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Keywords = cpDNA haplotypes

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17 pages, 3095 KiB  
Article
Haplotypes, Genotypes, and DNA Methylation Levels of Neuromedin U Gene Are Associated with Cardio-Metabolic Parameters: Results from the Moli-sani Study
by Fabrizia Noro, Annalisa Marotta, Simona Costanzo, Benedetta Izzi, Alessandro Gialluisi, Amalia De Curtis, Antonietta Pepe, Sarah Grossi, Augusto Di Castelnuovo, Chiara Cerletti, Maria Benedetta Donati, Giovanni de Gaetano, Francesco Gianfagna and Licia Iacoviello
Biomedicines 2025, 13(8), 1906; https://doi.org/10.3390/biomedicines13081906 - 5 Aug 2025
Viewed by 278
Abstract
Background/Objectives: Neuromedin U (NMU) is a highly conserved gene encoding a neuropeptide involved in the regulation of feeding behavior and energy homeostasis. We aimed to analyze the association between NMU genetic and epigenetic variations and cardio-metabolic parameters in an Italian population to identify [...] Read more.
Background/Objectives: Neuromedin U (NMU) is a highly conserved gene encoding a neuropeptide involved in the regulation of feeding behavior and energy homeostasis. We aimed to analyze the association between NMU genetic and epigenetic variations and cardio-metabolic parameters in an Italian population to identify the role of these variants in cardio-metabolic risk. Methods: A total of 4028 subjects were randomly selected from the Moli-sani study cohort. NMU haplotypes were estimated using seven SNPs located in the gene body and in the promoter region; DNA methylation levels in the promoter region, previously associated with lipid-related variables in the same population, were also used. Results: Among the haplotypes inferred, the haplotype carrying the highest number of minor variants (frequency 16.6%), when compared with the most frequent haplotype, was positively associated with insulin levels, HOMA-IR, and diastolic blood pressure, and negatively with HDL-cholesterol. The multivariable analysis that considered methylation levels along with their interactions with SNPs showed that increased methylation levels in two close CpG sites were associated with higher levels of lipid-related variables. Conclusions: This study supports a role for NMU as a regulator of human metabolism. This finding suggests that NMU could be a potential target for preventive interventions against coronary and cerebrovascular diseases, and that NMU genetic and epigenetic variability may serve as a biomarker for cardio-metabolic risk. Full article
(This article belongs to the Special Issue Epigenetics and Metabolic Disorders)
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18 pages, 3587 KiB  
Article
Phylogeography and Population Demography of Parrotia subaequalis, a Hamamelidaceous Tertiary Relict ‘Living Fossil’ Tree Endemic to East Asia Refugia: Implications from Molecular Data and Ecological Niche Modeling
by Yunyan Zhang, Zhiyuan Li, Qixun Chen, Yahong Wang, Shuang Wang, Guozheng Wang, Pan Li, Hong Liu, Pengfu Li, Chi Xu and Zhongsheng Wang
Plants 2025, 14(12), 1754; https://doi.org/10.3390/plants14121754 - 7 Jun 2025
Viewed by 804
Abstract
The diverse topography and mild monsoon climate in East Asia are considered to be important drivers for the long-term ecological success of the Tertiary relict ‘living fossil’ plants during the glacial/interglacial cycles. Here we investigated the phylogeographic pattern and demographic history of a [...] Read more.
The diverse topography and mild monsoon climate in East Asia are considered to be important drivers for the long-term ecological success of the Tertiary relict ‘living fossil’ plants during the glacial/interglacial cycles. Here we investigated the phylogeographic pattern and demographic history of a hamamelidaceous Tertiary relict ‘living fossil’ tree (Parrotia subaequalis) endemic to the subtropical forests of eastern China, employing molecular data and ecological niche modeling. In the long evolutionary history, P. subaequalis has accumulated a high haplotype diversity. Weak gene flow by seeds, geographical isolation, and heterogeneous habitats have led to a relatively high level of genetic differentiation in this species. The divergence time of two cpDNA lineages of P. subaequalis was dated to the late Miocene of the Tertiary period, and the diversification of haplotypes occurred in the Quaternary period. Paleo-distribution modeling suggested that P. subaequalis followed the pattern of ‘glacial expansion-interglacial compression’. The Dabie Mountain and Yellow Mountain in Anhui Province and the Tianmu Mountain and Simin Mountain in Zhejiang Province were inferred to be multiple glacial refugia of P. subaequalis in East Asia and have been proposed to be protected as ‘Management Units’. Collectively, our study offers insights into the plant evolution and adaptation of P. subaequalis and other Tertiary relict ‘living fossil’ trees endemic to East Asia refugia. Full article
(This article belongs to the Special Issue Origin and Evolution of the East Asian Flora (EAF)—2nd Edition)
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17 pages, 4095 KiB  
Article
Case Study: Genetic and In Silico Analysis of Familial Pancreatitis
by Yash Sharma and Deborah J. Good
Genes 2025, 16(5), 603; https://doi.org/10.3390/genes16050603 - 20 May 2025
Viewed by 836
Abstract
Background/Objectives: Chronic pancreatitis (CP) is a progressive inflammatory condition of the pancreas that leads to irreversible changes in pancreatic structure. The pancreatic α and β cells secrete hormones such as insulin and glucagon into the bloodstream. The pancreatic acinar cells secrete digestive enzymes [...] Read more.
