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Super-resolution reconstruction of γ-ray CT images for PET-enabled dual-energy CT imaging. 用于 PET 双能 CT 成像的 γ 射线 CT 图像超分辨率重建。
IF 2.7 3区 生物学
Genome Pub Date : 2024-02-01 Epub Date: 2023-04-07 DOI: 10.1117/12.2654431
Yansong Zhu, Benjamin A Spencer, Zhaoheng Xie, Edwin K Leung, Reimund Bayerlein, Negar Omidvari, Simon R Cherry, Jinyi Qi, Ramsey D Badawi, Guobao Wang
{"title":"<ArticleTitle xmlns:ns0=\"http://www.w3.org/1998/Math/MathML\">Super-resolution reconstruction of <ns0:math><ns0:mstyle><ns0:mstyle><ns0:mi>γ</ns0:mi></ns0:mstyle></ns0:mstyle></ns0:math>-ray CT images for PET-enabled dual-energy CT imaging.","authors":"Yansong Zhu, Benjamin A Spencer, Zhaoheng Xie, Edwin K Leung, Reimund Bayerlein, Negar Omidvari, Simon R Cherry, Jinyi Qi, Ramsey D Badawi, Guobao Wang","doi":"10.1117/12.2654431","DOIUrl":"10.1117/12.2654431","url":null,"abstract":"<p><p>Dual-energy computed tomography (DECT) enables material decomposition for tissues and produces additional information for PET/CT imaging to potentially improve the characterization of diseases. PET-enabled DECT (PDECT) allows the generation of PET and DECT images simultaneously with a conventional PET/CT scanner without the need for a second x-ray CT scan. In PDECT, high-energy <math><mstyle><mi>γ</mi></mstyle></math>-ray CT (GCT) images at 511 keV are obtained from time-of-flight (TOF) PET data and are combined with the existing x-ray CT images to form DECT imaging. We have developed a kernel-based maximum-likelihood attenuation and activity (MLAA) method that uses x-ray CT images as a priori information for noise suppression. However, our previous studies focused on GCT image reconstruction at the PET image resolution which is coarser than the image resolution of the x-ray CT. In this work, we explored the feasibility of generating super-resolution GCT images at the corresponding CT resolution. The study was conducted using both phantom and patient scans acquired with the uEXPLORER total-body PET/CT system. GCT images at the PET resolution with a pixel size of 4.0 mm × 4.0 mm and at the CT resolution with a pixel size of 1.2 mm × 1.2 mm were reconstructed using both the standard MLAA and kernel MLAA methods. The results indicated that the GCT images at the CT resolution had sharper edges and revealed more structural details compared to the images reconstructed at the PET resolution. Furthermore, images from the kernel MLAA method showed substantially improved image quality compared to those obtained with the standard MLAA method.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":"32 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10947795/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86818310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Environmental drivers behind the genetic differentiation in mountain chickadees (Poecile gambeli). 山鸡遗传分化背后的环境驱动因素(Poecile gambeli)。
IF 3.1 3区 生物学
Genome Pub Date : 2024-02-01 Epub Date: 2023-11-03 DOI: 10.1139/gen-2023-0067
P Srikanthan, T M Burg
{"title":"Environmental drivers behind the genetic differentiation in mountain chickadees (<i>Poecile gambeli</i>).","authors":"P Srikanthan, T M Burg","doi":"10.1139/gen-2023-0067","DOIUrl":"10.1139/gen-2023-0067","url":null,"abstract":"<p><p>Anthropogenic climate change has a large impact on wildlife populations and the scale of the impacts has been increasing. In this study, we utilised 3dRAD sequence data to investigate genetic divergence and identify the environmental drivers of genetic differentiation between 12 populations of mountain chickadees, family Paridae, sampled across North America. To examine patterns of genetic variation across the range, we conducted a discriminant analysis of principal components (DAPC), admixture analysis, and calculated pairwise Fst values. The DAPC revealed four clusters: southern California, eastern Rocky Mountains, northwestern Rocky Mountains, and Oregon/northern California. We then used BayeScEnv to highlight significant outlier SNPs associated with the five environmental variables. We identified over 150 genes linked to outlier SNPs associated with more than 15 pathways, including stress response and circadian rhythm. We also found a strong signal of isolation by distance and local temperature was highly correlated with genetic distance. Maxent simulations showed a northward range shift over the next 50 years and a decrease in suitable habitat, highlighting the need for immediate conservation action.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"53-63"},"PeriodicalIF":3.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran. 伊朗本土牛品种的遗传多样性和积极选择特征。
