Genome‐wide SNP identification in Fraxinus linking genetic characteristics to tolerance of Agrilus planipennis

Abstract Background Ash ( Fraxinus spp.) is one of the most widely distributed tree genera in North America. Populations of ash in the United States and Canada have been decimated by the introduced pest, Agrilus planipennis (Coleoptera: Buprestidae; emerald ash borer), having both negative impacts on forest ecosystems and economic interests. The majority of trees succumb to attack by A. planipennis , but some trees have been found to be tolerant to infestation despite years of exposure. Restriction site-associated DNA (RAD) sequencing was used to sequence ash individuals, both tolerant and susceptible to A. planipennis attack, in order to identify SNP patterns related to tolerance and health declines.Results A de novo reference genome was assembled and single nucleotide polymorphisms (SNPs) were called using SAMtools. After filtering criteria were implemented, a set of 17,807 SNPs were generated. Principle component analysis (PCA) of SNPs aligned individual trees into clusters related to geography, however, five tolerant trees clustered together despite geographic diversity. A subset of 32 outlier SNPs identified within this group, as well as a subset of 17 SNPs identified based on vigor rating, are candidates for selection on host tolerance.Conclusions Identifying genetic markers associated with host tolerance through genome-wide association has the potential to restore populations with cultivars that are able to withstand A. planipennis infestation. This study was successful in using RAD-sequencing in order to identify SNPs that are potential candidates to identify tolerance to A. planipennis . This was a first step toward uncovering the genetic basis for host tolerance to A. planipennis . Future studies are needed to identify the functionality of the loci where these SNPs occur and how they may be related to tolerance of A. planipennis attack.

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Reassortment Network of Influenza A Virus

Frontiers in Microbiology ◽

10.3389/fmicb.2021.793500 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xingfei Gong ◽

Mingda Hu ◽

Wei Chen ◽

Haoyi Yang ◽

Boqian Wang ◽

...

Keyword(s):

Influenza A Virus ◽

Influenza A ◽

Phylogenetic Trees ◽

Minimum Spanning Tree ◽

Comprehensive Understanding ◽

Genome Sequences ◽

Genetic Characteristics ◽

Time Period ◽

Genome Wide ◽

History Of

Influenza A virus (IAV) genomes are composed of eight single-stranded RNA segments. Genetic exchange through reassortment of the segmented genomes often endows IAVs with new genetic characteristics, which may affect transmissibility and pathogenicity of the viruses. However, a comprehensive understanding of the reassortment history of IAVs remains lacking. To this end, we assembled 40,296 whole-genome sequences of IAVs for analysis. Using a new clustering method based on Mean Pairwise Distances in the phylogenetic trees, we classified each segment of IAVs into clades. Correspondingly, reassortment events among IAVs were detected by checking the segment clade compositions of related genomes under specific environment factors and time period. We systematically identified 1,927 possible reassortment events of IAVs and constructed their reassortment network. Interestingly, minimum spanning tree of the reassortment network reproved that swine act as an intermediate host in the reassortment history of IAVs between avian species and humans. Moreover, reassortment patterns among related subtypes constructed in this study are consistent with previous studies. Taken together, our genome-wide reassortment analysis of all the IAVs offers an overview of the leaping evolution of the virus and a comprehensive network representing the relationships of IAVs.

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The Association of TMPRSS6 Gene Polymorphism and Iron Intake with Iron Status among Under-Two-Year-Old Children in Lombok, Indonesia

Nutrients ◽

10.3390/nu11040878 ◽

2019 ◽

Vol 11 (4) ◽

pp. 878

Author(s):

Dewi Shinta ◽

Chris Adhiyanto ◽

Min Htet ◽

Umi Fahmida ◽

Keyword(s):