Background/Objectives: Chronic pancreatitis (CP) is a progressive inflammatory condition of the pancreas that leads to irreversible changes in pancreatic structure. The pancreatic α and β cells secrete hormones such as insulin and glucagon into the bloodstream. The pancreatic acinar cells secrete digestive enzymes that break down macromolecules. When these digestive enzymes do not function properly, maldigestion, malabsorption, and malnutrition may result. Presented here is a case study of an individual newly diagnosed with chronic pancreatitis, along with a genetic analysis of his son and an in-silico analysis of two of the variant proteins. Methods: This study was conducted using human subjects, namely, the proband (father) and his son. Medical genetic testing of the proband (father) identified the presence of two variants in the cystic fibrosis transmembrane receptor gene (CFTR): variant rs213950, resulting in a single amino acid change (p. Val470Met), and variant rs74767530, a nonsense variant (Arg1162Ter) with known pathogenicity for cystic fibrosis. Medical testing also revealed an additional missense variant, rs515726209 (Ala73Thr), in the CTRC gene. Cheek cell DNA was collected from both the proband and his son to determine the inheritance pattern and identify any additional variants. A variant in the human leukocyte antigen (rs7454108), which results in the HLA-DQ8 haplotype, was examined in both the proband and his son due to its known association with autoimmune disease, a condition also linked to chronic pancreatitis. In silico tools were subsequently used to examine the impact of the identified variants on protein function. Results: Heterozygosity for all variants originally identified through medical genetic testing was confirmed in the proband and was absent in the son. Both the proband and his son were found to have the DRB1*0301 (common) haplotype for the HLA locus. However, the proband was also found to carry a linked noncoding variant, rs2647088, which was absent in the son. In silico analysis of variant rs213950 (Val470Met) in CFTR and rs515726209 (Ala73Thr) in CTRC revealed distinct changes in predicted ligand binding for both proteins, which may affect protein function and contribute to the development of CP. Conclusions: This case study of a proband and his son provides additional evidence for a polygenic inheritance pattern in CP. The results also highlight new information on the role of the variants on protein function, suggesting additional testing of ligand binding for these variants should be done to confirm the functional impairments. Full article
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17 pages, 3496 KiB  
Article
Unraveling the Evolutionary Tales of Yunnanopilia longistaminea (Opiliaceae): Insights from Genetic Diversity, Climate Adaptation, and Conservation Strategies
by Guansong Yang, Liu Yang, Shikang Shen, Yuehua Wang and Yuying Wang
Plants 2025, 14(5), 706; https://doi.org/10.3390/plants14050706 - 26 Feb 2025
Viewed by 495
Abstract
The evolutionary history of Yunnanopilia longistaminea, a vulnerable plant endemic to the Yuanjiang-Honghe River Valley in southwestern China, was investigated using cpDNA and nrDNA sequences along with ecological niche modeling. Understanding the genetic diversity and population structure of Y. longistaminea is crucial [...] Read more.
