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Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non‐native species meet. Hybridization can threaten native species via competition (with vigorous hybrids), reproductive resource wastage and gene introgression. The latter, in particular, could result in increased fitness in invasive species, decreased fitness of natives and compromise reintroduction or recovery conservation practices. In this study, we use a combination of RAD sequencing and microsatellites for a range‐wide sample set of 1366 fish to evaluate the potential for hybridization and introgression between native crucian carp (Carassius carassius) and three non‐native taxa (Carassius auratus auratus, Carassius auratus gibelio and Cyprinus carpio) in European water bodies. We found hybridization between native and non‐native taxa in 82% of populations with non‐natives present, highlighting the potential for substantial ecological impacts from hybrids on crucian carp populations. However, despite such high rates of hybridization, we could find no evidence of introgression between these taxa. The presence of triploid backcrosses in at least two populations suggests that the lack of introgression among these taxa is likely due to meiotic dysfunction in hybrids, leading to the production of polyploid offspring which are unable to reproduce sexually. This result is promising for crucian reintroduction programs, as it implies limited risk to the genetic integrity of source populations. Future research should investigate the reproductive potential of triploid hybrids and the ecological pressures hybrids impose on C. carassius. [ABSTRACT FROM AUTHOR]

Summary: Meiotic crossovers (COs) generate genetic diversity and are crucial for viable gamete production. Plant COs are typically limited to 1–3 per chromosome pair, constraining the development of improved varieties, which in wheat is exacerbated by an extreme distal localisation bias. Advances in wheat genomics and related technologies provide new opportunities to investigate, and possibly modify, recombination in this important crop species. Here, we investigate the disruption of FIGL1 in tetraploid and hexaploid wheat as a potential strategy for modifying CO frequency/position.We analysed figl1 mutants and virus‐induced gene silencing lines cytogenetically. Genetic mapping was performed in the hexaploid.FIGL1 prevents abnormal meiotic chromosome associations/fragmentation in both ploidies. It suppresses class II COs in the tetraploid such that CO/chiasma frequency increased 2.1‐fold in a figl1 msh5 quadruple mutant compared with a msh5 double mutant. It does not appear to affect class I COs based on HEI10 foci counts in a hexaploid figl1 triple mutant. Genetic mapping in the triple mutant suggested no significant overall increase in total recombination across examined intervals but revealed large increases in specific individual intervals.Notably, the tetraploid figl1 double mutant was sterile but the hexaploid triple mutant was moderately fertile, indicating potential utility for wheat breeding. See also the Commentary on this article by Phillips & Lloyd, 244: 341–343. [ABSTRACT FROM AUTHOR]

Copyright of Jurnal Produksi Tanaman is the property of Brawijaya University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The genome sizes of angiosperms decreased significantly more than the genome sizes of their ancestors (pteridophytes and gymnosperms). Decreases in genome size involve a highly complex process, with remnants of the genome size reduction scattered across the genome and not directly linked to specific genomic structures. This is because the associated mechanisms operate on a much smaller scale than the mechanisms mediating increases in genome size. This review thoroughly summarizes the available literature regarding the molecular mechanisms underlying genome size reductions and introduces Utricularia gibba and Arabidopsis thaliana as model species for the examination of the effects of these molecular mechanisms. Additionally, we propose that phosphorus deficiency and drought stress are the major external factors contributing to decreases in genome size. Considering these factors affect almost all land plants, angiosperms likely gained the mechanisms for genome size reductions. These environmental factors may affect the retention rates of deletions, while also influencing the mutation rates of deletions via the functional diversification of the proteins facilitating double-strand break repair. The biased retention and mutation rates of deletions may have synergistic effects that enhance deletions in intergenic regions, introns, transposable elements, duplicates, and repeats, leading to a rapid decrease in genome size. We suggest that these selection pressures and associated molecular mechanisms may drive key changes in angiosperms during recurrent cycles of genome size decreases and increases.Key message: Genome shrinkage in angiosperms is driven by intricate molecular mechanisms and abiotic stress factors, reshaping our understanding of genome size and structural evolution. [ABSTRACT FROM AUTHOR]

The genome sizes of angiosperms decreased significantly more than the genome sizes of their ancestors (pteridophytes and gymnosperms). Decreases in genome size involve a highly complex process, with remnants of the genome size reduction scattered across the genome and not directly linked to specific genomic structures. This is because the associated mechanisms operate on a much smaller scale than the mechanisms mediating increases in genome size. This review thoroughly summarizes the available literature regarding the molecular mechanisms underlying genome size reductions and introduces Utricularia gibba and Arabidopsis thaliana as model species for the examination of the effects of these molecular mechanisms. Additionally, we propose that phosphorus deficiency and drought stress are the major external factors contributing to decreases in genome size. Considering these factors affect almost all land plants, angiosperms likely gained the mechanisms for genome size reductions. These environmental factors may affect the retention rates of deletions, while also influencing the mutation rates of deletions via the functional diversification of the proteins facilitating double-strand break repair. The biased retention and mutation rates of deletions may have synergistic effects that enhance deletions in intergenic regions, introns, transposable elements, duplicates, and repeats, leading to a rapid decrease in genome size. We suggest that these selection pressures and associated molecular mechanisms may drive key changes in angiosperms during recurrent cycles of genome size decreases and increases.Key message: Genome shrinkage in angiosperms is driven by intricate molecular mechanisms and abiotic stress factors, reshaping our understanding of genome size and structural evolution. [ABSTRACT FROM AUTHOR]

The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods. [ABSTRACT FROM AUTHOR]

