Autosomal Research Articles

Karyological Examination of Ornithogalum orthophyllum Ten. and Ornithogalum oligophyllum E. D. Clarke

In this study, two species of Ornithogalum L. genus (Ornithogalum orthophyllum Ten. and Ornithogalum oligophyllum E. D. Clarke), one of the important genus of the Asparagaceae family, were examined in terms of karyological aspects. The plant materials used in the study were collected from the natural distribution areas of the plants around Elazığ 2019. Some of the collected samples were turned into herbarium samples and stocked in the FU herbarium. Bulbs obtained from the collected samples were used in cytotaxonomic studies. As a result of the studies carried out in dividing somatic cells, chromosome counts and karyotype analyzes of the species were made and their ideograms were drawn. Chromosome number were determined as 2n=20 and karyotype formula M+3m+3sm+3st in Ornithogalum oligophyllum, Ornithogalum orthophyllum species as 2n=14 and karyotype formula as 3m+2sm+2st.

Identification of Disease-Relevant, Sex-Based Proteomic Differences in iPSC-Derived Vascular Smooth Muscle Cells.

The prevalence of cardiovascular disease varies with sex, and the impact of intrinsic sex-based differences on vasculature is not well understood. Animal models can provide important insights into some aspects of human biology; however, not all discoveries in animal systems translate well to humans. To explore the impact of chromosomal sex on proteomic phenotypes, we used iPSC-derived vascular smooth muscle cells from healthy donors of both sexes to identify sex-based proteomic differences and their possible effects on cardiovascular pathophysiology. Our analysis confirmed that differentiated cells have a proteomic profile more similar to healthy primary aortic smooth muscle cells than iPSCs. We also identified sex-based differences in iPSC-derived vascular smooth muscle cells in pathways related to ATP binding, glycogen metabolic process, and cadherin binding as well as multiple proteins relevant to cardiovascular pathophysiology and disease. Additionally, we explored the role of autosomal and sex chromosomes in protein regulation, identifying that proteins on autosomal chromosomes also show sex-based regulation that may affect the protein expression of proteins from autosomal chromosomes. This work supports the biological relevance of iPSC-derived vascular smooth muscle cells as a model for disease, and further exploration of the pathways identified here can lead to the discovery of sex-specific pharmacological targets for cardiovascular disease.

Taxonomy, karyomorphology and pollen viability of Hymenocallis littoralis (Jacq.) Salisb. (Amaryllidaceae)

The present study offers the taxonomy, karyomorphology, and pollen-pistil interactions in the bulbous species Hymenocallis littoralis (Jacq.) Salisb. of the family Amaryllidaceae. The genus Hymenocallis is closely allied to Pancratium, however, differs from the later by filament, number and shape of ovule, and seed characteristics. Detailed descriptions and illustrations of H. littoralis are provided, alongside information on its habitat, distribution, examined specimens, and economic significance. A new somatic chromosome number of 2n = 50 is reported for H. littoralis, and this count was not found to be consistent with any of the earlier reports, offering additional insights into its chromosomal characteristics. Furthermore, the study reveals a high pollen viability of 95% in H. littoralis. Bangladesh J. Plant Taxon. 31(2): 265-273, 2024 (December)

Search for a genetic cause of variably protease-sensitive prionopathy.

Prion disease is caused by misfolding of the prion protein (PrP), and can be either sporadic genetic, or acquired. Acquired cases arising from infection through dietary or medical routes are exceedingly rare today (<1% of cases). Sporadic cases occur apparently at random, without any major genetic risk factors, and are not passed down to subsequent generations. All cases of genetic prion disease to date have been traced to DNA changes that alter the amino acid sequence of PrP, and children of people with genetic prion disease are at 50/50 risk of inheriting these autosomal dominant DNA changes. Variably protease sensitive prionopathy, or VPSPr, is a rare and unusual subtype of prion disease, in which there are no changes in PrP's amino acid sequence, and yet, a high proportion of patients appear to have a family history of dementia, although none to date have had family members diagnosed with prion disease specifically. VPSPr is currently categorized as a sporadic prion disease, but it has been speculated that it may have a genetic cause in a different gene or in a region of the PrP gene that does not change the amino acid sequence. Here we performed DNA sequencing on 67 VPSPr cases to search for a genetic cause. We found no DNA changes that could potentially cause VPSPr. While it is difficult to prove the negative - a causal genetic change could still exist in some part of the genome where we did not search - our data support the notion that VPSPr is truly sporadic in nature, and that risk of VPSPr is not transmitted in families.