Iron Status ◽

Association Studies ◽

Iron Concentration ◽

Hemoglobin Concentration ◽

Minor Allele ◽

Genome Wide Association Studies ◽

Iron Intake ◽

Genetic Characteristics ◽

Genome Wide ◽

Hb Concentration

Multiple common variants in transmembrane protease serine 6 (TMPRSS6) were associated with the plasma iron concentration in genome-wide association studies, but their effect in young children where anemia and iron deficiency (ID) were prevalent has not been reported, particularly taking account of iron intake. This study aims to investigate whether TMPRSS6 SNPs (rs855791 and rs4820268) and iron intake are associated with a low iron and hemoglobin concentration in under-two-year-old children. The study analyzed the baseline of a randomized trial (NUPICO, ClinicalTrials.gov NCT01504633) in East Lombok, Indonesia. Children aged 6–17 months (n = 121) were included in this study. The multiple linear regressions showed that TMPRSS6 decreased serum ferritin (SF) by 4.50 g/L per copy minor allele (A) of rs855791 (p = 0.08) and by 5.00 μg/L per copy minor allele (G) of rs4820268 (p = 0.044). There were no associations between rs855791 and rs4820268 with soluble transferrin receptor (sTfR) and hemoglobin (Hb) concentration (rs855791; p = 0.38 and p = 0.13, rs4820268; p = 0.17 and p = 0.33). The finding suggests the need for further studies to explore whether the nutrient recommendation for iron should be based on genetic characteristics, particularly for children who have mutation in TMPRSS6.

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Biological properties and genetic characteristics of experimental diagnostic Vibrio cholerae bacteriophages

Journal of microbiology epidemiology immunobiology ◽

10.36233/0372-9311-39 ◽

2021 ◽

Vol 98 (3) ◽

pp. 290-297

Author(s):

M. P. Pogozhova ◽

N. E. Gayevskaya ◽

A. S. Vodopyanov ◽

R. V. Pisanov ◽

A. O. Anoprienko ◽

...

Keyword(s):

Life Cycle ◽

Morphological Structure ◽

Biological Properties ◽

Sequencing Data ◽

Genetic Characteristics ◽

Resistance Factors ◽

Prophylactic Drugs ◽

Genome Wide ◽

El Tor ◽

Experimental Cholera

Background. Currently, the researches focused on the design of new diagnostic and preventive preparations based on bacteriophages are underway, so it is importatnt to study the biological properties of cholera phages along with their genetic structure. This information is necessary to predict the phage life cycle and assess the prospects of its practical use in experiments, phagodiagnostics and phagoprophylaxis.Materials and methods. The presence or absence of genes characteristic of temperate bacteriophages was tested using a database created by the authors and developed software "PhageAnalyzer", which allows for rapid analysis of bacteriophage genome-wide sequencing data and prediction of their life cycle.Results and discussion. The morphological structure of experimental diagnostic cholera phages is represented by head bacteriophages of various morphogroups. Negative colonies phage differed in diameter, shape and degree of transparency. No genetic determinants of resistance factors and toxins have been found in the genomes of bacteriophages Rostov-1, Rostov-6, Rostov 7, and Rostov M3. Results of phylogenetic analysis demonstrated that the studied experimental cholera bacteriophages resemble headphages from the genus Vibrio, but are unique, since they lie outside “cluster groups”. Vibrio phages Rostov-1 and Rostov M3 are appeared to be lytic. Genes characteristic of moderate bacteriophages were found in cholera phages Rostov-6 and Rostov 7.Conclusion. The experimental cholera bacteriophage Rostov-1 can be used to differentiate cholera vibrion O1 the serogroup of the El Tor biovar, and Vibrio phage Rostov M3 can be used to differentiate the Classical biovar. Both bacteriophages are lytic and promising components for creating prophylactic drugs against cholera. Vibrio phages Rostov-6 and Rostov 7 can be successfully used only in experimental activities, as well as for monitoring cholera vibrions in the environment. Complete genomic sequences are deposited and available in the international database Genbank (NCBI).