All flowering plants are now recognized as diploidized paleopolyploids (Jiao et al., 2011; One Thousand Plant Transcriptomes Initiative, 2019), and polyploid species comprise approximately 30% of contemporary plant species (Wood et al., 2009; Barker et al., 2016a). A major implication of these discoveries is that, to appreciate the evolution of plant diversity, we need to understand the fundamental biology of polyploids and diploidization. This need is broadly recognized by our community as there is a continued, growing interest in polyploidy as a research topic. Over the past 25 years, the sequencing and analysis of plant genomes has revolutionized our understanding of the importance of polyploid speciation to the evolution of land plants. [ABSTRACT FROM AUTHOR]

Lilium rosthornii Diels, commonly known as the Nanchuan lily in China, is a unique wild lily species with potential medicinal or ornamental value. The development and utilization are mainly restricted to its highly efficient regeneration and the scarcity of new germplasm. In this study, an efficient plant regeneration method for Nanchuan lily was established based on embryogenic callus induction, adventitious bud sprouting, and shoot proliferation and rooting. The results showed that Murashige and Skoog (MS) media supplemented with 0.5 mg L−1 picloram (PIC) and 1.0 mg L−1 1-naphthaleneacetic acid (NAA) were suitable for embryogenic callus induction using outer bulblet scales (78.89% rate), and MS supplemented with 0.5 mg L−1 6-benzylaminopurine (6-BA), 1.0 mg L−1 NAA, and 75.0 mg L−1 ascorbic acid in darkness was optimal for embryogenic callus proliferation (2.62 coefficient). Moreover, callus inoculation in MS medium supplemented with 1.0 mg L−1 thidiazuron (TDZ) and 0.1 mg L−1 NAA significantly promoted shoot induction (3.16 coefficient) under relatively low light conditions. The shoot proliferation and rooting of MS plants treated with 0.1 mg L−1 NAA and 0.5 mg L−1 TDZ were greatest under light conditions at 93.33% and 98.89%, respectively. In addition, bulblet growth was induced by treatment with different combinations of colchicine at different concentrations for different durations. Focusing on the bulblet centre, 100% morphological changes were achieved for in vitro induction using 0.15% colchicine for 72 h of treatment. Compared with the control, three stable mutagenic plants with greater guard cells and reduced stomatal density were generated and were identified as chimaeras by flow cytometry analysis. These results provide support for improving tissue reproduction and breeding autotetraploid germplasm in Nanchuan lily. [ABSTRACT FROM AUTHOR]

Copyright of Acta Prataculturae Sinica is the property of Acta Prataculturae Sinica Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Bulletin of Botanical Research is the property of Bulletin of Botanical Research Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Summary: The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation.Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification.Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species.Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non‐model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity. [ABSTRACT FROM AUTHOR]

To induce polyploidy in rhododendrons, different experimental materials of four Rhododendron species (2n = 2x = 26) were treated with colchicine and oryzalin as chemical mutagens. Three materials from R. fortunei, namely, seeds, cotyledons, and adventitious buds, were treated, and the highest tetraploid induction rate (15.64%) was observed in cotyledons treated with 20 mg·L− 1 oryzalin for 4 d. Two materials (stem tips and stem bases) were treated in R. simsii, and the highest tetraploid induction rate (4.04%) was achieved with 0.14% colchicine after soaking the stem tips for 48 h. However, when we treated the stem bases, the chimerism occurrence rate was up to 30.00%. In addition, polyploidy induction in R. ovatum was carried out at two colchicine concentrations (0.12 and 0.14%) with two materials (stem tip and stem base), which resulted in a higher chimeric rate. Three materials (stem tip, stem base, and adventitious buds) of R. molle were used, but no polyploidy was found. Polyploid identification was performed through stomatal observation and flow cytometry. Polyploid plants had larger and sparser stomata than diploid plants. Furthermore, morphological measurements revealed that the size of the stomata and leaves in tetraploid plants was larger than that in diploid plants. Stomatal density was decreased in tetraploid plants compared to diploid plants. Flow cytometry analysis identified tetraploids in the mutant plants of R. fortunei and R. simsii. Phenotypic analyses showed that tetraploid plants had smaller, rounder leaves and darker leaf colors than diploid plants. In summary, we compared the induced polyploid rhododendrons using different methods, which is of great significance for cultivating new rhododendron varieties with good ornamental properties and high resistance and for developing the rhododendron industry in China.Key message: In this research, we have tested various methods and different materials for the polyploidy induction in rhododendrons, and analyzed the morphological characteristics of polyploid plants. [ABSTRACT FROM AUTHOR]

As one of the most influential environmental factors, drought stress greatly impacts the development and production of plants. Triploid-induced Passiflora edulis Sims 'Mantianxing' is an important new cultivar for multi-resistance variety selective breeding, which is one of the P. edulis breeding essential targets. However, the performance of triploid 'Mantianxing' under drought stress is unknown. In order to study the drought resistance of triploid 'Mantianxing', our study compared drought-related indicators in diploids and triploids under natural drought experiments, including morphological, physiological, and biochemical characteristics. Results showed that triploid P. edulis 'Mantianxing' showed variable responses to drought treatment. Compared with diploids, triploids showed higher photosynthesis and chlorophyll fluorescence, osmotic adjustment substances, and antioxidant enzyme activity under drought stress and faster chlorophyll biosynthesis and growth recovery after rewatering. Generally speaking, these results indicate that the drought resistance of triploid P. edulis is superior to diploid. This study provides scientific information for breeding stress tolerance variety of P. edulis 'Mantianxing' new cultivar. [ABSTRACT FROM AUTHOR]