Beyond the "Dominant" and "Recessive" Patterns of Inheritance.

This study aimed to investigate whether genes with different modes of inheritance differ in the presence of promoter-enriched CGI loci. For each autosomal chromosome, the author searched for variations in the total number of diseases' phenotypes with autosomal dominant (AD) and recessive (AR) inheritance for a list of promoter-poor CGI (CGI-) and promoter-enriched CGI (CGI+) genes using the OMIM database. Then, the CGI- and CGI+ genes displaying random allelic or bi-allelic expression were examined. The author evaluated whether there was a distinct distribution of AD and AR diseases in the groups of chromosomes based on their SNP hotspot density. The same analysis was conducted for the X chromosome. The SPSS statistical package was utilized. The distribution of AD and AR diseases between CGI- and CGI+ bi-allelic genes significantly differed in autosomal chromosomes 6 and 17, which show intermediate SNP hotspot density. Additionally, a statistically significant difference was observed in AD and AR diseases in the remaining autosomal chromosomes with low SNP hotspots between their randomly allelic expressed CGI- and CGI+ genes. Specifically, AD diseases were related to CGI- genes, while AR diseases were associated with CGI+ genes. In the X chromosome, X-linked dominant (XLD) diseases were mainly found in CGI+ genes, and X-linked recessive (XLR) diseases were found in CGI- genes, regardless of the X-inactivation process. It is essential to study inheritance and classify genetic variants in a more stochastic way than the terms "Dominant" and "Recessive," and their derivatives, such as "Codominant" and "Incomplete Dominant," are applied in Mendelian and non-Mendelian inheritance. This concept may further explain the "Reduced Penetrance" and "Variable Expressivity" in certain human diseases. All the above suggests a need to reassess how genetic and epigenetic data are studied and utilized for genetic counseling or precision medicine.

Universal Single Copy Knock-In System in Caenorhabditis elegans : One Plasmid to Target All Chromosomes.

Successful transgenesis in model organisms has dramatically helped us understand gene function, regulation, genetic networks, and potential applications. Here, we introduce the universal single-copy knock-in system (Universal SKI System or U-SKI), designed for inserting any transgene by CRISPR/Cas9 in the Caenorhabditis elegans genome. The Universal SKI System takes advantage of a plasmid (pSKI), which can also be used for extrachromosomal arrays, to facilitate the insertion of a transgene at specific safe harbor loci on each autosomal chromosome. The pSKI plasmid contains multiple restriction sites for easy cloning and serves as a CRISPR/Cas9-based insertion repair template because it has two synthetic and long homology arms that recombine with the SKI cassettes. This system also uses a single crRNA guide, which acts as a Co-CRISPR enrichment marker. Overall, the Universal SKI System is highly flexible; with the same Universal SKI cassette on each autosome, researchers can select the insertion site and streamline tracking while reducing the complexity of expressing single-copy transgenes in C. elegans .

Cell-cycle and Age-Related Modulations of Mouse Chromosome Stiffness.

Chromosome structure is complex, and many aspects of its organization remain poorly understood. Measuring chromosome stiffness offers valuable insight into their structural properties. In this study, we analyzed the stiffness of chromosomes from metaphase I (MI) and metaphase II (MII) oocytes. Our results revealed a ten-fold increase in stiffness (Young's modulus) of MI chromosomes compared to somatic chromosomes. Furthermore, the stiffness of MII chromosomes was lower than that of MI chromosomes. We examined the role of meiosis-specific cohesin complexes in regulating chromosome stiffness. Surprisingly, chromosomes from three meiosis-specific cohesin mutants exhibited stiffness comparable to that of wild-type chromosomes, indicating that these cohesins are not the primary determinants of chromosome stiffness. Additionally, our findings revealed an age-related increase in chromosome stiffness in MI oocytes. Since aging is associated with elevated levels of DNA damage, we investigated the impact of etoposide-induced DNA damage on oocyte chromosome stiffness and found that it led to a reduction in MI chromosome stiffness. Overall, our study underscores the dynamic and cyclical nature of chromosome stiffness, modulated by both the cell cycle and age-related factors.