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Evolution, heterogeneity and global dispersal of cosmopolitan genotype: The most widespread genotype of Dengue Virus type 2

10.21203/rs.3.rs-389331/v1 ◽

2021 ◽

Author(s):

Surya Pavan Yenamandra ◽

Carmen Koo ◽

Suzanna Chiang ◽

Lim Han Shi Jeri ◽

Zhen Yuan Yeo ◽

...

Keyword(s):

Dengue Virus ◽

Virus Type ◽

Genomic Analysis ◽

Envelope Gene ◽

Genetic Characteristics ◽

Fitness Advantage ◽

Genome Wide ◽

The Tropics ◽

Dengue Virus Type 2

Abstract Dengue virus type 2 (DENV-2) contributes substantially to the dengue burden and dengue-related mortality in the tropics and sub-tropics. DENV-2 includes six genotypes, among which cosmopolitan genotype is the most widespread. The present study investigated the evolution, intra-genotype heterogeneity and dispersal of cosmopolitan genotype to understand unique genetic characteristics that have shaped the molecular epidemiology and distribution of cosmopolitan lineages. The spatial analysis demonstrated a wide geo-distribution of cosmopolitan genotype through an extensive inter-continental network, anchored in Southeast Asia and Indian sub-continent. Intra-genotype analyses using 2,392 envelope gene sequences revealed six distinct lineages within the cosmopolitan genotype, namely the Indian sub-continent lineage and five other lineages. Indian sub-continent lineage was the most diverged among six lineages and has almost reached the nucleotide divergence threshold of 6% within E gene to qualify as a separate genotype. Genome wide amino acid signatures and selection pressure analyses further suggested differences in evolutionary characteristics between the Indian sub-continent lineage and other lineages. The present study narrates a comprehensive genomic analysis of cosmopolitan genotype and presents notable genetic characteristics that occurred during its evolution and global expansion. Whether those characteristics conferred a fitness advantage to cosmopolitan genotype in different geographies warrant further investigations.

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A Correlation Study on In Vitro Physiological Activities of Soybean Cultivars, 19 Individual Isoflavone Derivatives, and Genetic Characteristics

Antioxidants ◽

10.3390/antiox10122027 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2027

Author(s):

Han-Na Chu ◽

Su-Ji Lee ◽

Xiaohan Wang ◽

Sang-Hoon Lee ◽

Hye-Myeong Yoon ◽

...

Keyword(s):

Genome Wide Association Study ◽

Correlation Study ◽

Genetic Characteristics ◽

Soybean Cultivars ◽

Genome Wide ◽

A Genome ◽

Estrogen Activity ◽

Er Alpha ◽

The Relationship

The functionality of soybeans is an important factor in the selection and utilization of excellent soybean cultivars, and isoflavones are representative functional substances in soybeans, which exhibit effects on antioxidants, estrogen activity, and cancer, and prevent cardiovascular diseases. This study analyzed ABTS, DPPH, estrogen, ER (ER) alpha, UCP-1, and NO inhibition activities in 48 types of soybean cultivars, as well as the relationship with 19 isolated types of individual isoflavone derivatives. Statistical analysis was conducted to find individual isoflavone derivatives affecting physiological activities, revealing the high correlation of three types of derivatives: genistein 7-O-(6″-O-acetyl)glucoside (6″-O-acetylgenistin), genistein 7-O-(2″-O-apiosyl)glucoside, and glycitein. Based on these results, 15 types of soybean cultivars were selected (one control type, seven yellow types, six black types, and one green type), which have both high physiological activities and a high content of individual isoflavone derivatives. In addition, these high correlations were further verified through a genome-wide association study (GWAS) to determine the association between activities, substances, and genetic characteristics. This study comprehensively describes the relationship between the specific physiological activities of soybean resources, individual isoflavone derivative substances, and SNPs, which will be utilized for in-depth research, such as selection of excellent soybean resources with specific physiological activities.