There are thousands of Narcissus cultivars, however; their genome compositions are not so clear, except that their ploidy levels are extensively investigated. The present study analyzed eight popular cultivars using GISH or/and FISH. The present results clearly revealed their genome compositions: 'Bridal Crown' was diploid (2n = 2x = 17 = 10 + 7 = AE) rather than aneuploid, 'Jinzhanyintai' was autotriploid (2n = 3x = 30 = 10 + 10 + 10 = AAA) rather than allotetraploid or hexaploid, 'Tête-à-Tête' was allotriploid (2n = 3x = 24 + B = 10 + 7 + 7 + B = AEE), 'Cultivar X' was also allotriploid (2n = 3x = 24 = 10 + 7 + 7 = AEX), and 'Dutch Master', 'Replete' and 'Queen's Day' were all autotetraploid (2n = 4x = 28 = 7 + 7 + 7 + 7 = EEEE). Together with other reports, we concluded that 'Tête-à-Tête' contained one genome of Narcissus tazetta, one genome of Narcissus cyclamineus, and one genome of Narcissus pseudonarcissus, and that 'Pink Parasol' was aneu-autotetraploid (2n = 4x + 2 = 30 = 7 + 7 + 7 + 7 + 2 = EEEE+2) rather allotetraploid (2n = 4x = 10 + 10 + 5 + 5 = CCDD). Based on the cultivar's genome composition and origin, it is concluded that distant hybridization, sexual polyploidization and chromosome doubling play different roles in breeding modern Narcissus cultivars. [ABSTRACT FROM AUTHOR]

An initial cross of V. darrowii 'Johnblue' (Darrow's blueberry) × V. vitis-idaea 'Red Sunset' (lingonberry) produced more than 30 true intersectional diploid hybrids as confirmed by molecular markers. The most vigorous of these hybrids was extensively evaluated. This hybrid, US 2535-A, was floriferous and morphologically intermediate to the respective parents. Examination of pollen suggested low male fertility. Numerous crosses using the hybrid as a female reflected similarly low fertility and potential crossing barriers. Stylar examination suggested blockage of pollen tube growth in self-pollinations and significantly retarded growth in backcross pollinations. Nonetheless, two confirmed hybrid offspring were produced using the F1 hybrid as a female in crosses with V. vitis-idaea and V. darrowii, respectively. In a second set of crosses utilizing additional V. darrowii and V. vitis-idaea genotypes, another 23 verified hybrids in seven parental combinations were produced. Hybrids such as the ones presented offer the potential for generating de novo interspecific fruit types in blueberry and/or broadening the adaptation of lingonberry. [ABSTRACT FROM AUTHOR]

The Asiatic hybrid lily cultivar Lilium dazzling (family Liliaceae) is a perennial herbaceous bulbous plant with bright yellow flowers of ornamental values. It also shows resistance to diseases and abiotic stress, making it an ideal parent for breeding studies. This study established a sterile culture system using scales of dazzling lily as explants to induce polyploidy. Adventitious buds growing to 1 cm were treated with different concentrations of colchicine (125, 250 and 500 μmol·L-1), pendimethalin or trifluralin (100, 200 and 300 μmol·L-1 respectively) for 12, 24 and 36 h. Flow cytometry and chromosome counting were used to identify ploidy, and the phenotype of the polyploids was examined by stomatal observation and leaf index determination. With increasing mutagen concentration and exposure time, the mortality and mutagenic rate increased. The optimal treatment group was: 300 μmol·L-1 trifluralin for 12 h, which resulted in 15.55% mortality rate and 42.22% induction rate. The polyploid plants showed a significant increase in stomata length, leaf length and leaf width, with a decrease in stomatal density compared with the control plants. This study provided a basis for polyploid breeding. [ABSTRACT FROM AUTHOR]

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species. [ABSTRACT FROM AUTHOR]

Summary: Although polyploid plants have lower stomatal density than their diploid counterparts, the molecular mechanisms underlying this difference remain elusive.Here, we constructed a network based on the triploid poplar transcriptome data and triple‐gene mutual interaction algorithm and found that PpnMYC2 was related to stomatal development‐related genes PpnEPF2, PpnEPFL4, and PpnEPFL9. The interactions between PpnMYC2 and PagJAZs were experimentally validated. PpnMYC2‐overexpressing poplar and Arabidopsis thaliana had reduced stomatal density. Poplar overexpressing PpnMYC2 had higher water use efficiency and drought resistance.RNA‐sequencing data of poplars overexpressing PpnMYC2 showed that PpnMYC2 promotes the expression of stomatal density inhibitors PagEPF2 and PagEPFL4 and inhibits the expression of the stomatal density‐positive regulator PagEPFL9. Yeast one‐hybrid system, electrophoretic mobility shift assay, ChIP‐qPCR, and dual‐luciferase assay were employed to substantiate that PpnMYC2 directly regulated PagEPF2, PagEPFL4, and PagEPFL9. PpnMYC2, PpnEPF2, and PpnEPFL4 were significantly upregulated, whereas PpnEPFL9 was downregulated during stomatal formation in triploid poplar.Our results are of great significance for revealing the regulation mechanism of plant stomatal occurrence and polyploid stomatal density, as well as reducing stomatal density and improving plant water use efficiency by overexpressing MYC2. [ABSTRACT FROM AUTHOR]

This study delves into the exploration of genetic diversity and phylogenetic relationships within Camellia reticulata cultivars, providing a vital reference for horticultural research on this hetero-hexaploid species. Utilizing available transcriptome data from C. reticulata, novel low-copy nuclear gene sequences were successfully identified. With tailored primer design, these genes were amplified and sequenced from 100 C. reticulata cultivars originating from Kunming, Chuxiong, Dali, and Tengchong in China. Five distinct low-copy nuclear gene sequences were found to collectively span 3481 bp, showcasing 71 polymorphic mutation sites (Pi = 0.0077) and 91 haplotypes (Hd = 0.9974). The genetic diversity among cultivars from the four provenances ranked Tengchong > Dali > Kunming > Chuxiong. AMOVA analysis revealed that 96.50% of the genetic variation exists within the provenances. Low genetic distance and differentiation (Fst= 0.0199) were observed among cultivars from the four provenances. Ninety-nine cultivars were clustered into four clades, corresponding to the three ancestors of C. reticulata (diploid C. reticulata, C. pitardii, and C. saluenensis). The novel low-copy nuclear gene sequence markers developed in this study provide an effective tool for analyzing genetic diversity, phylogenetic relationships, and origination of C. reticulata cultivars. [ABSTRACT FROM AUTHOR]

Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited, rich in beneficial nutrients, rapid softening and tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, and decaploid. Here we report a haplotype-resolved tetraploid genome (A. arguta cv. 'Longcheng No.2') containing four haplotypes, each with 40,859, 41,377, 39,833 and 39,222 protein-coding genes. We described the phased genome structure, synteny, and evolutionary analyses to identify and date possible WGD events. Ks calculations for both allelic and paralogous genes pairs throughout the assembled haplotypic individuals showed its tetraploidization is estimated to have formed ~ 1.03 Mya following Ad-α event occurred ~ 18.7 Mya. Detailed annotations of NBS-LRRs or CBFs highlight the importance of genetic variations coming about after polyploidization in underpinning ability of immune responses or environmental adaptability. WGCNA analysis of postharvest quality indicators in combination with transcriptome revealed several transcription factors were involved in regulating ripening kiwi berry texture. Taking together, the assembly of an A. arguta tetraploid genome provides valuable resources in deciphering complex genome structure and facilitating functional genomics studies and genetic improvement for kiwifruit and other crops. [ABSTRACT FROM AUTHOR]

BACKGROUND: Recently, suspected cyhalofop‐butyl‐resistant populations of allohexaploid weed Echinochloa crus‐galli var. crus‐galli were discovered in rice fields in Aichi Prefecture, Japan. Analyzing the target‐site ACCase genes of cyhalofop‐butyl helps understand the resistance mechanism. However, in E. crus‐galli, the presence of multiple ACCase genes and the lack of detailed gene investigations have complicated the analysis of target‐site genes. Therefore, in this study, we characterized the herbicide response of E. crus‐galli lines and thoroughly characterized the ACCase genes, including the evaluation of gene mutations in the ACCase genes of each line. RESULT: Four suspected resistant lines collected from Aichi Prefecture showed varying degrees of resistance to cyhalofop‐butyl and other FOP‐class ACCase inhibitors but were sensitive to herbicides with other modes of action. Through genomic analysis, six ACCase loci were identified in the E. crus‐galli genome. We renamed each gene based on its syntenic relationship with other ACCase genes in the Poaceae species. RNA‐sequencing analysis revealed that all ACCase genes, except the pseudogenized copy ACCase2A, were transcribed at a similar level in the shoots of E. crus‐galli. Mutations known to confer resistance to FOP‐class herbicides, that is W1999C, W2027C/S and I2041N, were found in all resistant lines in either ACCase1A, ACCase1B or ACCase2C. CONCLUSION: In this study, we found that the E. crus‐galli lines were resistant exclusively to ACCase‐inhibiting herbicides, with a target‐site resistance mutation in the ACCase gene. Characterization of ACCase loci in E. crus‐galli provides a basis for further research on ACCase herbicide resistance in Echinochloa spp. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Purpose: Primary central nervous system, diffuse large B-cell lymphoma, post-transplant lymphoproliferative disorder in the cerebellopontine angle after an allogeneic stem cell transplantation has never been reported in the literature. Typically, diffuse large B-cell lymphoma is non-polyploid. We report the first case of a patient with polyploid post-transplant lymphoproliferative disorder in the cerebellopontine angle who presented with back pain. Case presentation: A 45-year-old man with a history of nodular sclerosing classic Hodgkin lymphoma stage IIB treated with systemic chemotherapy, external radiation and autologous stem cell transplant and double umbilical cord allogeneic transplant presented with several weeks of back pain. He was found to have a small right cerebellopontine angle mass thought to be consistent with a meningioma. Patient presented again two weeks later with acute onset of severe headache, right sided ptosis, right facial numbness, weakness and possible seizure event. Repeat MRI scans showed an interval and significant increase of the right cerebellopontine angle lesion. Biopsy of the cerebellopontine angle lesion was planned with suspicion of lymphoma. Intraoperative pathology consultation findings were not consistent with an acoustic neuroma, meningioma, or epidermoid cyst. Lymphoma could not be definitively identified by intra-operative frozen section. However, it was suspected, and a portion of fresh specimen was submitted for flow cytometry analysis. A near total resection of the tumor and decompression of the brainstem was achieved. Final pathologic analysis was positive for post-transplant lymphoproliferative disorder, monomorphic type, diffuse large B-cell lymphoma, non-germinal center B-cell type, EBV+, post-transplant (allogeneic stem cell) setting (post-transplant lymphoproliferative disorder (PTLD), monomorphic type, diffuse large B-cell lymphoma, non-germinal center B-cell type (non-GCB), EBV-positive under pre-2022 WHO terminology). The patient began a high-dose methotrexate-based regimen (the MATRIX regimen). Conclusions: Our case illustrates an unusual presentation of post-transplant lymphoproliferative disorder in the cerebellopontine angle in a patient with a remote history of allogeneic stem cell transplantation. It demonstrates the importance of keeping primary central nervous system post-transplant lymphoproliferative disorder on the differential for patients who present with back pain or headache that have a history of allogeneic stem cell transplant. [ABSTRACT FROM AUTHOR]

