IF 3.1 3区生物学

Genome Pub Date : 2024-04-01 Epub Date: 2024-02-05 DOI: 10.1139/gen-2023-0082

Alan Moura de Oliveira, Guilherme Mota Souza, Gustavo Akira Toma, Natalia Dos Santos, Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, Geize Aparecida Deon, Princia Grejo Setti, Fábio Porto-Foresti, Ricardo Utsunomia, Ricardo José Gunski, Analía Del Valle Garnero, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer, Marcelo de Bello Cioffi

{"title":"Satellite DNAs, heterochromatin, and sex chromosomes of the wattled jacana (Charadriiformes; Jacanidae): a species with highly rearranged karyotype.","authors":"Alan Moura de Oliveira, Guilherme Mota Souza, Gustavo Akira Toma, Natalia Dos Santos, Rodrigo Zeni Dos Santos, Caio Augusto Gomes Goes, Geize Aparecida Deon, Princia Grejo Setti, Fábio Porto-Foresti, Ricardo Utsunomia, Ricardo José Gunski, Analía Del Valle Garnero, Edivaldo Herculano Correa de Oliveira, Rafael Kretschmer, Marcelo de Bello Cioffi","doi":"10.1139/gen-2023-0082","DOIUrl":"10.1139/gen-2023-0082","url":null,"abstract":"Charadriiformes, which comprises shorebirds and their relatives, is one of the most diverse avian orders, with over 390 species showing a wide range of karyotypes. Here, we isolated and characterized the whole collection of satellite DNAs (satDNAs) at both molecular and cytogenetic levels of one of its representative species, named the wattled jacana (Jacana jacana), a species that contains a typical ZZ/ZW sex chromosome system and a highly rearranged karyotype. In addition, we also investigate the in situ location of telomeric and microsatellite repeats. A small catalog of 11 satDNAs was identified that typically accumulated on microchromosomes and on the W chromosome. The latter also showed a significant accumulation of telomeric signals, being (GA)10 the only microsatellite with positive hybridization signals among all the 16 tested ones. These current findings contribute to our understanding of the genomic organization of repetitive DNAs in a bird species with high degree of chromosomal reorganization contrary to the majority of bird species that have stable karyotypes.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"109-118"},"PeriodicalIF":3.1,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691652","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

Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries. 研究多胎和单胎雌羊卵巢中生育调节lncrna的表达。

IF 3.1 3区生物学

Genome Pub Date : 2024-03-01 Epub Date: 2023-11-20 DOI: 10.1139/gen-2023-0055

Shahram Hosseinzadeh, Ali Akbar Masoudi

{"title":"Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries.","authors":"Shahram Hosseinzadeh, Ali Akbar Masoudi","doi":"10.1139/gen-2023-0055","DOIUrl":"10.1139/gen-2023-0055","url":null,"abstract":"Sheep is the primary source of animal protein in Iran. Birth type is one of the significant features that determine total meat output. Little is known about how long non-coding RNAs (LncRNAs) affect litter size. The purpose of this research is to investigate the DE-LncRNAs in ovarian tissue between multiparous and uniparous Shal ewes. Through bioinformatics analyses, LncRNAs with variable expression levels between ewes were discovered. Target genes were annotated using the DAVID database, and STRING and Cytoscape software were used to evaluate their interactions. The expression levels of 148 LncRNAs were different in the multiparous and uniparous ewe groups (false discovery rate (FDR) < 0.05). Eight biological process terms, nine cellular component terms, 10 molecular function terms, and 38 KEGG pathways were significant (FDR < 0.05) in the GO analysis. One of the most significant processes impacting fertility is mitogen-activated protein kinase (MAPK) signaling pathway, followed by oocyte meiosis, gonadotropin-releasing hormone signaling pathway, progesterone-mediated oocyte maturation, oxytocin signaling pathway, and cAMP signaling pathway. ENSOARG00000025710, ENSOARG00000025667, ENSOARG00000026034, and ENSOARG00000026632 are LncRNAs that may affect litter size and fertility. The most crucial hub genes include MAPK1, BRD2, GAK, RAP1B, FGF2, RAP1B, and RAP1B. We hope that this study will encourage researchers to further investigate the effect of LncRNAs on fertility.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"78-89"},"PeriodicalIF":3.1,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138175995","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 chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes. 应用寡核苷酸探针荧光原位杂交技术鉴定陆地棉染色体。

IF 3.1 3区生物学

Genome Pub Date : 2024-03-01 Epub Date: 2023-11-03 DOI: 10.1139/gen-2023-0051

Min Xu, Haiyue Guo, Yingying Wang, Baoliang Zhou

{"title":"Identification of chromosomes by fluorescence in situ hybridization in Gossypium hirsutum via developing oligonucleotide probes.","authors":"Min Xu, Haiyue Guo, Yingying Wang, Baoliang Zhou","doi":"10.1139/gen-2023-0051","DOIUrl":"10.1139/gen-2023-0051","url":null,"abstract":"Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3-7, and 9-13) in A subgenome and 7 (Chrs. 1-2, 4-5, and 7-9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"64-77"},"PeriodicalIF":3.1,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434217","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

The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia. 马兜铃科植物芳奇的完整叶绿体基因组为马兜铃科植物的系统发育和物种鉴定提供了见解。

IF 3.1 3区生物学

Genome Pub Date : 2024-03-01 Epub Date: 2023-12-13 DOI: 10.1139/gen-2023-0068

Qingqun Cai, Shiyin Feng, Xiasheng Zheng

{"title":"The complete chloroplast genome of Aristolochia fangchi provided insights into the phylogeny and species identification of Aristolochia.","authors":"Qingqun Cai, Shiyin Feng, Xiasheng Zheng","doi":"10.1139/gen-2023-0068","DOIUrl":"10.1139/gen-2023-0068","url":null,"abstract":"Aristolochia fangchi is an important species within the family Aristolochiaceae, most of which contain nephrotoxic aristolochic acid. The inadvertent use of Aristolochiaceae plants as raw ingredients in the manufacturing of patent medicine poses a significant risk warranting considerable attention. In this study, we assembled and analyzed the complete chloroplast genome of Aristolochia fangchi, which is a 159 867 bp long circular molecule. Functional annotation of the A. fangchi plastome unveiled a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Subsequently, a series of genome structure and characteristic evaluations were conducted against the A. fangchi plastome. Further phylogenetic analysis suggested that a plausible phylogenetic relationship among Aristolochiaceae derived from the concatenated sequences of shared conserved genes rather than from the entire chloroplast genome with one IR copy. Finally, a DNA polymorphism assessment against a dozen Aristolochia plastomes yielded multiple potential regions for biomarker designation. Six pairs of primers were generated and underwent both in silico and actual PCR validations. In conclusion, this study identified the unique characteristics of the A. fangchi plastome, providing invaluable insights for further investigations on species identification and the phylogeny evolution between A. fangchi and its related species.","PeriodicalId":12809,"journal":{"name":"Genome","volume":" ","pages":"90-98"},"PeriodicalIF":3.1,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802845","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

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":"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.","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 (Poecile gambeli).","authors":"P Srikanthan, T M Burg","doi":"10.1139/gen-2023-0067","DOIUrl":"10.1139/gen-2023-0067","url":null,"abstract":"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.","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":"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, FST, 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.","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":"Saffron, the stigma of Crocus sativus 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).","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 Pasteurella multocida 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":"Pasteurella multocida 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 nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 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 P. multocida of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.","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":"Studies on the northeastern American native hops (Humulus lupulus ssp. lupuloides) 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 H. lupulus ssp. lupuloides 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.","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

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