Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains

2006 ◽  
Vol 291 (6) ◽  
pp. C1183-C1192 ◽  
Author(s):  
Nancy E. Schlick ◽  
Michael I. Jensen-Seaman ◽  
Kimberly Orlebeke ◽  
Anne E. Kwitek ◽  
Howard J. Jacob ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Model System ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Rat Strains ◽  
Single Nucleotide ◽  
Inbred Rat Strains ◽  
Wild Rat ◽  
Inbred Rat

Rat remains a major biomedical model system for common, complex diseases. The rat continues to gain importance as a model system with the completion of its full genomic sequence. Although the genomic sequence has generated much interest, only three complete sequences of the rat mitochondria exist. Therefore, to increase the knowledge of the rat genome, the entire mitochondrial genomes (16,307–16,315 bp) from 10 inbred rat strains (that are standard laboratory models around the world) and 2 wild rat strains were sequenced. We observed a total of 195 polymorphisms, 32 of which created an amino acid change (nonsynonymous substitutions) in 12 of the 13 protein coding genes within the mitochondrial genome. There were 11 single nucleotide polymorphisms within the tRNA genes, six in the 12S rRNA, and 12 in the 16S rRNA including 3 insertions/deletions. We found 14 single nucleotide polymorphisms and 2 insertion/deletion polymorphisms in the D-loop. The inbred rat strains cluster phylogenetically into three distinct groups. The wild rat from Tokyo grouped closely with five inbred strains in the phylogeny, whereas the wild rat from Milwaukee was not closely related to any inbred strain. These data will enable investigators to rapidly assess the potential impact of the mitochondria in these rats on the physiology and the pathophysiology of phenotypes studied in these strains. Moreover, these data provide information that may be useful as new animal models, which result in novel combinations of nuclear and mitochondrial genomes, are developed.

scholarly journals Analysis of the genetic diversity of Phalaenopsis orchids with single nucleotide polymorphisms and snap markers derived from the Pto gene

2021 ◽  
Vol 53 (4) ◽  
pp. 620-631
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Nucleotide Polymorphisms ◽  
Multiple Sequence ◽  
Functional Link ◽  
Single Nucleotide ◽  
Functional Changes ◽  
Interspecies Variability

The Pto gene is a plant gene that has been reported to be involved in resistance to bacterial pathogens. A partial genomic sequence corresponding to Pto (~449 bp) was isolated from 16 species and four hybrids of Phalaenopsis during 2017 at the Department of Agronomy and Horticulture, IPB University, Bogor, Indonesia. Multiple sequence analysis was performed to find putative single nucleotide polymorphisms (SNPs) and design the corresponding single nucleotide-amplified polymorphism (SNAP) markers, which were in turn used to estimate the genetic diversity of 25 Phalaenopsis species. In total, 20 SNPs, of which 14 were nonsynonymous, were identified from the partial Pto sequences. Eighteen SNAP primers were then developed based on these 14 nonsynonymous and four synonymous SNPs. Validation results showed that 15 SNAP primers showed a polymorphism information content exceeding 0.3, suggesting the existence of more than two alleles for this locus. Upon their use, the SNAP markers described 86% of all interspecies variability. The Pto 52, Pto 349, Pto 229, and Pto 380 SNAP markers were very informative in the determination of genetic diversity. Notably, the existence of these nonsynonymous SNPs implied the possibility of functional changes within the amino acid sequence of the putative PTO protein. Thus, the resulting differences in the activity of the PTO protein may be used to breed tolerance to pathogen infection. Further work may be required to establish a functional link between tolerance to pathogens and the presence of Pto-SNAP markers in Phalaenopsis properly.

scholarly journals Single-Nucleotide Polymorphisms in Soybean

Genetics ◽  
2003 ◽  
Vol 163 (3) ◽  
pp. 1123-1134 ◽  
Author(s):  
Y L Zhu ◽  
Q J Song ◽  
D L Hyten ◽  
C P Van Tassell ◽  
L K Matukumalli ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genomic Dna ◽  
Nucleotide Diversity ◽  
Genomic Sequence ◽  
Haplotype Diversity ◽  
Pcr Primers ◽  
Dna Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cultivated Soybean

Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

Investigating the likely association between genetic ancestry and COVID-19 manifestation (Preprint)