The evolutionary history of Yunnanopilia longistaminea, a vulnerable plant endemic to the Yuanjiang-Honghe River Valley in southwestern China, was investigated using cpDNA and nrDNA sequences along with ecological niche modeling. Understanding the genetic diversity and population structure of Y. longistaminea is crucial for developing effective conservation strategies and managing its genetic resources. This study comprehensively sampled 295 individuals from 16 populations, which represent the species’ entire global distribution range, ensuring a thorough and representative analysis of its genetic diversity and population structure. The results revealed high genetic diversity and population structure, with significant genetic differentiation among populations. Specifically, the total nucleotide diversity was 2.40 × 10−3 for cpDNA and 1.51 × 10−3 for nrDNA, while the total haplotype diversity was 0.605 for cpDNA and 0.526 for nrDNA. The divergence time of ancestral haplotypes of Y. longistaminea was estimated to be around 2.19 million years ago based on nrDNA and 2.72 million years ago based on cpDNA. These divergence times are comparable to those of other ancient plant species, suggesting a long evolutionary history. The population size of Y. longistaminea was found to have significantly declined around 30,000 years ago. The current distribution model suggests that Y. longistaminea primarily inhabits the warm temperate zone of China, and the LGM distribution model predicts a concentration of the species in Yuanjiang-Honghe River Valley in southwestern China. This study concludes that the southwestern region of China may have served as a glacial refuge for Y. longistaminea. These findings suggest that establishing protected areas in these regions and creating gene banks for ex situ conservation could be effective strategies to preserve the genetic diversity of Y. longistaminea. Further research on its population dynamics and genetic adaptation to climate change is valuable for understanding the species’ evolutionary history and conservation. Full article
(This article belongs to the Section Plant Ecology)
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22 pages, 6621 KiB  
Article
Orogeny and High Pollen Flow as Driving Forces for High Genetic Diversity of Endangered Acer griseum (Franch.) Pax Endemic to China
by Xinhe Xia, Xuedan Yu, Yuxia Wu, Jia Liao, Xinyue Pan, Yongqi Zheng and Chuanhong Zhang
Int. J. Mol. Sci. 2025, 26(2), 574; https://doi.org/10.3390/ijms26020574 - 11 Jan 2025
Viewed by 1149
Abstract
Acer griseum (Franch.) Pax is an endangered species endemic to China, mainly scattered in the Qinling–Daba Mountains. The genetic diversity of 17 natural populations were analyzed by nuclear DNA (nDNA) and chloroplast DNA (cpDNA) to explore the driving forces for its microevolution. A [...] Read more.
Acer griseum (Franch.) Pax is an endangered species endemic to China, mainly scattered in the Qinling–Daba Mountains. The genetic diversity of 17 natural populations were analyzed by nuclear DNA (nDNA) and chloroplast DNA (cpDNA) to explore the driving forces for its microevolution. A high level of genetic diversity (nDNA: He = 0.296, cpDNA: Ht = 0.806) was found in A. griseum. Genetic variation was mainly within populations (92.52%) based on nDNA, while it was mainly among populations (96.26%) based on cpDNA. The seventeen populations were divided into two groups, corresponding to the subtropical zone (Group I) and temperate zone (Group II), with haplotype 4 (Hap4) and Hap5 being the most common haplotypes, respectively. Consequently, genes associated with heat and heavy metal stress were identified in Group I, while genes related to salt and drought stress were identified in Group II. Haplotype differentiation was driven by the heterogeneous microenvironment caused by the uplifting of the Qinling-Daba Mountains, which was a vital source of its high genetic diversity. Furthermore, the uplifted Qinling–Daba mountains may bridge high pollen flow among populations, whereas rivers can result in low seed flow among populations, which has led to the incongruent genetic structure between nDNA and cpDNA. This study represents a new perspective that geological events, especially orogeny, play an important role in plant microevolution through the establishment of maternal genetic structure and provides a meaningful conservation strategy for A. griseum. Overall, the Qinling–Daba Mountains not only are cradles for the genetic diversity of A. griseum but also provided refugia for it during the Quaternary glacial period. Full article
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19 pages, 9488 KiB  
Article
Species Differentiation of Prunus serrulata and Prunus xueluoensis Based on Combined Analysis of SSR and cpDNA Markers
by Shucheng Gao, Xiangzhen Chen, Zhiqi Peng, Xinglin Zeng, Yingke Yun, Xianrong Wang and Xiangui Yi
Forests 2024, 15(11), 1927; https://doi.org/10.3390/f15111927 - 31 Oct 2024
Cited by 1 | Viewed by 1144
Abstract
Prunus xueluoensis C. H. Nan & X. R. Wang is a new species of the Subg. Cerasus Mill., described by C. H. Nan and X. R. Wang in 2013. Since the publication of P. xueluoensis, its taxonomic status has been the subject [...] Read more.
