdeiocoleaceae and Joinvilleaceae was recovered as the sister group of Poaceae. Within the xyrid clade, Mayacaceae and Erioaculaceae + Xyridaceae successively diverged along the backbone of Poales. The topology of [Aristidoideae, ((Micrairoideae, Panicoideae), (Arundinoideae, (Chloridoideae, Danthonioideae)))] within the PACMAD clade has received strong support from multiple findings. We also delved into the underlying biological factors that contributed to the conflicting nodes observed in the phylogenetic analysis. Apart from the uncertainty regarding the sister group of Poaceae caused by cytonuclear discordance, frequent hybridization and polyploidy may have contributed to other conflicting nodes. We identified 26 putative whole-genome duplication (WGD) events within Poales. However, apart from the σ-WGD and the ρ-WGD, we did not observe any potential polyploid events that could be directly linked to the species diversification in specific lineages. Furthermore, there was a significant increase in the net diversification rate of Poales following the K-Pg boundary.

Pratylenchus neglectus and P. thornei are among the most destructive root lesion nematodes of wheat in the Pacific Northwest, United States of America and throughout the world. The aim of this study was to determine whether both nematode species were similar in their ability to induce defense genes in roots of wheat genotype Scarlet, and whether a combination of both species induced a different pattern of gene induction than each species alone. The long-term aspect of the research was to identify nematode-inducible promoters for deploying defense genes in roots in breeding programs. The root transcriptomes of genotype Scarlet were obtained after a one-week infection period with each nematode species separately, or both species combined. Root defense gene expression was induced for all three treatments relative to the no-nematode control, but P. thornei affected expression to a greater extent compared to P. neglectus. The species combination induced the highest number of defense genes. This result was not predicted from nematode enumeration studies, in which P. thornei colonization was substantially lower than that of P. neglectus, and the nematode combination did not show a significant difference. Quantitative real time polymerase chain reaction (qRT-PCR) assays for Dehydrin2, Glucan endo-1,3-beta-glucosidase, 1-cys-Peroxiredoxin, Pathogenesis-related protein 1 and Late embryogenesis-abundant proteins 76 and group 3 authenticated the induction observed in the transcriptome data. In addition, a near-isogenic line of Scarlet harboring genetic resistance to fungal soilborne pathogens, called Scarlet-Rz1, showed similar or higher levels of defense gene expression compared to fungus-susceptible Scarlet in qRT-PCR assays. Finally, transcriptome expression patterns revealed nematode-inducible promoters that are responsive to both P. neglectus and P. thornei.

Human cytomegalovirus (HCMV) infection is common in tumor tissues across different types of cancer. While HCMV has not been recognized as a cancer-causing virus, numerous studies hint at its potential role in cancer development where its presence in various cancers corresponds with the hallmarks of cancer. Herein, we discuss and demonstrate that high-risk HCMV-DB and BL strains have the potential to trigger transformation in epithelial cells, including human mammary epithelial cells (HMECs), ovarian epithelial cells (OECs), and prostate epithelial cells (PECs), through the generation of polyploid giant cancer cells (PGCCs). A discussion is provided on how HCMV infection creates a cellular environment that promotes oncogenesis, supporting the continuous growth of CMV-transformed cells. The aforementioned transformed cells, named CTH, CTO, and CTP cells, underwent giant cell cycling with PGCC generation parallel to dedifferentiation, displaying stem-like characteristics and an epithelial-mesenchymal transition (EMT) phenotype. Furthermore, we propose that giant cell cycling through PGCCs, increased EZH2 expression, EMT, and the acquisition of malignant traits represent a deleterious response to the cellular stress induced by high-risk oncogenic HCMV strains, the latter being the origin of the transformation process in epithelial cells upon HCMV infection and leading to adenocarcinoma of poor prognosis.

Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato (Ipomoea batatas [L.] Lam) genome for molecular-marker-assisted breeding and genomic prediction. The creation of this marker panel has the potential to bring cost-effective and rapid genotyping capabilities to sweetpotato breeding programs worldwide. The open access provided by this platform will allow the genetic datasets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of sweetpotato.

Polyploid wheats include a group of tetraploids known as Timopheevii (AuAuGG), which are represented by two subspecies: Triticum timopheevii ssp. timopheevii (cultivated) and Triticum timopheevii ssp. araraticum (wild). The combined use of electrophoretic (SDS-PAGE) and chromatographic (RP-HPLC) techniques carried out on high-molecular-weight glutenin subunits (HMW-GSs) permitted the association of different x- and y-type subunits to the A and G genomes and the assessment of allelic variation present at corresponding loci. The results also revealed that in both subspecies, accessions are present that possess expressed y-type subunits at the Glu-A1 locus. Genes corresponding to these subunits were amplified and amplicons corresponding to x- and y-type genes associated with the A genome were detected in all accessions, including those without expressed x- and y-type subunits. The comparison with genes of polyploid wheats confirmed the structural characteristics of typical y-type genes, with the presence of seven cysteine residues and with hexapeptide and nonapeptide repeat motifs. The identification of wild and cultivated T. timopheevii with both x- and y-type glutenin subunits at the Glu-A1 and Glu-G1 loci represents a useful source for the modification of the allelic composition of HMW-GSs in cultivated wheats with the ultimate objective of improving technological properties.

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.

Fludioxonil, an antifungal agent used as a pesticide, leaves a measurable residue in fruits and vegetables. It has been identified to cause endocrine disruption, interrupt normal development, and cause various diseases such as cancers. In this study, fludioxonil was examined for its effects on the development and metastasis of breast cancer cells. On fludioxonil exposure (10-5 M) for 72 h, mutant p53 (mutp53) MDA-MB-231 triple-negative breast cancer (TNBC) cells significantly inhibited cell viability and developed into polyploid giant cancer cells (PGCCs), with an increase in the number of nuclei and expansion in the cell body size. Fludioxonil exposure disrupted the normal cell cycle phase ratio, resulting in a new peak. In addition, PGCCs showed greater motility than the control and were resistant to anticancer drugs, i.e., doxorubicin, cisplatin, and 5-fluorouracil. Cyclin E1, nuclear factor kappa B (NF-κB), and p53 expressions were remarkably increased, and the expression of cell cycle-, epithelial-mesenchymal-transition (EMT)-, and cancer stemness-related proteins were increased in the PGCCs. The daughter cells obtained from PGCCs had the single nucleus but maintained their enlarged cell size and showed greater cell migration ability and resistance to the anticancer agents. Consequently, fludioxonil accumulated Cyclin E1 and promoted the inflammatory cytokine-enriched microenvironment through the up-regulation of TNF and NF-κB which led to the transformation to PGCCs via abnormal cell cycles such as mitotic delay and mitotic slippage in mutp53 TNBC MDA-MB-231 cells. PGCCs and their daughter cells exhibited significant migration ability, chemo-resistance, and cancer stemness. These results strongly suggest that fludioxonil, as an inducer of potential genotoxicity, may induce the formation of PGCCs, leading to the formation of metastatic and stem cell-like breast cancer cells.