2020 ◽  
Author(s):  
Ranajit Das ◽  
Sudeep D Ghate
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Wide Association Study ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antiviral Response ◽  
Genetic Ancestry ◽  
Recovery Ratio ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
A Genome

UNSTRUCTURED The novel coronavirus 2019-nCoV/SARS-CoV-2 infection has shown discernible variability across the globe. While in some countries people are recovering relatively quicker, in others, recovery times have been comparatively longer and numbers of those succumbing to it high. In this study, we aimed to evaluate the likely association between an individual’s ancestry and the extent of COVID-19 manifestation employing Europeans as the case study. We employed 10,215 ancient and modern genomes across the globe assessing 597,573 single nucleotide polymorphisms (SNPs). Pearson’s correlation coefficient (r) between various ancestry proportions of European genomes and COVID-19 death/recovery ratio was calculated and its significance was statistically evaluated. We found significant positive correlation (p=0.03) between European Mesolithic hunter gatherers (WHG) ancestral fractions and COVID-19 death/recovery ratio and a marginally significant negative correlation (p=0.06) between Neolithic Iranian ancestry fractions and COVID-19 death/recovery ratio. We further identified 404 immune response related single nucleotide polymorphisms (SNPs) by comparing publicly available 753 genomes from various European countries against 838 genomes from various Eastern Asian countries in a genome wide association study (GWAS). Prominently, we identified that SNPs associated with Interferon stimulated antiviral response, Interferon-stimulated gene 15 mediated antiviral mechanism and 2′-5′ oligoadenylate synthase mediated antiviral response show large differences in allele frequencies between Europeans and East Asians. Overall, to the best of our knowledge, this is the first study evaluating the likely association between genetic ancestry and COVID-19 manifestation. While our current findings improve our overall understanding of the COVID-19, we note that the development of effective therapeutics will benefit immensely from more detailed analyses of individual genomic sequence data from COVID-19 patients of varied ancestries.

scholarly journals Single-Nucleotide Polymorphisms (SNPs) Both Associated with Hypertension and Contributing to Accelerated-Senescence Traits in OXYS Rats

2020 ◽  
Vol 21 (10) ◽  
pp. 3542 ◽  
Author(s):  
Vasiliy A. Devyatkin ◽  
Olga E. Redina ◽  
Natalia A. Muraleva ◽  
Nataliya G. Kolosova
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Relationships ◽  
Accelerated Aging ◽  
Oxys Rats ◽  
Nucleotide Polymorphisms ◽  
Rat Strains ◽  
Single Nucleotide ◽  
Hypertensive Rat ◽  
Age Related ◽  
Accelerated Senescence

Aging is a major risk factor of numerous human diseases. Adverse genetic variants may contribute to multiple manifestations of aging and increase the number of comorbid conditions. There is evidence of links between hypertension and age-related diseases, although the genetic relationships are insufficiently studied. Here, we investigated the contribution of hypertension to the development of accelerated-senescence syndrome in OXYS rats. We compared transcriptome sequences of the prefrontal cortex, hippocampus, and retina of OXYS rats with the genotypes of 45 rat strains and substrains (which include models with hypertension) to find single-nucleotide polymorphisms (SNPs) both associated with hypertension and possibly contributing to the development of age-related diseases. A total of 725 polymorphisms were common between OXYS rats and one or more hypertensive rat strains/substrains being analyzed. Multidimensional scaling detected significant similarities between OXYS and ISIAH rat genotypes and significant differences between these strains and the other hypertensive rat strains/substrains. Nonetheless, similar sets of SNPs produce a different phenotype in OXYS and ISIAH rats depending on hypertension severity. We identified 13 SNPs causing nonsynonymous amino-acid substitutions having a deleterious effect on the structure or function of the corresponding proteins and four SNPs leading to functionally significant structural rearrangements of transcripts in OXYS rats. Among them, SNPs in genes Ephx1, Pla2r1, and Ccdc28b were identified as candidates responsible for the concomitant manifestation of hypertension and signs of accelerated aging in OXYS rats.