Prunus xueluoensis C. H. Nan & X. R. Wang is a new species of the Subg. Cerasus Mill., described by C. H. Nan and X. R. Wang in 2013. Since the publication of P. xueluoensis, its taxonomic status has been the subject of ongoing debate. This study focuses on wild populations of P. xueluoensis and Prunus serrulata (Lindley) London, utilizing 18 pairs of SSR molecular markers and variations in chloroplast DNA sequences (matK, trnD-E, and trnS-G) to delineate the relationship between the two species. The results showed that P. serrulate (N = 12.400, Na = 5.144, H = 0.578, I = 1.129, Ho = 0.493) and P. xueluoensis (N = 13.625, Na = 6.264, H = 0.614, I = 1.342, Ho = 0.495) populations exhibit rich genetic diversity, which may be related to their wide geographical distribution. The CpDNA genetic diversities of P. serrulata (Hd = 0.553, Pi = 0.00136) and P. xueluoensis (Hd = 0.496, Pi = 0.00180) are at a high level within the Subg. Cerasus Mill. The UPGMA clustering, along with MP and ML phylogenetic trees, show that the unique haplotypes of P. xueluoensis cluster separately as a terminal branch in the evolutionary tree with high support. The shared haplotypes and unique haplotypes of P. serrulata are predominantly located at the base of the phylogenetic tree, suggesting that the two species have diverged. In the TCS haplotype network, the central and key node haplotypes are primarily unique to P. serrulata and shared haplotypes, while the unique haplotypes of P. xueluoensis are all distributed along the network’s periphery. Both P. serrulata (Nst = 0.254, Gst = 0.103, Nst/Gst = 2.466, p < 0.05) and P. xueluoensis (Nst = 0.366, Gst = 0.268, Nst/Gst = 1.366, p < 0.05) exhibit phylogeographic structures. However, when considered as a whole, the combined entity of P. serrulata and P. xueluoensis does not show a significant phylogeographic structure (Nst = 0.317, Gst = 0.400, Nst/Gst = 0.793, p < 0.05), which supports the classification of these as two distinct species. The estimate of the average age of the latest common ancestor of P. serrulata and P. xueluoensis is 3.22 mya (PP = 1; 95% HPD: 3.07~3.46 mya). Due to environmental differences in altitude, the group of P. serrulata differentiated in the expansion into the cold and humid alpine environment and gradually formed P. xueluoensis. The findings support the classification of P. serrulata and P. xueluoensis as two distinct species. Full article
(This article belongs to the Section Genetics and Molecular Biology)
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17 pages, 2194 KiB  
Article
DNA Sequence Variations Affecting Serotonin Transporter Transcriptional Regulation and Activity: Do They Impact Alcohol Addiction?
by Giampiero Ferraguti, Silvia Francati, Claudia Codazzo, Giovanna Blaconà, Giancarlo Testino, Antonio Angeloni, Marco Fiore, Mauro Ceccanti and Marco Lucarelli
Int. J. Mol. Sci. 2024, 25(15), 8089; https://doi.org/10.3390/ijms25158089 - 25 Jul 2024
Cited by 3 | Viewed by 2100
Abstract
Genetic features of alcohol dependence have been extensively investigated in recent years. A large body of studies has underlined the important role of genetic variants not only in metabolic pathways but also in the neurobiology of alcohol dependence, mediated by the neuronal circuits [...] Read more.
Genetic features of alcohol dependence have been extensively investigated in recent years. A large body of studies has underlined the important role of genetic variants not only in metabolic pathways but also in the neurobiology of alcohol dependence, mediated by the neuronal circuits regulating reward and craving. Serotonin transporter (5-HTT), encoded by the SLC6A4 gene (Solute carrier family 6-neurotransmitter transporter-member 4), is targeted by antidepressant drugs such as selective serotonin reuptake inhibitors (SSRIs) and plays a pivotal role in serotoninergic transmission; it has been associated with psychiatric diseases and alcohol dependence. Transcriptional regulation and expression of 5-HTT depend not only on epigenetic modifications, among which DNA methylation (CpG and non-CpG) is primarily involved, but also on sequence variations occurring in intron/exon regions and in untranslated regions in 5′ and 3′, being the first sequences important for the splicing machinery and the last for the binding of transcription factors and micro RNAs. This work intends to shed light on the role of sequence variations known to affect the expression or function of 5-HTT in alcohol-dependent individuals. We found a statistically significant difference in the allelic (p = 0.0083) and genotypic (p = 0.0151) frequencies of the tri-allelic polymorphism, with higher function alleles and genotypes more represented in the control population. Furthermore, we identified three haplotypes more frequent in subjects with AUD (p < 0.0001) and one more frequent in the control population (p < 0.0001). The results obtained for the tri-allelic polymorphism in alcohol dependence confirm what is already present in part of the literature. The role of haplotypes requires further studies to be clarified. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Control of Disease Occurrence)
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15 pages, 3821 KiB  
Article
Chloroplast Spacer DNA Analysis Revealed Insights into Phylogeographical Structure of Phoebe chekiangensis
by Xiankun Wu, Yan Chen, Chenhui Nan, Shucheng Gao, Xiangzhen Chen and Xiangui Yi
Forests 2024, 15(7), 1073; https://doi.org/10.3390/f15071073 - 21 Jun 2024
Cited by 2 | Viewed by 1260
Abstract
Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and [...] Read more.