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Evidence for heightened genetic instability in precancerous spasmolytic polypeptide expressing gastric glands

Journal of Medical Genetics ◽

10.1136/jmedgenet-2018-105752 ◽

2019 ◽

Vol 57 (6) ◽

pp. 385-388 ◽

Cited By ~ 4

Author(s):

Jiangrong Chen ◽

Chunchao Zhu ◽

Chaojie Wang ◽

Chuansheng Hu ◽

Daniel M Czajkowsky ◽

...

Keyword(s):

Genetic Instability ◽

Clinical Sample ◽

Clinical Samples ◽

Gastric Glands ◽

Genetic Characteristics ◽

Helicobacter Felis ◽

Genome Wide ◽

Spasmolytic Polypeptide ◽

Trefoil Factor 2 ◽

Cancer Tissues

BackgroundSpasmolytic polypeptide-expressing metaplasia (SPEM) is present in more than 90% of resected gastric cancer tissues. However, although widely regarded as a pre-cancerous tissue, its genetic characteristics have not been well studied.MethodsImmunohistochemistry using Trefoil factor 2 (TFF2) antibodies was used to identify TFF2-positive SPEM cells within SPEM glands in the stomach of Helicobacter felis (H. felis) -infected mice and human clinical samples. Laser microdissection was used to isolate specific cells from both the infected mice and the human samples. The genetic instability in these cells was examined by measuring the lengths of microsatellite (MS) markers using capillary electrophoresis. Also, genome-wide genetic variations in the SPEM cells from the clinical sample was examined using deep whole-exome sequencing.ResultsSPEM cells indeed exhibit not only heightened MS instability (MSI), but also genetic instabilities that extend genome-wide. Furthermore, surprisingly, we found that morphologically normal, TFF2-negative cells also contain a comparable degree of genomic instabilities as the co-resident SPEM cells within the SPEM glands.ConclusionThese results, for the first time, clearly establish elevated genetic instability as a critical property of SPEM glands, which may provide a greater possibility for malignant clone selection. More importantly, these results indicate that SPEM cells may not be the sole origin of carcinogenesis in the stomach and strongly suggest the common progenitor of these cells, the stem cells, as the source of these genetic instabilities, and thus, potential key players in carcinogenesis.

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Genome-wide association analysis in host genetic characteristics of progression to high-grade cervical intraepithelial neoplasia or higher for women with human papillomavirus infection and normal cytology.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.6033 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. 6033-6033

Author(s):

Chyong-Huey Lai ◽

Su-Wei Chang ◽

Lan-Yan Yang ◽

Shuen-Iu Hung ◽

Chiao-Yun Lin ◽

...

Keyword(s):