A case of double aneuploidy of Down and Klinefelter syndrome in an Indian infant: a detailed case report

BackgroundA variation in the number of chromosomes can lead to chromosomal disorders. These chromosomal aberrations might be related to autosomes or sex chromosomes. The most common chromosomal aberrations that are sex-linked and autosomal are Klinefelter syndrome and Down syndrome, respectively. However, the worldwide occurrence of double chromosomal aneuploidy in a single individual is relatively exceptional event and random meiotic nondisjunction events result in double aneuploidy, which causes trisomy of two distinct chromosomes. The clinical manifestations vary depending on whether aneuploidy is dominant or an amalgam of both. Moreover, double aneuploidy including autosome and sex chromosome is not often documented. In this paper, we document a case of Down–Klinefelter double aneuploidy syndrome in an Indian infant hospitalized to the neonatal care unit.Case presentationA full-term 9-month-old male infant born to a 36-year-old female with classical clinical signs of Down syndrome like epicanthus, a depressed nasal bridge, a flat face, small ears, an open mouth, thick lower lip vermilion, a protruding tongue, and a short neck was referred for cytogenetic examination, revealing a rare karyotype of 48, XXY, + 21.ConclusionDown–Klinefelter syndrome is a rare chromosomal anomaly with unique characteristics, often displaying only Down syndrome-like traits at birth. Early diagnosis can be challenging due to the lack of noticeable symptoms until puberty. Early cytogenetic investigation can detect double aneuploidy, improving the affected person's quality of life and educating family members about potential medical and psychosocial difficulties.

The Who’s, What’s, and “Y”s: Y Sex Chromosome Loss and Methylation for Analysis in Male Aging and Mortality and Forensic Science Applications

The Y chromosome plays a crucial role in understanding the overall landscape of male health. Incorporating the Y chromosome into genomic and epigenomic research may elucidate the male-specific mechanisms behind aging and the pathogenesis of certain conditions, both acute and chronic. Present epigenetic research focuses on the effects of modifications like methylation on autosomal chromosomes. However, little research has been conducted to further these investigations in sex chromosomes, especially the Y chromosome. Epigenetic analyses can identify age-associated CpG sites that may offer potential biomarkers for age estimation and disease risk assessment, among others. This review emphasizes interdisciplinary efforts that have been made in the construction of an assembly and the application of “epigenetic clocks” to the Y chromosome. The studies reviewed here examined the effects of aging on genes such as NLGN4Y, DDX3Y, and TBL1Y, and on male-specific health disparities and disease etiologies, as well as the potential for the use of these genes to assess the diagnostic and age algorithmic potential of Y-specific genes.

Roadmap and Considerations for Genome Editing in a Non-Model Organism: Genetic Variations and Off-Target Profiling.

The CRISPR/Cas genome editing approach in non-model organisms poses challenges that remain to be resolved. Here, we demonstrated a generalized roadmap for a de novo genome annotation approach applied to the non-model organism Macrobrachium rosenbergii. We also addressed the typical genome editing challenges arising from genetic variations, such as a high frequency of single nucleotide polymorphisms, differences in sex chromosomes, and repetitive sequences that can lead to off-target events. For the genome editing of M. rosenbergii, our laboratory recently adapted the CRISPR/Cas genome editing approach to embryos and the embryonic primary cell culture. In this continuation study, an annotation pipeline was trained to predict the gene models by leveraging the available genomic, transcriptomic, and proteomic data, and enabling accurate gene prediction and guide design for knock-outs. A next-generation sequencing analysis demonstrated a high frequency of genetic variations in genes on both autosomal and sex chromosomes, which have been shown to affect the accuracy of editing analyses. To enable future applications based on the CRISPR/Cas tool in non-model organisms, we also verified the reliability of editing efficiency and tracked off-target frequencies. Despite the lack of comprehensive information on non-model organisms, this study provides an example of the feasibility of selecting and editing specific genes with a high degree of certainty.

Clinal variation in autosomal satellite DNA clusters across a contact zone in Barker Frogs.

Contact zones between genetically divergent lineages offer a unique opportunity to explore gene flow and speciation dynamics. Because satellite DNAs (satDNAs) have high evolutionary rates, they may be useful for comparing related taxa and assessing contact zones. Here, we analyzed the distribution of chromosomal clusters of PcP190 satDNA across a contact zone between two distinct genetic lineages of a Neotropical species complex of frogs. The parental lineages, Physalaemus ephippifer and lineage 1B (L1B), exhibited pronounced divergence in the number of PcP190 clusters. We further expanded the geographic scope of this species complex by including two additional Brazilian localities in previously available cytogenetic and mitochondrial DNA datasets. The contact zone exhibited remarkable variation in the chromosomal distribution of PcP190 clusters among the autosomes; the only fixed autosomal site was found on chromosome 3. The highest numbers of PcP190 clusters were observed in specimens collected at sites near (approximately 320 km from) the distribution of L1B, whereas specimens from Dom Eliseu, which is near (approximately 330 km from) the distribution of P. ephippifer, had the lowest numbers of such clusters. Mitochondrial haplotypes also exhibited geographical variation across sites. Our findings expand the known contact zone of these Physalaemus lineages from 1,500 km2 to over 6,200 km2, demonstrating its extensive area, and emphasize the usefulness of satDNAs in studying contact zones.