Research studies on the conservation genetics of endangered plants play a crucial role in establishing management plans for biodiversity conservation. Phoebe chekiangensis is a precious and scarce tree species resource in the East China region. To comprehend the origin, evolutionary history, geographical, and historical factors that has contributed to the current distribution pattern of Phoebe chekiangensis in the East China region, we conducted a phylogeographic analysis that utilized intergenic spacers of chloroplast DNA (cpDNA). We amplified and sequenced three spacer regions of cpDNA (psbC-trnS, trnL-Intro, and Ycf3) intergenic spacer regions of 306 individuals from 11 populations, encompassing the majority of its geographical range in China. Our analysis revealed a total of 11 haplotypes. The research findings show that the spacer regions of the cpDNA genetic diversity of Phoebe chekiangensis was Hd = 0.423, and the nucleotide diversity was Pi × 10−3 = 0.400. At the species level, the population differentiation index Fst = 0.25610 (p < 0.05), and the gene flow Nm = 0.73. The genetic variation between populations was 29.14%, while within populations, it was 70.86%, with the inter-population genetic variation much lower than the within-population variation. The divergence time between the genera Phoebe and Machilus was estimated to be approximately 37.87 mya (PP = 1; 95%HPD: 25.63–44.54 mya), and the crown group time of the genus Phoebe was estimated to be 21.30 mya (PP = 1; 95%HPD: 9.76–34.94 mya). The common ancestor of the 11 Phoebe chekiangensis haplotypes was 7.85 mya, while the H7, H8, and H10 haplotypes of Phoebe chekiangensis (northern region) differentiated relatively late, with a divergence time of 1.90 mya. Neutrality tests (NTs) and mismatch distribution analysis (MDA) suggest that the time frame for Phoebe chekiangensis to expand southwestward along Wuyishan was relatively short and its adaptability to the environment was low, thereby limiting the formation of new haplotypes. These results suggest that Phoebe chekiangensis exhibited greater adaptation to the northern subtropics than to the central subtropics, offering valuable insights for the conservation and utilization of germplasm resources. Full article
(This article belongs to the Section Genetics and Molecular Biology)
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31 pages, 12783 KiB  
Article
Chloroplast Haplotype Diversity in the White Oak Populations of the Italian Peninsula, Sicily, and Sardinia
by Romeo Di Pietro, Luca Quaranta, Claudia Mattioni, Marco Cosimo Simeone, Piera Di Marzio, Elisa Proietti and Paola Fortini
Forests 2024, 15(5), 864; https://doi.org/10.3390/f15050864 - 15 May 2024
Cited by 4 | Viewed by 1921
Abstract
A phylogeographic study on the chloroplast DNA of natural white oak forests (Quercus subgen. Quercus, sect. Quercus) was carried out to identify possible haplotype-structured distribution within the Italian Peninsula, Sicily, and Sardinia. Sixty white oak populations belonging to Q. frainetto [...] Read more.
A phylogeographic study on the chloroplast DNA of natural white oak forests (Quercus subgen. Quercus, sect. Quercus) was carried out to identify possible haplotype-structured distribution within the Italian Peninsula, Sicily, and Sardinia. Sixty white oak populations belonging to Q. frainetto, Q. robur and the collective groups Q. petraea and Q. pubescens were considered and analyzed by combining five Chloroplast Simple Sequence Repeat (cpSSR) markers. A total of 28 haplotypes were detected. Central and southern Italy displayed the highest variability (14 and 10 haplotypes, respectively), followed by northern Italy (7), Sardinia (7), and Sicily (5). A complex geographical structure of the haplotype distribution emerged, highlighting (i) a high number of low-frequency haplotypes; (ii) the marked isolation of Sardinia; (iii) the occurrence of haplotypes widely distributed throughout the Italian Peninsula; (iv) the idiosyncrasy of Sicily, which exhibits exclusive haplotypes, and haplotypes shared with Sardinia and the rest of the Italian Peninsula. The haplotype distribution was also found to be partially related to the taxonomic identity of the specimens, with the following features emerging: a geographic separation between the central Italy and southern Italy Q. frainetto populations, an unexpected discontinuity between the Calabrian and Sicilian Q. petraea subsp. austrotyrrhenica populations, and the absence of the most common haplotype among the Q. pubescens populations of central and southern Italy. Full article
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19 pages, 7951 KiB  
Article
Population Variation and Phylogeography of Cherry Blossom (Prunus conradinae) in China
by Jingjing Dong, Xiangui Yi, Xianrong Wang, Meng Li, Xiangzhen Chen, Shucheng Gao, Wenyi Fu, Siyu Qian, Xinglin Zeng and Yingke Yun
Plants 2024, 13(7), 974; https://doi.org/10.3390/plants13070974 - 28 Mar 2024
Cited by 3 | Viewed by 1973
Abstract
Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae [...] Read more.