Summary: Mutations affecting crossover (CO) frequency and distribution lead to the presence of univalents during meiosis, giving rise to aneuploid gametes and sterility. These mutations may have a different effect after chromosome doubling. The combination of altered ploidy and mutations could be potentially useful to gain new insights into the mechanisms and regulation of meiotic recombination; however, studies using autopolyploid meiotic mutants are scarce.Here, we have analyzed the cytogenetic consequences in colchicine‐induced autotetraploids (colchiploids) from different Arabidopsis mutants with an altered CO frequency.We have found that there are three types of mutants: mutants in which chiasma frequency is doubled after chromosome duplication (zip4, mus81), as in the control; mutants in which polyploidy leads to a higher‐than‐expected increase in chiasma frequency (asy1, mer3, hei10, and mlh3); and mutants in which the rise in chiasma frequency produced by the presence of two extrachromosomal sets is less than doubled (msh5, fancm). In addition, the proportion of class I/class II COs varies after chromosome duplication in the control.The results obtained reveal the potential of colchiploid meiotic mutants for better understanding of the function of key proteins during plant meiosis. This is especially relevant considering that most crops are polyploids. [ABSTRACT FROM AUTHOR]

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab. [ABSTRACT FROM AUTHOR]

Background: Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. Results: In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. Conclusions: This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding. [ABSTRACT FROM AUTHOR]

Summary: Numerous staple crops exhibit polyploidy and are difficult to genetically modify. However, recent advances in genome sequencing and editing have enabled polyploid genome engineering. The hexaploid black nightshade species Solanum nigrum has immense potential as a beneficial food supplement. We assembled its genome at the scaffold level. After functional annotations, we identified homoeologous gene sets, with similar sequence and expression profiles, based on comparative analyses of orthologous genes with close diploid relatives Solanum americanum and S. lycopersicum. Using CRISPR‐Cas9‐mediated mutagenesis, we generated various mutation combinations in homoeologous genes. Multiple mutants showed quantitative phenotypic changes based on the genotype, resulting in a broad‐spectrum effect on the quantitative traits of hexaploid S. nigrum. Furthermore, we successfully improved the fruit productivity of Boranong, an orphan cultivar of S. nigrum suggesting that engineering homoeologous genes could be useful for agricultural improvement of polyploid crops. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

After polyploid species are formed, interactions between diploid and polyploid lineages may generate additional diversity in novel cytotypes and phenotypes. In anurans, mate choice by acoustic communication is the primary method by which individuals identify their own species and assess suitable mates. As such, the evolution of acoustic signals is an important mechanism for contributing to reproductive isolation and diversification in this group. Here, we estimate the biogeographical history of the North American grey treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid Hyla versicolor, focusing specifically on the geographical origin of whole genome duplication and the expansion of lineages out of glacial refugia. We then test for lineage‐specific differences in mating signals by applying comparative methods to a large acoustic data set collected over 52 years that includes >1500 individual frogs. Along with describing the overall biogeographical history and call diversity, we found evidence that the geographical origin of H. versicolor and the formation of the midwestern polyploid lineage are both associated with glacial limits, and that the southwestern polyploid lineage is associated with a shift in acoustic phenotype relative to the diploid lineage with which they share a mitochondrial lineage. In H. chrysoscelis, we see that acoustic signals are largely split by Eastern and Western lineages, but that northward expansion along either side of the Appalachian Mountains is associated with further acoustic diversification. Overall, results of this study provide substantial clarity on the evolution of grey treefrogs as it relates to their biogeography and acoustic communication. [ABSTRACT FROM AUTHOR]

Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the comigration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate the double reduction rate given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U‐statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U‐statistic to test for equilibrium. We validate our methods on both simulated and real data. [ABSTRACT FROM AUTHOR]

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Understanding the factors determining species' geographical and environmental range is a central question in evolution and ecology, and key for developing conservation and management practices. Shortly after the discovery of polyploidy, just over 100 years ago, it was suggested that polyploids generally have greater range sizes and occur in more extreme conditions than their diploid congeners. This suggestion is now widely accepted in the literature and is attributed to polyploids having an increased capacity for genetic diversity that increases their potential for adaptation and invasiveness. However, the data supporting this idea are mixed. Here, we compare the niche of allopolyploid plants to their progenitor species to determine whether allopolyploidization is associated with increased geographic range or extreme environmental tolerance. Our analysis includes 123 allopolyploid species that exist as only one known ploidy level, with at least one known progenitor species, and at least 50 records in the Global Biodiversity Information Facility (GBIF) database. We used GBIF occurrence data and range modeling tools to quantify the geographic and environmental distribution of these allopolyploids relative to their progenitors. We find no indication that allopolyploid plants occupy more extreme conditions or larger geographic ranges than their progenitors. Data evaluated here generally indicate no significant difference in range between allopolyploids and progenitors, and where significant differences do occur, the progenitors are more likely to exist in extreme conditions. We concluded that the evidence from these data indicate allopolyploidization does not result in larger or more extreme ranges. Thus, allopolyploidization does not have a consistent effect on species distribution, and we conclude it is more likely the content of an allopolyploid's genome rather than polyploidy per se that determines the potential for invasiveness. Understanding the factors shaping a species' geographical and environmental range is a central question in evolution and ecology, and polyploidization has been cited as a process that results in tolerance to a larger range of or more extreme conditions. Here, we compare the niche of 123 allopolyploid plants to their progenitor species to determine whether allopolyploidization is associated with this type of change using records in the Global Biodiversity Information Facility database. We find no indication that allopolyploid plants occupy more extreme conditions or larger geographic ranges than their progenitors. [ABSTRACT FROM AUTHOR]