Genome content in the non-model ciliate Chilodonella uncinata: insights into nuclear architecture, gene-sized chromosomes among the total DNA in their somatic macronuclei during their development.

Ciliates are a model lineage for studies of genome architecture given their unusual genome structures. All ciliates have both somatic macronuclei (MAC) and germline micronuclei (MIC), both of which develop from a zygotic nucleus following sex (i.e., conjugation). Nuclear developmental stages are not as well explored among non-model ciliate genera, including Chilodonella uncinata (Class- Phyllopharyngea), the focus of our work. Here, we characterize nuclear architecture and genome dynamics in C. uncinata by combining DAPI (4',6-diamidino-2-phenylindole) staining and fluorescence in situ hybridization (FISH) techniques with confocal microscopy. We developed a telomere probe for staining alongside DAPI, which allows for the identification of fragmented somatic chromosomes among the total DNA in the nuclei. We quantify both total DNA and telomere-bound signals to explore changes in DNA content and chromosome maturation across Chilodonella's nuclear life cycle. Specifically, we find that MAC developmental stages in the ciliate C. uncinata are different than the data reported from other ciliate species. These data provide insights into nuclear dynamics during nuclear development and enrich our understanding of genome evolution in non-model ciliates.

Genetic and cytogenetic analysis of Moringa oleifera short and long capsule phenotypes

Cytogenetic and molecular studies hold significant importance in plant breeding programs. In the case of moringa, such studies are scarce. Therefore, the objective of this research was to determine the chromosomal number and genetic diversity parameters in two phenotypes of Moringa oleifera Lam. (short and long capsule) using chromosomal analysis and ISSR markers, respectively. Cytogenetic analyses were conducted using the “Somatic chromosomes in root apices” technique, with acetocarmine and papain for staining. It was possible to identify 2N = 28 chromosomes in a single cell of the long capsule phenotype, ranging in size from 0.05 to 0.10 μm. Cells in both moringa phenotypes were observed in prophase, metaphase, anaphase, and telophase. High genetic variability was found in both phenotypes of moringa, as indicated by a Shannon index of 0.81. Additionally, the principal component analysis and UPGMA (Unweighted Pair-Group Method with Arithmetic) groups revealed genetic isolation between the studied moringa phenotypes. The significant polymorphism obtained with most primers suggests that the tested ISSR markers are highly useful for studying genetic diversity in moringa. These findings provide a robust foundation for future research in genetic improvement and conservation of moringa, highlighting the relevance of cytogenetic and molecular studies in this species.

Parent Narratives Provide Perspectives on the Experience of Care in Trisomy 18.

Trisomy 18 syndrome, also known as Edwards syndrome, is the second most common autosomal chromosome syndrome after Down syndrome. Trisomy 18 is a serious medical disorder due to the increased occurrence of structural defects, the high neonatal and infant mortality, and the disabilities observed in older children. Interventions, including cardiac surgery, remain controversial, and the traditional approach is to pursue pure comfort care. While the medical challenges have been well-characterized, there are scant data on the parental views and perspective of the lived experience of rearing a child with trisomy 18. Knowledge of the parental viewpoints can help clinicians guide families through decision-making. Our aim was to identify parents' perspectives by analyzing a series of narratives. In this qualitative study, we collected 46 parent narratives at the 2015 and 2016 conferences of the Support Organization for Trisomy 18 & 13 (SOFT). The participants were asked to "Tell us a story about your experience." Inductive content analysis and close reading were used to identify themes from the stories. Dedoose, a web-based application to analyze qualitative data, was used to code themes more systematically. Of the identified themes, the most common included Impact of trisomy 18 diagnosis and Surpassing expectations. Other themes included Support from professionals, A child, not a diagnosis, and Trust/lack of trust. We examined the voice and the perspectives of the parents in their challenges in caring for their children with this life-limiting condition. The exploration of the themes can ideally guide clinicians in their approach to the counseling and care of the child in a shared decision-making approach.