Prunus conradinae (subgenus Cerasus, Rosaceae) is a significant germplasm resource of wild cherry blossom in China. To ensure the comprehensiveness of this study, we used a large sample size (12 populations comprising 244 individuals) which involved the fresh leaves of P. conradinae in Eastern, Central, and Southwestern China. We combined morphological and molecular evidence (three chloroplast DNA (cpDNA) sequences and one nuclear DNA (nr DNA) sequence) to examine the population of P. conradinae variation and differentiation. Our results revealed that Central, East, and Southwest China are important regions for the conservation of P. conradinae to ensure adequate germplasm resources in the future. We also found support for a new variant, P. conradinae var. rubrum. We observed high genetic diversity within P. conradinae (haplotype diversity [Hd] = 0.830; ribotype diversity [Rd] = 0.798), with novel genetic variation and a distinct genealogical structure among populations. There was genetic variation among populations and phylogeographic structure among populations and three geographical groups (Central, East, and Southwest China). The genetic differentiation coefficient was the lowest in the Southwest region and the gene exchange was obvious, while the differentiation was obvious in Central China. In the three geographic groups, we identified two distinct lineages: an East China lineage (Central China and East China) and a Southwest China lineage ((Central China and Southwest China) and East China). These two lineages originated approximately 4.38 million years ago (Mya) in the early Pliocene due to geographic isolation. P. conradinae expanded from Central China to East China at 3.32 Mya (95% HPD: 1.12–5.17 Mya) in the Pliocene. The population of P. conradinae spread from East China to Southwest China, and the differentiation time was 2.17 Mya (95% (HPD: 0.47–4.54 Mya), suggesting that the population of P. conradinae differentiated first in Central and East China. The population of P. conradinae experienced differentiation from Central China to Southwest China around 1.10 Mya (95% HPD: 0.11–2.85 Mya) during the early Pleistocene of the Quaternary period. The southeastern region of East China, near Mount Wuyi, likely serves as a refuge for P. conradinae. This study establishes a theoretical foundation for the classification, identification, conservation, and exploitation of germplasm resources of P. conradinae. Full article
(This article belongs to the Special Issue Origin and Evolution of the East Asian Flora (EAF))
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18 pages, 6993 KiB  
Article
Interspecific Sharing of Closely Related Chloroplast Genome Haplotypes among Sclerophyllous Oaks in the Hot-Dry Valley of the Jinsha River, Southwestern China
by Yao Li, Chao Tan, Wenxu Zhang, Lu Wang, Zhi Yang, Yanming Fang, Yong Yang and Lingfeng Mao
Forests 2024, 15(3), 537; https://doi.org/10.3390/f15030537 - 14 Mar 2024
Cited by 1 | Viewed by 1525
Abstract
Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale [...] Read more.
Evergreen sclerophyllous oak forests (ESOFs) in southwestern China are a special vegetation type developed in response to the expansion of arid habitats after the uplift of the Himalayas. Here, we used chloroplast (cp) DNA and nuclear ribosomal (nr) DNA to investigate the fine-scale genetic variation patterns of six sympatric oaks (Quercus, Fagaceae) in the hot-dry valley ESOFs of the Jinsha River, southwestern China. Three cp genomes were assembled for each species. Nine cp genome haplotypes and 16 nrDNA haplotypes were identified based on single-nucleotide variants and indels. Our results demonstrated that discordance existed between the cpDNA and nrDNA phylogenies of the sclerophyllous oaks in section Ilex. The nrDNA phylogeny was consistent with species boundaries, while the cpDNA phylogeny was decoupled from taxonomy. Interspecific sharing of closely related cp genome haplotypes was detected between Quercus cocciferoides and the other two sclerophyllous oaks, Q. longispica and Q. franchetii. Specifically, Q. cocciferoides and Q. longispica sampled in a mixed stand exhibited two haplotypes that differed by a 9 bp indel. The local distribution of the two highly similar haplotypes suggested that they may have arisen from ancient introgression. Given that the two species have diverged for a long time, it is possible that the ancestral cp genome of one species was captured by another species through asymmetric introgression in early times, and an indel event occurred subsequently. Phylogenetic analyses using more previously published cp genome sequences indicated that Q. cocciferoides and Q. franchetii shared multiple cpDNA lineages of Ilex oaks, which may be caused by shared ancestral polymorphism and/or ancient introgression. Our study showed that at least three highly variable regions (ψycf1, ndhF-rpl32, and trnKUUU-rps16 or rpl32-trnLUAG) can distinguish the nine haplotypes identified by whole-cp genome sequences. These markers are useful for the evolutionary studies of the maternal lineages of oaks in hot-dry valley ESOFs. Full article
(This article belongs to the Section Genetics and Molecular Biology)
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17 pages, 2914 KiB  
Article
Ecological and Biogeographical Imprints in a Beech Glacial Refugium
by Ioannis Tsiripidis, Stavroula Stamellou, Aristotelis C. Papageorgiou and Andreas D. Drouzas
Diversity 2024, 16(3), 152; https://doi.org/10.3390/d16030152 - 27 Feb 2024
Viewed by 1596
Abstract
The distribution of vascular plant species and assemblages existing in beech (Fagus sylvatica L.) forests was compared with the distribution of beech chloroplast DNA (cpDNA) haplotypes, aiming to identify possible interpretable trends of co-occurrence, on a small geographical scale, and to infer [...] Read more.
