scholarly journals When polymorphism and monomorphism meet: discordant genomic and phenotypic clines across a lizard contact zone

2019 ◽  
Author(s):  
Caroline M. Dong ◽  
Claire A. McLean ◽  
Adam Elliott ◽  
Adnan Moussalli ◽  
Devi Stuart-Fox
Keyword(s):  
Contact Zone ◽  
Rapid Evolution ◽  
F1 Hybrids ◽  
Nucleotide Polymorphisms ◽  
Incipient Speciation ◽  
Single Nucleotide ◽  
High Frequencies ◽  
Uv Reflectance ◽  
Genomic Introgression ◽  
Insight Into

AbstractColour polymorphism can promote rapid evolution and speciation, particularly when populations differ in the number or composition of morphs. The contact zone between Ctenophorus modestus (swift dragon) and C. decresii (tawny dragon) is a compelling study system in which to examine evolutionary processes and outcomes when polymorphic and monomorphic populations meet. Ctenophorus modestus is polymorphic for male throat coloration and lacks ultraviolet (UV) reflectance while C. decresii is monomorphic with UV-blue throats. We characterised genomic and phenotypic clines across the contact zone based on single nucleotide polymorphisms, the mitochondrial ND4 gene, and male colour traits, and concurrently assessed the phenotype of captive-bred F1 hybrids. Our results indicate that genomic introgression is asymmetric, with high frequencies of backcrossing to C. modestus but not C. decresii, accompanied by the prevalence of the C. modestus mtDNA haplotype in hybrids. The clines for throat phenotype are abrupt and displaced towards the range of C. decresii, relative to the genetic and dorsolateral phenotype clines. By contrast, both throat and dorsolateral phenotypes in captive-bred F1 hybrids are intermediate. Our results are consistent with the hypothesis that throat coloration, a polymorphic sexual signal in C. modestus, is the target of selection during incipient speciation and provide insight into the microevolutionary processes that may link polymorphism and speciation.

scholarly journals Interactions of COMT and ALDH2 Genetic Polymorphisms on Symptoms of Parkinson’s Disease

2021 ◽  
Vol 11 (3) ◽  
pp. 361
Author(s):  
Rwei-Ling Yu ◽  
Shao-Ching Tu ◽  
Ruey-Meei Wu ◽  
Pei-An Lu ◽  
Chun-Hsiang Tan
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Detrimental Effect ◽  
Personal Hygiene ◽  
Nucleotide Polymorphisms ◽  
Monoamine Neurotransmitters ◽  
Single Nucleotide ◽  
Detrimental Impact ◽  
Reduced Activity ◽  
Insight Into

(1) Background: Monoamine neurotransmitters play essential roles in the normal functioning of our nervous system. However, the metabolism of monoamine neurotransmitters is accompanied by the production of neurotoxic metabolites, and inefficient removal of the metabolites has been suggested to cause neurodegeneration. (2) Methods: To examine the effect of reduced activity of catechol-O-methyltransferase (COMT) and aldehyde dehydrogenase 2 (ALDH2) conferred by single nucleotide polymorphisms COMT rs4680(A) and ALDH2 rs671(A) on the symptoms of patients with Parkinson’s disease (PD), a total of 114 PD patients were recruited cross-sectionally and received genotyping for rs4680 and rs671 along with MDS-UPDRS evaluation. (3) Results: We found that patients carrying rs4680(A) had more severe bradykinesia in the upper extremity and rest tremor. Besides, patients carrying rs671(A) had more difficulty maintaining personal hygiene, while patients with genotype rs671(GG) had higher scores in the item “depressed mood.” More importantly, we found the effect of rs4680 to be moderated by rs671 SNP for the symptom of “hand movements.” The detrimental impact of rs4680(A) is more pronounced in the presence of genotype rs671(GG). (4) Conclusions: This study facilitates a deeper understanding of the detrimental effect of reduced activity of COMT and ALDH2 conferred by genetic variation and provides novel insight into the interactions between enzymes metabolizing monoamine neurotransmitters in the pathogenesis of PD.

Single nucleotide polymorphisms in piRNA-pathway genes: an insight into genetic determinants of human diseases

2019 ◽  
Vol 295 (1) ◽  
pp. 1-12 ◽  
Author(s):  
Jyoti Roy ◽  
Kalyani Anand ◽  
Swati Mohapatra ◽  
Rojalin Nayak ◽  
Trisha Chattopadhyay ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Human Diseases ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Single Nucleotide ◽  
Pirna Pathway ◽  
Insight Into

scholarly journals Transcriptome Analysis, Marker Discovery and Pigment Biosynthesis of Red-leaf Juglans regia