Development of a qPCR assay for the quantification of canine autosomal DNA recovered from livestock attacks

The absence of a standardised method to quantify canine DNA recovered from livestock attacks leaves forensic providers without an important quality control step to help support their decision making. Typically used to normalise the amount of DNA for STR amplification, modern forensic DNA quantification approaches use qPCR of target genes and can also include an Internal Positive Controls (IPC) to determine the presence of PCR inhibitors. The co-amplification of livestock DNA alongside canine DNA has meant that previously developed qPCR methods are not suitable for use so a standardised approach is needed. This research describes the development of a Taq-man multiplex qPCR assay that simultaneously quantifies the autosomal MC1R and Y-specific SRY gene to determine the concentration of canine DNA recovered from attacked livestock. Data suggests that the method is robust and reproducible with no significant difference in the standard curves produced from multiple runs or from different DNA standards derived from different canines. Assay sensitivity of between 15 and 31 pg is consistent with other forensic quantification assays and also in line with the sensitivity of the two tested canine STR kits, Canine Genotype 2.1 Kit and CaDNAP Panels 1 and 2. The assay is highly specific to canines when tested against 163 different dogs representing 33 different breeds and no cross-amplification of non-target species’ DNA was observed even from livestock DNA tested at 31.25 ng/µl. This strongly suggests that any DNA detected on evidence collected from attacked livestock is canine. The assay also shows robust tolerance to common livestock inhibitors continuing to amplify when inhibitor-spiked DNA samples were tested. Both mixed and inhibited DNA samples underwent STR typing using two canine forensic STR kits with data showing the Canine Genotype 2.1 Kit displaying pronounced cross-amplification of livestock DNA and and/or extensive PCR inhibition leading to the complete loss of amplification when using this kit. Conversely the CaDNAP Panels 1 and 2 showed little cross-amplification of livestock DNA and improved inhibitor tolerance suggesting that this approach was better suited for the analysis of livestock attack samples. Findings are discussed and the impact of the observations on future work in this area are explored.

Genus Zingiber: A Review on Botanical, Major Bioactivities and Genetic Diversity

Zingiberaceae is a perennial plant family that is found across the tropics, particularly in Southeast Asia from low land to hill forests. In Peninsular Malaysia, it is believed that 160 ginger species are widely distributed belonging to 18 genera. Most of the Zingiber species in Peninsular Malaysia are less investigated and less understood taxonomically, thus remaining as under-utilized crops. The description of their morphologies in parallel with phytochemicals and molecular information are crucial to provide valuable information for further discovery of potent compounds, identification of potential new sources of genetic variation, as well as to provide insight into the domestication and breeding of ginger. The majority of Zingiber species are perennial herbs with a fragrant scent, an upright stem, and a fibrous rhizome. The presence of volatile components such as monoterpenoids, sesquiterpenes, sesquiterpenoids and some non-volatile compounds like gingerols, shagaols, and zingerone have contributed to the strong scent of the ginger oils. Among the dominant components of Zingiber are α-zingiberene, geranial, neral, camphene, neral, neric acid, α-curcumene, and zerumbone. The crude extracts and essential oils of Zingiber have proven to show some biological activities such as antimicrobial, anti-bacterial, insecticidal, larvicidal, anti-cancer, anti-inflammatory, anti-ulceration, antioxidant, anti-fungal, immunomodulatory, and anti-nociceptive. Most Zingiber species are known to have 22 somatic chromosomes (2n=22) which is the lowest among genera in Zingiberaceae. This study underscores the crucial significance of breeding programs and germplasm conservation, specifically emphasizing the potential of common ginger as a prominent contributor.

Units containing telomeric repeats are prevalent in subtelomeric regions of a Mesorhabditis isolate collected from the Republic of Korea.