IF 3.1 3区 生物学
Genome Pub Date : 2024-02-01 Epub Date: 2023-11-14 DOI: 10.1139/gen-2022-0106
Nader Forough Ameri, Hasan Moradian, Ali Esmailizadeh Koshkoiyeh, Mahdiyeh Montazeri, Elaheh Rostamzadeh Madabi, Masood Asadi Fozi
{"title":"Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran.","authors":"Nader Forough Ameri, Hasan Moradian, Ali Esmailizadeh Koshkoiyeh, Mahdiyeh Montazeri, Elaheh Rostamzadeh Madabi, Masood Asadi Fozi","doi":"10.1139/gen-2022-0106","DOIUrl":"10.1139/gen-2022-0106","url":null,"abstract":"<p><p>Animal domestication, climate changes over time, and artificial selection have played significant roles in shaping the genome structure of various animal species, including cattle. These processes have led to the emergence of several indigenous cattle breeds with distinct genetic characteristics. This study focused on unraveling the genetic diversity and identifying candidate genomic regions in eight indigenous cattle breeds of Iran. The data consisted of ∼777 962 single nucleotide polymorphisms (SNPs) of 89 animals from Iranian indigenous cattle scattered throughout the country. We employed various methods, including integrated haplotype score, <i>F</i><sub>ST</sub>, and cross-population composite likelihood ratio, to conduct a genome scan for detecting selection signals within and between cattle populations. Average observed heterozygosity across the populations was 0.36, with a range of 0.32-0.40. In addition, negative and low rates of inbreeding (FIS) in the populations were observed. The genome-wide analysis revealed several genomic regions that harbored candidate genes associated with production traits (e.g., MFSD1, TYW5, ADRB2, BLK, and CRTC3), adaptation to local environmental constraints (CACNA2D1, CXCL3, and GRO1), and coat color (DYM). Finally, the study of the reported quantitative trait loci (QTL) regions in the cattle genome demonstrated that the identified regions were associated with QTL related to important traits such as milk composition, body weight, daily gain, feed conversion, and residual feed intake. Overall, this study contributes to a better understanding of the genetic diversity and potential candidate genes underlying important traits in Iranian indigenous cattle breeds, which can inform future breeding and conservation efforts.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"31-42"},"PeriodicalIF":3.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92153577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of adulteration in the market samples of saffron using morphology, HPLC, HPTLC, and DNA barcoding methods. 用形态学、高效液相色谱、高效薄层色谱和DNA条形码方法鉴定市场藏红花样品中的掺假。
IF 3.1 3区 生物学
Genome Pub Date : 2024-02-01 Epub Date: 2023-11-03 DOI: 10.1139/gen-2022-0059
Varadharajan Bhooma, Sophie Lorraine Vassou, Ilango Kaliappan, Madasamy Parani
{"title":"Identification of adulteration in the market samples of saffron using morphology, HPLC, HPTLC, and DNA barcoding methods.","authors":"Varadharajan Bhooma, Sophie Lorraine Vassou, Ilango Kaliappan, Madasamy Parani","doi":"10.1139/gen-2022-0059","DOIUrl":"10.1139/gen-2022-0059","url":null,"abstract":"<p><p>Saffron, the stigma of <i>Crocus sativus</i> L., is the most expensive spice used for culinary, medicinal, dye, and cosmetics purposes. It is highly adulterated because of its limited production and high commercial value. In this study, 104 saffron market samples collected from 16 countries were tested using morphology, high-performance liquid chromatography (HPLC), high-performance thin-layer chromatography (HPTLC), and deoxyribonucleic acid (DNA) barcoding. Overall, 45 samples (43%) were adulterated. DNA barcoding identified the highest number of adulterated saffron (44 samples), followed by HPTLC (39 samples), HPLC (38 samples), and morphology (32 samples). Only DNA barcoding identified the adulterated samples containing saffron and other plants' parts as bulking agents. In addition, DNA barcoding identified 20 adulterant plant species, which will help develop quality control methods and market surveillance. Some of the adulterant plants are unsafe for human consumption. The HPLC method helped identify the saffron samples adulterated with synthetic safranal. HPLC and HPTLC methods will help identify the samples adulterated with other parts of the saffron plant (auto-adulteration).</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"43-52"},"PeriodicalIF":3.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comparative genome analysis of Pasteurella multocida strains of porcine origin. 猪源多杀性巴氏杆菌菌株的比较基因组分析。
IF 3.1 3区 生物学
Genome Pub Date : 2024-01-01 Epub Date: 2023-08-28 DOI: 10.1139/gen-2023-0021