The distribution of vascular plant species and assemblages existing in beech (Fagus sylvatica L.) forests was compared with the distribution of beech chloroplast DNA (cpDNA) haplotypes, aiming to identify possible interpretable trends of co-occurrence, on a small geographical scale, and to infer the relevant historical factors. Vegetation and genetic (cpSSR) data were collected from 60 plots on Mt. Menikio (northeastern Greece). Classification and ordination analyses were applied on the vegetation data, while on the cpSSR data, diversity measures and genetic structure analyses were employed. A probabilistic co-occurrence analysis was performed on haplotypes and taxa. The results show that a plant biogeographical border exists on Mt. Menikio which, in addition, has acted both as a refugium and as a meeting point of lineages for more than one glacial cycle. Significant associations of co-occurrence between haplotypes and vascular taxa were found but no common distribution patterns between the former and species assemblages were identified. The combined consideration of the distribution profiles of species assemblages, plant species and cpDNA haplotypes (corresponding to the three levels of biodiversity) provides concrete information on historical events, leading to a comprehensive understanding of the evolutionary and biogeographical processes that have shaped specific spatial patterns of biodiversity. Full article
(This article belongs to the Section Biogeography and Macroecology)
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18 pages, 2404 KiB  
Article
Glucocorticoid Receptor Gene (NR3C1) Polymorphisms and Metabolic Syndrome: Insights from the Mennonite Population
by Kathleen Liedtke Kolb, Ana Luiza Sprotte Mira, Eduardo Delabio Auer, Isabela Dall’Oglio Bucco, Carla Eduarda de Lima e Silva, Priscila Ianzen dos Santos, Valéria Bumiller-Bini Hoch, Luana Caroline Oliveira, Aline Borsato Hauser, Jennifer Elisabeth Hundt, Alan R. Shuldiner, Fabiana Leão Lopes, Teide-Jens Boysen, Andre Franke, Luis Felipe Ribeiro Pinto, Sheila Coelho Soares-Lima, Gabriela Canalli Kretzschmar and Angelica Beate Winter Boldt
Genes 2023, 14(9), 1805; https://doi.org/10.3390/genes14091805 - 15 Sep 2023
Cited by 8 | Viewed by 4185
Abstract
The regulation of the hypothalamic-pituitary-adrenal (HPA) axis is associated with polymorphisms and the methylation degree of the glucocorticoid receptor gene (NR3C1) and is potentially involved in the development of metabolic syndrome (MetS). In order to evaluate the association between MetS with [...] Read more.