2017 ◽  
Vol 5 (2) ◽  
pp. 20
Author(s):  
Xin Chen ◽  
Li Xu ◽  
Xiao-juan Zong ◽  
Hai-rong Wei ◽  
Jia-wei Wang ◽  
...  
Keyword(s):  
Juglans Regia ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Leaf Trait ◽  
Search Tool ◽  
Pigment Biosynthesis ◽  
Marker Discovery ◽  
Insight Into

Red-leaf trait rarely occurs in Juglans regia, and the genetic mechanism underlying this phenomenon is still unknown. In this study, we attempted to provide insight into the comprehensive transcriptome of red-leaf J. regia by RNA-Seq using Illumina SeqTM2000 platform. A total of 33,488,602 high-quality reads (3.35G cleans bases) were obtained and assembled into 53,782 unigenes. A total of 3,683 unigenes were annotated by using basic local alignment search tool to search against protein databases, All the matched unigenes were categorized by gene ontology analysis, and 3,466 were assigned to metabolism, among which 74 were mapped to anthocyanin, carotenoid, and betalain biosynthetic pathways by Kyoto Encyclopedia of Genes and Genomes analysis. Approximately 656 transcription factors were isolated including MYB, NAC, and bHLH. Additionally, a total of 13,981 simple sequence repeats, 41,088 single nucleotide polymorphisms, and 5,860 insertions and deletions were determined from J. regia transcriptome. Therefore, the current J. regia transcriptome provides deep insight into the molecular basis of red-leaf breeding of J. regia.

scholarly journals Highly Heritable and Functionally Relevant Breed Differences in Dog Behavior

2019 ◽  
Author(s):  
Evan L MacLeant ◽  
Noah Snyder-Mackler ◽  
Bridgett M. vonHoldt ◽  
James A. Serpell
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Architecture ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Biological Basis ◽  
Behavioral Traits ◽  
Breed Differences ◽  
The Brain ◽  
Insight Into

AbstractVariation across dog breeds presents a unique opportunity for investigating the evolution and biological basis of complex behavioral traits. We integrated behavioral data from more than 17,000 dogs from 101 breeds with breed-averaged genotypic data (N = 5,697 dogs) from over 100,000 loci in the dog genome. Across 14 traits, we found that breed differences in behavior are highly heritable, and that clustering of breeds based on behavior accurately recapitulates genetic relationships. We identify 131 single nucleotide polymorphisms associated with breed differences in behavior, which are found in genes that are highly expressed in the brain and enriched for neurobiological functions and developmental processes. Our results provide insight into the heritability and genetic architecture of complex behavioral traits, and suggest that dogs provide a powerful model for these questions.

scholarly journals Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

2020 ◽  
Author(s):  
Nicolae Sapoval ◽  
Medhat Mahmoud ◽  
Michael D. Jochum ◽  
Yunxi Liu ◽  
R. A. Leo Elworth ◽  
...  
Keyword(s):  
High Variability ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Dna Viruses ◽  
Small Indels ◽  
Qrt Pcr ◽  
The World ◽  
Pcr Diagnostics ◽  
Insight Into

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

scholarly journals Impact of COL6A4P2 gene polymorphisms on the risk of lung cancer in a Chinese Han population

2020 ◽  
Author(s):  
Ying Duan ◽  
Gaowen Liu ◽  
Fanglin Niu ◽  
Jing Li ◽  
Mengdan Yan ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Odds Ratio ◽  
Gene Polymorphisms ◽  
Additive Model ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Han Population ◽  
Codominant Model ◽  
Insight Into

Abstract Background The aim of this study was to investigate the effects of COL6A4P2 polymorphisms on lung cancer (LC) in Chinese Han population.Methods To examine whether variants of COL6A4P2 contribute to LC, five single nucleotide polymorphisms (SNPs) of COL6A4P2 were genotyped by Agena MassARRAY in 510 LC patients and 495 controls. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated by logistic regression.Results We found that COL6A4P2 rs34445363 significantly increased the risk of LC in the alleles model (OR = 1.26, 95%CI: 1.01 - 1.58, p = 0.038). And rs34445363 also increased the LC risk under the log-additive model (OR = 1.26, 95%CI: 1.01 - 1.58, p = 0.041) with the multigene model analysis. Further stratification analysis showed that rs34445363 increased the LC risk under the log-additive model (OR = 1.42, 95%CI: 1.03 - 1.95, p = 0.033) in people aged ≤ 61; and rs61733464 was associated with a decreased LC risk in the log-additive model (OR = 0.72, 95%CI: 0.52 - 0.99, p = 0.048) in people aged ≤ 61. We also found that the mutations of rs34445363 and rs77941834 were associated with increased LC risk in the codominant model (rs34445363, GA vs. GG, OR = 1.73, 95%CI: 1.04 - 2.86, p = 0.034; rs77941834, TA vs. TT, OR = 1.88, 95%CI: 1.06 - 3.34, p = 0.032) in females.Conclusions This study provided an evidence for polymorphisms of COL6A4P2 gene associated to the development of LC, also a new insight into etiology of LC.