Awadhesh Prajapati, Revanaiah Yogisharadhya, Nihar Nalini Mohanty, Suresh Kumar Mendem, Mohammed Mudassar Chanda, Shivakumara Siddaramappa, Sathish Bhadravati Shivachandra
{"title":"Comparative genome analysis of <i>Pasteurella multocida</i> strains of porcine origin.","authors":"Awadhesh Prajapati, Revanaiah Yogisharadhya, Nihar Nalini Mohanty, Suresh Kumar Mendem, Mohammed Mudassar Chanda, Shivakumara Siddaramappa, Sathish Bhadravati Shivachandra","doi":"10.1139/gen-2023-0021","DOIUrl":"10.1139/gen-2023-0021","url":null,"abstract":"<p><p><i>Pasteurella multocida</i> causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182-2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of <i>nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB</i>, and <i>omp87</i> in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters. In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of <i>P. multocida</i> of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"13-23"},"PeriodicalIF":3.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10483893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure and genetic diversity of Canadian Maritimes wild hops. 加拿大Maritimes野生啤酒花的结构和遗传多样性。
IF 3.1 3区 生物学
Genome Pub Date : 2024-01-01 Epub Date: 2023-09-22 DOI: 10.1139/gen-2023-0045
Ashok Somalraju, Braulio Soto-Cerda, Kaushik Ghose, Jason McCallum, Ron Knox, Bourlaye Fofana
{"title":"Structure and genetic diversity of Canadian Maritimes wild hops.","authors":"Ashok Somalraju, Braulio Soto-Cerda, Kaushik Ghose, Jason McCallum, Ron Knox, Bourlaye Fofana","doi":"10.1139/gen-2023-0045","DOIUrl":"10.1139/gen-2023-0045","url":null,"abstract":"<p><p>Studies on the northeastern American native hops (<i>Humulus lupulus</i> ssp<i>.</i> <i>lupuloides</i>) from the Canadian Maritimes are scarce. This study aimed to evaluate the genetic structure and diversity among 25 wild-collected hops from three Canadian Maritime provinces using microsatellite (simple sequence repeat (SSR)) markers. Based on 43 SSR markers, four distinct subgroups were found, with a low molecular variance (19%) between subgroups and a high variance (81%) within subgroups. The Nei's unbiased genetic distance between clusters ranged from 0.01 to 0.08, the genetic distance between clusters 2 and 3 being the farthest and that between clusters 1 and 2 the closest. Cluster 2 captured the highest overall diversity. A total of 18 SSR markers clearly discriminated hop clones by detecting putative subspecies-specific haplotypes, differentiating clones of native-wild <i>H. lupulus</i> ssp<i>. lupuloides</i> from the naturalized old and modern hop cultivars. Seven of the 18 SSR markers also differentiated two clones from the same site from one another. The study is the first, using molecular markers, to identify SSR markers with potential for intellectual property protection in Canadian Maritimes hops. The SSR markers herein used can be prime tools for hop breeders and growers in the region.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"24-30"},"PeriodicalIF":3.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41139899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location. 大豆反转录转座子SORE-1相邻区域胞嘧啶甲基化的频率取决于染色体位置。
IF 3.1 3区 生物学
Genome Pub Date : 2024-01-01 Epub Date: 2023-09-25 DOI: 10.1139/gen-2023-0044
Kenta Nakashima, Mashiro Yuhazu, Shun Mikuriya, Megumi Kasai, Jun Abe, Akito Taneda, Akira Kanazawa
{"title":"Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon <i>SORE-1</i> depends on chromosomal location.","authors":"Kenta Nakashima, Mashiro Yuhazu, Shun Mikuriya, Megumi Kasai, Jun Abe, Akito Taneda, Akira Kanazawa","doi":"10.1139/gen-2023-0044","DOIUrl":"10.1139/gen-2023-0044","url":null,"abstract":"<p><p>Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon <i>SORE-1</i>. We analyzed <i>SORE-1</i>, inserted in exon 1 of the <i>GmphyA2</i> gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 <i>SORE-1</i> elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of <i>SORE-1</i> was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of <i>SORE-1</i> coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of <i>SORE-1</i> on the adjacent regions is influenced by its location on the chromosome.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"1-12"},"PeriodicalIF":3.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41117856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Note of appreciation. 感谢信
IF 3.1 3区 生物学
Genome Pub Date : 2024-01-01 DOI: 10.1139/gen-2023-0092
{"title":"Note of appreciation.","authors":"","doi":"10.1139/gen-2023-0092","DOIUrl":"10.1139/gen-2023-0092","url":null,"abstract":"","PeriodicalId":12809,"journal":{"name":"Genome","volume":"67 1","pages":"i"},"PeriodicalIF":3.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139073798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico. 墨西哥肠炎沙门氏菌MLST群体结构和耐药基因的基因组分析。