Polyploid plants, an important source for the selection of ornamental plants for their advantages of faster growth, higher yields, and stronger adaptability to an adverse environment, play an essential role in the development of economic plants for agricultural stress. The methodology has been improved to decrease blindness and increase the efficiency of ornamental plants' polyploid breeding in the long term. The progress of research on ornamental plants related to natural polyploidy, chromosome doubling, the 2n gametes pathway, and plant ploidy identification are reviewed in this paper. The main routes in polyploid breeding are chromosome doubling and sexual hybridization. Screening of suitable induction methods and plant material should be enhanced in chromosome doubling to improve induction efficiency. Regarding polyploid breeding, the utilization and research on 2n gametes produced by natural conditions or artificial induction should be strengthened to shorten the breeding years. Therefore, further research should strengthen the combination of chromosome doubling and sexual hybridization to improve breeding efficiency and strengthen the research and application of polyploid plants. This thesis review provides some reference value for polyploid breeding in ornamental plants. [ABSTRACT FROM AUTHOR]

Taxa are traditionally identified using morphological proxies for groups of evolutionarily isolated populations. These proxies are common characters deemed by taxonomists as significant. However, there is no general rule on which character or sets of characters are appropriate to circumscribe taxa, leading to discussions and uncertainty. Birch species are notoriously hard to identify due to strong morphological variability and factors such as hybridization and the existence of several ploidy levels. Here, we present evidence for an evolutionarily isolated line of birches from China that are not distinguishable by traditionally assumed taxon recognition proxies, such as fruit or leaf characters. We have discovered that some wild material in China and some cultivated in the Royal Botanic Gardens Edinburgh, formerly recognized as Betula luminifera, differ from other individuals by having a peeling bark and a lack of cambial fragrance. We use restriction site-associated DNA sequencing and flow cytometry to study the evolutionary status of the unidentified Betula samples to assess the extent of hybridization between the unidentified Betula samples and typical B. luminifera in natural populations. Molecular analyses show the unidentified Betula samples as a distinct lineage and reveal very little genetic admixture between the unidentified samples and B. luminifera. This may also be facilitated by the finding that B. luminifera is tetraploid, while the unidentified samples turned out to be diploid. We therefore conclude that the samples represent a yet unrecognized species, which is here described as Betula mcallisteri. [ABSTRACT FROM AUTHOR]

Background and Aims Cultivated bananas resulted from inter(sub)specific hybridizations involving Musa species and subspecies (M. acuminata subspecies, M. schizocarpa , M. balbisiana) and the subsequent selection, centuries ago, of hybrids with parthenocarpic, seedless fruits. Cultivars have low fertility and are vegetatively propagated, forming groups of somaclones. Relatively few of them, mainly triploids, are grown on a large scale and characterization of their parental relationships may be useful for breeding strategies. Here we investigate parental relationships and gamete-type contributions among diploid and polyploid banana cultivars. Methods We used SNP genotyping data from whole-genome sequencing of 178 banana individuals, including 111 cultivars, 55 wild bananas and 12 synthetic F 1 hybrids. We analysed the proportion of SNP sites in accordance with direct parentage with a global statistic and along chromosomes for selected individuals. Key Results We characterized parentage relationships for 7 diploid cultivars, 11 triploid cultivars and 1 tetraploid cultivar. Results showed that both diploid and triploid cultivars could have contributed gametes to other banana cultivars. Diploids may have contributed 1 x or 2 x gametes and triploids 1 x to 3 x gametes. The Mchare diploid cultivar group, nowadays only found in East Africa, was found as parent of two diploid and eight triploid cultivars. In five of its identified triploid offspring, corresponding to main export or locally popular dessert bananas, Mchare contributed a 2 x gamete with full genome restitution without recombination. Analyses of remaining haplotypes in these Mchare offspring suggested ancestral pedigree relationships between different interspecific banana cultivars. Conclusions The current cultivated banana resulted from different pathways of formation, with implication of recombined or un-recombined unreduced gametes produced by diploid or triploid cultivars. Identification of dessert banana's parents and the types of gametes they contributed should support the design of breeding strategies. [ABSTRACT FROM AUTHOR]

The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions - an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC’s genetic diversity. The analysis of molecular variance confirmed the CCC’s diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count. [ABSTRACT FROM AUTHOR]

Genome duplication supplies raw genetic materials and has been thought to be essential for evolutionary innovation and ecological adaptation. Here, we select Kelch-like (klhl) genes to study the evolution of the duplicated genes in the polyploid Carassius complex, including amphidiploid C. auratus and amphitriploid C. gibelio. Phylogenetic, chromosomal location and read coverage analyses indicate that most of Carassius klhl genes exhibit a 2:1 relationship with zebrafish orthologs and confirm two rounds of polyploidy, an allotetraploidy followed by an autotriploidy, occurred during Carassius evolution. The lineage-specific expansion and biased retention/loss of klhl genes are also found in Carassius. Transcriptome analyses across eight adult tissues and seven embryogenesis stages reveal varied expression dominance and divergence between the two species. The expression of klhls in response to Carassius herpesvirus 2 infection shows different expression changes corresponding to distinct herpesvirus resistances in three C. gibelio gynogenetic clones. Finally, we find that most C. gibelio klhl genes possess three alleles except eight genes that have lost one or two alleles due to genome rearrangement. The allele expression bias is prosperous for Cgklhl genes and varies during embryogenesis owning to the sequential expression manner of the alleles. The current study provides global insights into the genomic and transcriptional evolution of duplicated genes in a given superfamily resulting from multiple rounds of polyploidization. [ABSTRACT FROM AUTHOR]