The regulation of the hypothalamic-pituitary-adrenal (HPA) axis is associated with polymorphisms and the methylation degree of the glucocorticoid receptor gene (NR3C1) and is potentially involved in the development of metabolic syndrome (MetS). In order to evaluate the association between MetS with the polymorphisms, methylation, and gene expression of the NR3C1 in the genetically isolated Brazilian Mennonite population, we genotyped 20 NR3C1 polymorphisms in 74 affected (MetS) and 138 unaffected individuals without affected first-degree relatives (Co), using exome sequencing, as well as five variants from non-exonic regions, in 70 MetS and 166 Co, using mass spectrometry. The methylation levels of 11 1F CpG sites were quantified using pyrosequencing (66 MetS and 141 Co), and the NR3C1 expression was evaluated via RT-qPCR (14 MetS and 25 Co). Age, physical activity, and family environment during childhood were associated with MetS. Susceptibility to MetS, independent of these factors, was associated with homozygosity for rs10482605*C (OR = 4.74, pcorr = 0.024) and the haplotype containing TTCGTTGATT (rs3806855*T_ rs3806854*T_rs10482605*C_rs10482614*G_rs6188*T_rs258813*T_rs33944801*G_rs34176759*A_rs17209258*T_rs6196*T, OR = 4.74, pcorr = 0.048), as well as for the CCT haplotype (rs41423247*C_ rs6877893*C_rs258763*T), OR = 6.02, pcorr = 0.030), but not to the differences in methylation or gene expression. Thus, NR3C1 polymorphisms seem to modulate the susceptibility to MetS in Mennonites, independently of lifestyle and early childhood events, and their role seems to be unrelated to DNA methylation and gene expression. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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12 pages, 1454 KiB  
Article
Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments
by Dan Wang, Yu Huang, Lu Rui, Huihui Du, Junsheng Qi, Mingguo Ma and Nong Zhou
Genes 2023, 14(9), 1754; https://doi.org/10.3390/genes14091754 - 2 Sep 2023
Cited by 1 | Viewed by 1516
Abstract
Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and [...] Read more.
Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Genetic structure and genetic differentiation were explored using haplotype distribution maps and genetic distance matrices. A total of 15 haplotypes were identified in the 32 populations of P. polyphylla var. yunnanensis. Five unique haplotypes were identified from the fourteen haplotypes of the cultivated populations, while only one unique haplotype was identified from the ten haplotypes of the wild populations. The haplotype richness and genetic diversity of the cultivated populations were higher than those of the wild populations (HT = 0.900 vs. 0.861). In addition, there were no statistically significant correlations between geographic distance and genetic distance in the cultivated populations (r = 0.16, p > 0.05), whereas there was a significant correlation between geographical distance and genetic structure in the wild populations (r = 0.32, p > 0.05), indicating that there was a geographical and genetic connection between the wild populations. There was only 2.5% genetic variation between the wild populations and cultivated populations, indicating no obvious genetic differentiation between the wild and cultivated populations. Overall, the genetic background of the cultivated populations was complex, and it was hypothesized that the unique haplotypes and higher diversity of the cultivated populations were caused by the mixed provenance of the cultivated populations. Full article
(This article belongs to the Special Issue Molecular Genetics and Resources of Medicinal Plants)
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17 pages, 1701 KiB  
Article
Genetic Structure of the Liriope muscari Polyploid Complex and the Possibility of Its Genetic Disturbance in Japan
by Keita Watanabe, Makoto Yaneshita, Tetsuo Denda, Masatsugu Yokota, Shun K. Hirota, Yoshihisa Suyama and Yoshihiko Tsumura
Plants 2022, 11(22), 3015; https://doi.org/10.3390/plants11223015 - 8 Nov 2022
Cited by 1 | Viewed by 2489
Abstract
Anthropogenic activities, such as the movement of plants through greening, can result in genetic disturbance that can interfere with local adaptation in wild populations. Although research is underway to prevent genetic disturbance associated with greening, genetic disturbance of intraspecific polyploidy, which is estimated [...] Read more.
Anthropogenic activities, such as the movement of plants through greening, can result in genetic disturbance that can interfere with local adaptation in wild populations. Although research is underway to prevent genetic disturbance associated with greening, genetic disturbance of intraspecific polyploidy, which is estimated to be present in 24% of vascular plants, has not been well studied. Liriope muscari is a polyploid complex with known diploid (2n = 36), tetraploid (2n = 72), and hexaploid (2n = 108) forms. The plants of this species tolerate dry and hot conditions and are therefore frequently used for greening and gardening. However, the distribution of this polyploid in Japan, its genetic structure, and genetic disturbance are not known. In this study, we investigated the polyploidy distribution and genetic structure in naturally distributed L. muscari in Japan using chloroplast DNA (cpDNA) haplotypes and nuclear DNA (nDNA). Commercially produced individuals were also studied and compared with natural populations to assess any genetic disturbance of the ploidy complex in this species. Chromosome counts, cpDNA, and nDNA results showed three genetically and cytologically distinct groups in Japan: first, a tetraploid group in mainland Japan; second, a hexaploid group in the Ryukyu Islands; and third, a diploid and tetraploid group in the Ryukyu Islands. Significant isolation by distance was also detected within the three groups (p = 0.001). Genetic disturbance due to greening and gardening should be avoided among the three groups. Genetic disturbance can be reduced by using individuals derived from natural populations that are close to the sites used for greening and gardening. For commercially produced individuals, genetic disturbance is unlikely in the Kanto region, an area of high usage, while genetic disturbance is thought possible in the Ryukyu Islands. Full article
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