IF 3.1 3区 生物学
Genome Pub Date : 2023-12-01 Epub Date: 2023-07-21 DOI: 10.1139/gen-2023-0007
Adrián Gómez-Baltazar, Angélica Godínez-Oviedo, Gerardo Vázquez-Marrufo, Ma Soledad Vázquez-Garcidueñas, Montserrat Hernández-Iturriaga
{"title":"Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with <i>Salmonella enterica</i> in Mexico.","authors":"Adrián Gómez-Baltazar, Angélica Godínez-Oviedo, Gerardo Vázquez-Marrufo, Ma Soledad Vázquez-Garcidueñas, Montserrat Hernández-Iturriaga","doi":"10.1139/gen-2023-0007","DOIUrl":"10.1139/gen-2023-0007","url":null,"abstract":"<p><p><i>Salmonella enterica</i> is one of the most commonly reported foodborne pathogens by public health agencies worldwide. In this study, the multilocus sequence typing (MLST) population structure and frequency of antimicrobial resistance (AMR) genes were evaluated in <i>S. enterica</i> strains from Mexico (<i>n</i> = 2561). The most common sources of isolation were food (44.28%), environment (27.41%), animal-related (24.83%), and human (3.48%). The most prevalent serovars were Newport (8.51%), Oranienburg (7.03%), Anatum (5.78%), Typhimurium (5.12%), and Infantis (4.57%). As determined by the 7-gene MLST scheme, the most frequent sequence types were ST23, ST64, and ST32. The core genome MLST scheme identified 132 HC2000 and 195 HC900 hierarchical clusters, with the HC2000_2 cluster being the most prevalent in Mexico (<i>n</i> = 256). A total of 78 different AMR genes belonging to 13 antimicrobial classes were detected in 638 genomic assemblies of <i>S. enterica</i>. The most frequent class was aminoglycosides (31.76%), followed by tetracyclines (12.53%) and sulfonamides (11.91%). These results can help public health agencies in Mexico prioritize their efforts and resources to increase the genomic sequencing of circulating <i>Salmonella</i> strains. Additionally, they provide valuable information for local and global public health efforts to reduce the impact of foodborne diseases and AMR.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"319-332"},"PeriodicalIF":3.1,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10069175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Glycolate oxidase gene family identification and functional analyses in cotton resistance to Verticillium wilt. 棉花抗黄萎病乙醇酸氧化酶基因家族鉴定及功能分析。
IF 3.1 3区 生物学
Genome Pub Date : 2023-12-01 Epub Date: 2023-07-20 DOI: 10.1139/gen-2023-0002
Lijun Dong, Xue Zhang, Meng Wang, Xiaohong Fu, Guixia Liu, Shuling Zhang
{"title":"Glycolate oxidase gene family identification and functional analyses in cotton resistance to <i>Verticillium</i> wilt.","authors":"Lijun Dong, Xue Zhang, Meng Wang, Xiaohong Fu, Guixia Liu, Shuling Zhang","doi":"10.1139/gen-2023-0002","DOIUrl":"10.1139/gen-2023-0002","url":null,"abstract":"<p><p>Glycolate oxidase (GOX) plays an important role in the regulation of photorespiration and photosynthesis in plants. However, as one of the main enzymes to produce the second messenger hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), its functions in response to pathogens are still poorly understood. In this study, we carried out genome-wide identification, and 14 GOX genes were identified in <i>Gossypium hirsutum</i>. These GOX genes are located on 10 chromosomes and divided into hydroxyacid-oxidases (HAOX) and GOX groups. After infection with <i>Verticillium dahliae</i> Kleb., six GOX gene expression levels were changed. Moreover, H<sub>2</sub>O<sub>2</sub>, salicylic acid (SA), and the content and activity of GOX increased in cotton. <i>GhHAOX2</i>-<i>D</i>-silenced plants showed more wilting than control plants after infection with <i>V. dahliae</i>. Additionally, H<sub>2</sub>O<sub>2</sub> accumulation and SA content were reduced in <i>GhHAOX2</i>-<i>D</i>-silenced plants. The expression levels of <i>GhPAL, GhPAD4</i>, and <i>GhPR1</i> and the lignin content of the silenced plants were significantly lower than those of the control plants. These results indicate that GhHAOX2-D is a positive regulator of <i>Verticillium</i> wilt tolerance in cotton and may promote H<sub>2</sub>O<sub>2</sub> accumulation via the synergistic effects of GOX genes and SA. Collectively, GOX genes play an important role in cotton resistance to <i>Verticillium</i> wilt.</p>","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"305-318"},"PeriodicalIF":3.1,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10101225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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