Background: Understanding the mechanisms underlining forage production and its biomass nutritive quality at the omics level is crucial for boosting the output of high-quality dry matter per unit of land. Despite the advent of multiple omics integration for the study of biological systems in major crops, investigations on forage species are still scarce. Results: Our results identified substantial changes in gene co-expression and metabolite-metabolite network topologies as a result of genetic perturbation by hybridizing L. perenne with another species within the genus (L. multiflorum) relative to across genera (F. pratensis). However, conserved hub genes and hub metabolomic features were detected between pedigree classes, some of which were highly heritable and displayed one or more significant edges with agronomic traits in a weighted omics-phenotype network. In spite of tagging relevant biological molecules as, for example, the light-induced rice 1 (LIR1), hub features were not necessarily better explanatory variables for omics-assisted prediction than features stochastically sampled and all available regressors. Conclusions: The utilization of computational techniques for the reconstruction of co-expression networks facilitates the identification of key omic features that serve as central nodes and demonstrate correlation with the manifestation of observed traits. Our results also indicate a robust association between early multi-omic traits measured in a greenhouse setting and phenotypic traits evaluated under field conditions. [ABSTRACT FROM AUTHOR]

Lectins are natural proteins in animals, plants, and microorganisms and can be divided into 12 families. These lectins play important roles in various environmental stresses. Some polyploid plants show tolerance to environmental stresses and to insect pests. However, the mechanism of stress tolerance is unclear. Tetraploid Robinia pseudoacacia (4×) under salt stress showed higher tolerance than diploid R. pseudoacacia (2×). As lectin can improve stress tolerance, it was questioned whether the stress resistance of polyploid plants was related to the lectin protein. In this study, salt resistance of lectin gene TRpL1 was verified by its over-expression in plants. In addition, salt resistance of lectin protein by E. coli strains was detected. The data revealed that the over-expression transgenic plants of TRpL1 showed better salt tolerance than control plants under salt stress, and the TRpL1-expressing strain also grew better in the medium with added NaCl. Therefore, tetraploid plants can resist salt stress through TRpL1 protein regulation. [ABSTRACT FROM AUTHOR]

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon. [ABSTRACT FROM AUTHOR]

SUMMARY: Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome‐scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at ~4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about ~0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element‐rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels. Significance Statement: We assembled the chromosome‐scale genome assembly of broomcorn millet and divided the allotetraploid genome into two subgenomes. The biased TE activity in the two subgenomes may have led to the expanded genome size in subgenome B before polyploidization and elevated levels of gene losses during diploidization. The present study suggests that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels. [ABSTRACT FROM AUTHOR]

Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-bysequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype. [ABSTRACT FROM AUTHOR]

The phenotypic variation of vegetative organs and reproductive organs of newly synthesized and natural Arabidopsis kamchatica genotypes was investigated in both a controlled environment and a natural environment in an experimental garden. When we compared the variation of their leaf shape as a vegetative organ, the synthetic A. kamchatica individuals grown in the garden showed larger variation compared with the individuals incubated in a growth chamber, suggesting enhanced phenotypic variation in a natural fluctuating environment. In contrast, the natural A. kamchatica genotypes did not show significant change in variation by growth condition. The phenotypic variation of floral organs by growth condition was much smaller in both synthetic and natural A. kamchatica genotypes, and the difference in variation width between the growth chamber and the garden was not significant in each genotype as well as among genotypes. The higher phenotypic variation in synthetic leaf may imply flexible transcriptomic regulation of a newly synthesized polyploid compared with a natural polyploid. [ABSTRACT FROM AUTHOR]

As a cancer type potentially dominated by copy number variations, ovarian cancer shows hyperploid karyotypes and large-scale chromosome alterations, which might be promising biomarkers correlated with tumor metastasis and chemoresistance. Experimental studies have provided more information about the roles of aneuploids and polyploids in ovarian cancer. However, ploidy evaluation of ovarian cancer cell lines is still limited, even in some ploidy-related research. Herein, the ploidy landscape of 51 ovarian cancer cell lines from the Cancer Cell Line Encyclopedia (CCLE) were analyzed, and the ploidy statuses of 13 human ovarian cancer cell lines and 2 murine cell lines were evaluated using G-banding and flow cytometry. Most human ovarian cancer cell lines were aneuploid, with modal numbers of 52–86 and numerical complexity ranging from 5 to 12. A2780, COV434 and TOV21G were screened as diploid cell lines, with a modal number of 46, a low aneuploid score and a near-diploid ploidy value. Two murine cell lines, both OV2944-HM1 and ID-8, were near-tetraploid. Integrated information on karyotypes, aneuploid score and ploidy value supplied references for a nondiploid model construction and a parallel analysis of diploid versus aneuploid. Moreover, the gene expression profiles were compared between diploid and aneuploid cell lines. The functions of differentially expressed genes were mainly enriched in terms of protein function regulation, TGF-β signaling and cell adhesion molecules. Genes downregulated in the aneuploid group were mainly related to metabolism and protein function regulation, and genes upregulated in the aneuploid group were mainly involved in immune regulation. Differentially expressed genes were randomly distributed on all chromosomes, while chromosome 1 alteration might contribute to immune-related alterations in aneuploid cell lines. Chromosome 19 alteration might be potentially significant for aneuploid ovarian cancer cell lines and patients, which needs further verification in ploidy research. [ABSTRACT FROM AUTHOR]

Background The Lycophyta species are the extant taxa most similar to early vascular plants that were once abundant on Earth. However, their distribution has greatly diminished. So far, the absence of chromosome-level assembled lycophyte genomes has hindered our understanding of evolution and environmental adaption of lycophytes. Findings We present the reference genome of the tetraploid aquatic quillwort, Isoetes sinensis , a lycophyte. This genome represents the first chromosome-level assembled genome of a tetraploid seed-free plant. Comparison of genomes between I. sinensis and Isoetestaiwanensis revealed conserved and different genomic features between diploid and polyploid lycophytes. Comparison of the I. sinensis genome with those of other species representing the evolutionary lineages of green plants revealed the inherited genetic tools for transcriptional regulation and most phytohormones in I. sinensis. The presence and absence of key genes related to development and stress responses provide insights into environmental adaption of lycophytes. Conclusions The high-quality reference genome and genomic analysis presented in this study are crucial for future genetic and environmental studies of not only I. sinensis but also other lycophytes. [ABSTRACT FROM AUTHOR]