Mesorhabditis is known for its somatic genome being only a small portion of the germline genome due to programmed DNA elimination. This phenotype may be associated with the maintenance of telomeres at the ends of fragmented somatic chromosomes. To comprehensively investigate the telomeric regions of Mesorhabditis nematodes at the sequence level, we endeavored to collect a Mesorhabditis nematode in the Republic of Korea and acquire its highly contiguous genome sequences. We isolated a Mesorhabditis nematode and assembled its 108-Mb draft genome using both 6.3Gb (53 ×) of short-read and 3.0Gb (25 × , N50 = 5.7kb) of nanopore-based long-read sequencing data. Our genome assembly exhibits comparable quality to the public genome of Mesorhabditis belari in terms of contiguity and evolutionary conserved genes. Unexpectedly, our Mesorhabditis genome has many more interstitial telomeric sequences (ITSs), specifically subtelomeric ones, compared to the genomes of Caenorhabditis elegans and M. belari. Moreover, several subtelomeric sequences containing ITSs had 4-26 homologous sequences, implying they are highly repetitive. Based on this highly repetitive nature, we hypothesize that subtelomeric ITSs might have accumulated through the action of transposable elements containing ITSs. It still remains elusive whether these ITS-containing units are associated with programmed DNA elimination, but they may facilitate new telomere formation after DNA elimination. Our genomic resources for Mesorhabditis can aid in understanding how its distinct phenotypes have evolved.

Chromosomal mapping of 5S rDNA in two species of the genus Acanthocephalus (Echinorhynchida)

Chromosomal mapping of 5S rDNA in two Acanthocephala species was performed for the first time using fluorescence in situ hybridization (FISH) with a 5S rDNA probe. The 5S rDNA PCR products from the genomes of both species were sequenced and aligned and an identical 141 bp long coding region was determined. The same patterns of 5S rDNA gene cluster distribution were observed, with FISH signal restricted to a single autosomal chromosome pair. A preference for distal positioning on the chromosomes (subtelomeric position) was observed in both species. In addition, two-color FISH was performed to examine the mutual positions of 5S and 18S rDNA on the chromosomes. Our knowledge of the organization of the Acanthocephala genome is extremely limited and its chromosomes are poorly studied. Any new information about the location of chromosomal markers as important features of the respective karyotype may be useful in solving evolutionary questions.

Notes on the Morphology, Anatomy, Palynology, and Karyology of Onobrychis argaea (Fabaceae), Endemic to Turkey

Onobrychis argaea belonging to the Fabaceae family, is an endangered plant species endemic to Turkey, distributed only in Kayseri Erciyes Mountain. This study represents the first comprehensive investigation into the morphology, anatomy, pollen and seed micromorphology, and chromosome characteristics of O. argaea. The previous description of the species has been expanded and modified. The pith of the root is covered with xylem tissue. In the stem cross-section, the protective tissue is periderm in the woody part and epiderm in the herbaceous part. The leaflets are amphistomatic and equifacial. The pollen grains are radially symmetric, isopolar, tricolpate, with prolate shape and reticulate-microreticulate ornamentation. The seeds are reniform, yellowish-brown, suboblate, and exhibit rugulate surface ornamentation. The number of somatic chromosomes in O. argaea is 2n = 14. The karyotype formula of this species consists of seven median chromosomes.

Induction of Tetraploids in Phellodendron amurense Rupr. and Its Effects on Morphology and Alkaloid Content

Phellodendron amurense Rupr. is a precious medicinal tree species in northeast China. However, P. amurense resources have been severely destroyed due to uncontrolled overharvest and the limited innovation of new germplasms by traditional cross-breeding. In this study, polyploid breeding was introduced to the improvement program of P. amurense. Fifty-four tetraploid plants of P. amurense were first produced by colchicine-induced adventitious bud chromosome doubling in stem segment explants. The induction frequency reached 36.16% (1.0 g L−1 colchicine solution for 48 h treatment) and 50.00% (2.0 g L−1 colchicine solution for 24 h treatment), respectively, showing the high efficiency of the somatic chromosome doubling based on the organogenesis system. Tetraploidization resulted in significant phenotypic variation, such as larger and thicker leaves, thicker stems, and bigger stomata. Ultra-performance liquid chromatography–mass spectrometry (UPLC–MS/MS) analysis identified 59 differentially accumulated alkaloids (DAAs) between the leaf and stem samples of tetraploids, including 32 upregulated and 27 downregulated in stems. For both leaf and stem samples, 18 DAAs were identified between diploids and tetraploids, with 16 DAAs upregulated in tetraploid leaves and 8 upregulated in tetraploid stems, suggesting that polyploidization caused significant alterations in alkaloid contents in leaves and stems of P. amurense. The contents of the main medicinal compounds, such as berberine, jatrorrhizine, phellodendrine, and palmatine, increased significantly in the leaf and/or stem samples after polyploidization. This finding implied that polyploid breeding might be an effective approach for improving P. amurense, beneficial to preserving and exploiting natural resources.