scholarly journals The Association between 5-Hydroxytryptamine Receptor 1B rs13212041 Polymorphism and Trait Anxiety in Chinese Han College Subjects

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 882
Author(s):  
Xiaofei Ruan ◽  
Suwen Fang ◽  
Qi Zheng ◽  
Senqing Qi ◽  
Yingfang Tian ◽  
...  
Keyword(s):  
Emotional Disorders ◽  
Trait Anxiety ◽  
Protective Factor ◽  
Anxiety And Depression ◽  
Personality Factor ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Development Of Anxiety ◽  
Insight Into

Trait anxiety is a vulnerable personality factor for anxiety and depression. High levels of trait anxiety confer an elevated risk for the development of anxiety and other psychiatric disorders. There is evidence that 5-hydroxytryptamine receptor 1B (5-HT1B) gene polymorphisms play an important role in emotional disorders. Genotyping for four single-nucleotide polymorphisms (SNP) (rs11568817, rs130058, rs6297, and rs13212041) was conducted for 388 high trait anxious (HTA) individuals and 463 low traitanxious (LTA) individuals in Chinese Han college subjects. The results showed that the frequencies of the C-allele and TC + CC genotype of rs13212041 in the LTA individuals were higher than that in the HTA individuals (p = 0.025 and p = 0.014, respectively). Both the C-allele and TC + CC genotype were associated with trait anxiety decreasing (OR = 0.771 and OR = 0.71, respectively). Furthermore, different gene model analysis also showed that the C allele was a protective factor for trait anxiety in Chinese Han college subjects. These findings suggest that 5-HT1B rs13212014 may play a role in trait anxiety among China Han college subjects. The rs13212014 polymorphism may be involved in decreasing the risk of trait anxiety. These results also provide a novel insight into the molecular mechanism underlying trait anxiety.

Insights Into Functional and Structural Impacts of nsSNPs in XPA-DNA Repairing Gene

2022 ◽  
Vol 12 (1) ◽  
pp. 1-12
Author(s):  
Nadeem Ahmad ◽  
Zubair Sharif ◽  
Sarah Bukhari ◽  
Omer Aziz
Keyword(s):  
Genetic Basis ◽  
Structure And Function ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Computational Tools ◽  
Project Hope ◽  
Structural Impacts ◽  
And Function ◽  
Protein Variants ◽  
Insight Into

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in people. SNPs are valuable resource for exploring the genetic basis of disease. The XPA gene provides a way to produce a protein used to repair damaged DNA. This study used the computational methods to classify SNPs and estimate their probability of being neutral or deleterious. The purpose of this analysis is to predict the effect of nsSNPs on the structure and function of XPA proteins. Data was collected from the NCBI hosted dbSNP. The authors examined the pathogenic effect of 194 nsSNPs in the XPA gene with computational tools. Four nsSNPs (C126S, C126W, R158S, and R227Q) those potentially effect on structure and function of the XPA protein were identified with combination of SIFT, PolyPhen, Provean, PHD-SNP, I-Mutant, ConSurf server and Project HOPE. This is the first comprehensive analysis in which XPA gene variants studied using in silico methods and this research able to gain further insight into XPA protein variants and function.

scholarly journals Performing post-genome-wide association study analysis: overview, challenges and recommendations

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1002
Author(s):  
Yagoub Adam ◽  
Chaimae Samtal ◽  
Jean-tristan Brandenburg ◽  
Oluwadamilare Falola ◽  
Ezekiel Adebiyi
Keyword(s):  
Complex Traits ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Single Phenotype ◽  
Insight Into

Genome-wide association studies (GWAS) provide  huge information on statistically significant single-nucleotide polymorphisms (SNPs) associated with various human complex traits and diseases. By performing GWAS studies, scientists have successfully identified the association of hundreds of thousands to  millions of SNPs to a single phenotype. Moreover, the association of some SNPs with rare diseases has been intensively tested. However, classic GWAS studies have not yet provided solid, knowledgeable insight into functional and biological mechanisms underlying phenotypes or mechanisms of diseases. Therefore, several post-GWAS (pGWAS) methods have been recommended. Currently, there is no simple scientific document to provide a quick guide for performing pGWAS analysis. pGWAS is a crucial step for a better understanding of the biological machinery beyond the SNPs. Here, we provide an overview to performing pGWAS analysis and demonstrate the challenges behind each method. Furthermore, we direct readers to key articles for each pGWAS method and present the overall issues in pGWAS analysis.  Finally, we include a custom pGWAS pipeline to guide new users when performing their research.

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