Background and Aims Polyploidy is an important process that often generates genomic diversity within lineages, but it can also cause changes that result in loss of genomic material. Island lineages, while often polyploid, typically show chromosomal stasis but have not been investigated in detail regarding smaller-scale gene loss. Our aim was to investigate post-polyploidization genome dynamics in a chromosomally stable lineage of Malvaceae endemic to New Zealand. Methods We determined chromosome numbers and used fluorescence in situ hybridization to localize 18S and 5S rDNA. Gene sequencing of 18S rDNA, the internal transcribed spacers (ITS) with intervening 5.8S rDNA, and a low-copy nuclear gene, GBSSI-1 , was undertaken to determine if gene loss occurred in the New Zealand lineage following polyploidy. Key Results The chromosome number for all species investigated was 2 n  = 42, with the first published report for the monotypic Australian genus Asterotrichion. The five species investigated all had two 5S rDNA signals localized interstitially on the long arm of one of the largest chromosome pairs. All species, except Plagianthus regius , had two 18S rDNA signals localized proximally on the short arm of one of the smallest chromosome pairs. Plagianthus regius had two additional 18S rDNA signals on a separate chromosome, giving a total of four. Sequencing of nuclear ribosomal 18S rDNA and the ITS cistron indicated loss of historical ribosomal repeats. Phylogenetic analysis of a low-copy nuclear gene, GBSSI-1 , indicated that some lineages maintained three copies of the locus, while others have lost one or two copies. Conclusions Although island endemic lineages show chromosomal stasis, with no additional changes in chromosome number, they may undergo smaller-scale processes of gene loss and concerted evolution ultimately leading to further genome restructuring and downsizing. [ABSTRACT FROM AUTHOR]

Summary: Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species‐special metabolites. Here, we report reference‐grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole‐genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high‐quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes. [ABSTRACT FROM AUTHOR]

Motivation: In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic diversity transmitted by the gametes. The genome-wide determination of the frequency and location of the recombination events can now be efficiently performed by genotyping the offspring's polymorphic markers. However, genotyping recombination in complex hybrid genomes with existing methods remains challenging because of their strain and ploidy specificity and the degree of diversity and complexity of the parental genomes, especially in > 2 n polyploids. Results: We present UGDR, a pipeline to genotype the polymorphisms of complex hybrid yeast genomes. It is based on optimal mapping strategies of NGS reads, comparative analyses of the allelic ratio variation and read depth coverage. We tested the UGDR pipeline with sequencing reads from recombined hybrid diploid yeast strains and various clinical strains exhibiting different degrees of ploidy. UGDR allows to plot the markers distribution and recombination profile per chromosome. Conclusion: UGDR detects and plots recombination events in haploids and polyploid yeasts, which facilitates the discovery and understanding of the yeast genetic recombination map and identify new out-performing recombinants. [ABSTRACT FROM AUTHOR]

Common wheat (Triticum aestivum, BBAADD) is an allohexaploid species combines the D genome from Ae. tauschii and with the AB genomes from tetraploid wheat (Triticum turgidum). Compared with tetraploid wheat, hexaploid wheat has wide-ranging adaptability to environmental adversity such as salt stress. However, little is known about the molecular basis underlying this trait. The plasma membrane Na+/H+ transporter Salt Overly Sensitive 1 (SOS1) is a key determinant of salt tolerance in plants. Here we show that the upregulation of TaSOS1 expression is positively correlated with salt tolerance variation in polyploid wheat. Furthermore, both transcriptional analysis and GUS staining on transgenic plants indicated TaSOS1-A and TaSOS1-B exhibited higher basal expression in roots and leaves in normal conditions and further up-regulated under salt stress; while TaSOS1-D showed markedly lower expression in roots and leaves under normal conditions, but significant up-regulated in roots but not leaves under salt stress. Moreover, transgenic studies in Arabidopsis demonstrate that three TaSOS1 homoeologs display different contribution to salt tolerance and TaSOS1-D plays the prominent role in salt stress. Our findings provide insights into the subgenomic homoeologs variation potential to broad adaptability of natural polyploidy wheat, which might effective for genetic improvement of salinity tolerance in wheat and other crops. [ABSTRACT FROM AUTHOR]

The fertility and crossing behavior of a tetraploid hybrid of 4x Andean blueberry (V. meridionale) and lingonberry (V. vitis-idaea) was evaluated through a series of crosses. Crosses of the hybrid with highbush blueberry produced divergent results. When used as a female with V. corymbosum males, virtually all offspring were hexaploid, most likely arising from 2n = 4x = 48 female gametes, and 1n = 2x = 24 male gametes. However, when used as a male, tetraploid hybrids were produced, resulting from 1n = 2x = 24 gametes from each parent. To further examine this crossing behavior, the 4x V. meridionale—V. vitis-idaea interspecific hybrid was pollinated with 6x V. virgatum (rabbiteye blueberry). Analogous to the previous crosses, 7x hybrids were produced from the joining of 2n = 4x = 48 female gametes with 1n = 3x = 36 male gametes. Such reciprocal crossing asymmetry is unprecedented. The ability to produce both 6x and 4x offspring from the same V. corymbosum parents allows the potential of bridging a V. meridionale hybrid genotype to both the tetraploid (V. corymbosum) and hexaploid (V. virgatum) commercial crop levels. [ABSTRACT FROM AUTHOR]