Human Papillomavirus ◽

Cervical Intraepithelial Neoplasia ◽

Roc Curve ◽

Intraepithelial Neoplasia ◽

Genome Wide Association ◽

Normal Cytology ◽

Genetic Characteristics ◽

Risk Alleles ◽

Genome Wide

6033 Background: Human papillomavirus (HPV) testing is widely used for cervical cancer screening. The hazard ratio of developing cervical intraepithelial neoplasia grade 2 or higher (CIN2+) in HPV-positive/ normal cytology women is 20–34 fold as compared to those with HPV-negative/normal cytology. HPV-positivity would cause substantial anxiety. Apart from viral factors such as high-risk (hr) types, it is important to identify host characteristics for predicting outcome. Methods: An initial genome-wide association study (GWAS) of single nucleotide polymorphisms (SNPs) by Affymetrix Axiom™ Genome-Wide Human Arrays was conducted on 505 cases with histological diagnosis of CIN2+ (group D1) versus 920 female controls. An additional set of 2315 female controls from the Taiwan Biobank genotype array were added in the discovery stage. The identified 29 CIN2+ -associated SNPs from GWAS (p < 5 x 10−6) were verified in an independent cohort (group D2 [n = 306] versus group N [n = 600]). Group N were HPV-negative/normal cytology women from a population-based cervical cytology and HPV co-test study. A cohort with HPV-positive/normal cytology (group P, n = 755) underwent follow-up and was served as the prediction set. The predictive validity was analyzed by logistic regression and receiver operating characteristic (ROC) curve analysis. Results: Thirty-three individuals of the group P progressed to CIN2+ (median follow-up: 23.7 months, range 4.0–122.1). A risk-predictive panel of 8 SNPs rs3097662, rs35979982, rs7763822, rs4282438, rs3128927, rs7759943, rs213194, rs17835649 which were significant in the replication (p < 0.05) was used to train models for disease risk prediction using the combination of GWAS and verification sets. Two prediction models were finalized and determined using 7 SNPs for hr- and low-risk (lr) HPV groups respectively (sensitivity 0.72 and 0.75, specificity 0.651 and 0.884, area under the ROC curve 0.703 and 0.701). Among group P with hr-HPV, those carried < 6 risk-alleles had significantly decreased hazard (log-rank p < 0·001) of progression to CIN2+ than those with ≧6 risk-alleles, while among group P with lr-HPV, those with predictive probability of ≥ 0·095 had a cumulative risk of progression of 10% at 3 years. Conclusions: Two risk-predictive SNP panels including 7 SNPs with hr- or lr-HPV groups can assist risk stratification among HPV-positive/ normal cytology women. These panels could be further tested in other ethnic populations.

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Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds

Animals ◽

10.3390/ani9090596 ◽

2019 ◽

Vol 9 (9) ◽

pp. 596 ◽

Cited By ~ 2

Author(s):

Fengwei Zhang ◽

Kaixing Qu ◽

Ningbo Chen ◽

Quratulain Hanif ◽

Yutang Jia ◽

...

Keyword(s):

Genetic Basis ◽

Genetic Characteristics ◽

Cattle Breeds ◽

Chinese Cattle ◽

Genome Wide ◽

Whole Genome Resequencing ◽

Immune Related Genes ◽

Go Terms ◽

Subtropical Environment

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

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The Loss of 1p as a Reliable Marker of Progression in a Child with Aggressive Meningioma: A 16-Year Follow-Up Case Report

Pediatric Neurosurgery ◽

10.1159/000512001 ◽

2020 ◽

pp. 1-8

Author(s):

Sina Hemmer ◽

Christoph Sippl ◽

Felix Sahm ◽

Joachim Oertel ◽

Steffi Urbschat ◽

...

Keyword(s):

Chromosome 1 ◽

Molecular Characteristics ◽

Genetic Characteristics ◽

Tumor Specimen ◽

Potential Marker ◽

Genome Wide ◽

A Genome ◽

History Of ◽

Reliable Marker

Background: Here, we present the case of a 32-year-old female with a progressing history of meningioma for 16 years starting with an ethmoidal lesion in 2002. The initial tumor specimen of this patient showed a deletion of the short arm of chromosome 1 through a translocation between chromosomes 1 and 11 (t[1; 11]) as well as additional chromosomal aberrations, including partial or complete monosomy of chromosomes 2, 6, 7, 11, 13, and 22. These molecular characteristics were already known to be associated with an aggressive course of the disease, and the patient was, therefore, included in a strict follow-up regime. From 2003 to 2019, the patient suffered multiple relapses and consecutive tumor resections. Methods: Tumor specimen from 2017 was examined using a genome-wide methylation analysis as well as a whole-genome sequencing. Results: These analyses confirmed the findings of 2002 and proved genetic alteration in the meningioma to be very stable over the time. Yet SMO and AKT1 mutations, which have been described to be paradigmatic in frontobasal meningioma, could not be found. Conclusions: Genetic characteristics seem to be very stable during progression of the disease. The loss of 1p represents to be a potential marker for the poor clinical course of our child meningioma. In 2019, our patient passed away due to the progress of her meningioma disease.

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