Single nucleotide polymorphism analysis reveals heterogeneity within a seedling tree population of a polyembryonic mango cultivar

Genome ◽  
2016 ◽  
Vol 59 (5) ◽  
pp. 319-325 ◽  
Author(s):  
Patrick Winterhagen ◽  
Jens-Norbert Wünsche
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genomic Sequence ◽  
Polymorphism Analysis ◽  
Ethylene Receptor ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Receptor Isoforms ◽  
Tree Population ◽  
Seedling Tree

Within a polyembryonic mango seedling tree population, the genetic background of individuals should be identical because vigorous plants for cultivation are expected to develop from nucellar embryos representing maternal clones. Due to the fact that the mango cultivar ‘Hôi’ is assigned to the polyembryonic ecotype, an intra-cultivar variability of ethylene receptor genes was unexpected. Ethylene receptors in plants are conserved, but the number of receptors or receptor isoforms is variable regarding different plant species. However, it is shown here that the ethylene receptor MiETR1 is present in various isoforms within the mango cultivar ‘Hôi’. The investigation of single nucleotide polymorphisms revealed that different MiETR1 isoforms can not be discriminated simply by individual single nucleotide exchanges but by the specific arrangement of single nucleotide polymorphisms at certain positions in the exons of MiETR1. Furthermore, an MiETR1 isoform devoid of introns in the genomic sequence was identified. The investigation demonstrates some limitations of high resolution melting and ScreenClust analysis and points out the necessity of sequencing to identify individual isoforms and to determine the variability within the tree population.

scholarly journals SINGLE NUCLEOTIDE POLYMORPHISMS IN THE D-LOOP REGION OF THE MITOCHONDRIAL GENOMES OF INDIVIDUALS FROM TWO ETHNIC GROUPS KINH AND MANG OF AUSTRO-ASIATIC LANGUAGE FAMILY

2018 ◽  
Vol 16 (2) ◽  
pp. 231-240
Author(s):  
Nguyen Thy Ngoc ◽  
Nguyen Bao Trang ◽  
Nguyen Quang Huy ◽  
Nguyen Dang Ton ◽  
Nguyen Thuy Duong
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Ethnic Group ◽  
Ethnic Groups ◽  
Mitochondrial Genomes ◽  
Nucleotide Polymorphisms ◽  
Language Family ◽  
Single Nucleotide ◽  
Loop Region ◽  
Pcr Products ◽  
D Loop

The two hypervariable regions HV-I and HV-II in the D-loop region are the most diverse region in the mitochondrial human genome. These DNA regions have an important role in population genetics and human evolution research. In this study, we identified single nucleotide polymorphisms (SNPs) in the D-loop region of the human mitochondrial DNA genomes of individuals in two Vietnamese ethnic groups: Kinh and Mang. 81 blood samples from 50 Kinh and 31 Mang unrelated individuals were collected for genomic DNA extraction. Using PCR and specific primers, we successfully amplified the two HV-I and HV-II regions with respective sizes of 693 bp and 689 bp. The PCR products then were purified and sequenced. After alignment to the reference mitochondrial genome rCRS (NC_012920.1), 96 SNPs were detected in the Kinh ethnic group, of which many polymorphisms were firstly found in this ethnic and 36 SNPs in the Mang ethnic group. Of the identified 132 SNPs, 16 SNPs were significantly different between the two ethnic groups (p < 0.05). Eight out of the 16 SNPs (T146C, T199C, A16182C, T16217C, T16297C, T16140C, A16183C, T16189C) were frequently found in the Kinh ethnic group but not or only rarely in the Mang ethnic group. On the other hand, 4 SNPs (C151T, A16162G, A16269G, T16271C) were commonly found in the Mang population but rarely in the Kinh population. These findings suggest that although Kinh and Mang belong to one language family (Austro-Asiatic), there is a noticeable diversity in the mitochondrial genomes between these two Vietnamese ethnic groups.

scholarly journals Investigatingthe likely association between genetic ancestry and COVID-19 manifestation

2020 ◽  
Author(s):  
Ranajit Das ◽  
Sudeep D. Ghate
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Wide Association Study ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antiviral Response ◽  
Genetic Ancestry ◽  
Recovery Ratio ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
A Genome

AbstractThe novel coronavirus 2019-nCoV/SARS-CoV-2 infection has shown discernible variability across the globe. While in some countries people are recovering relatively quicker, in others, recovery times have been comparatively longer and numbers of those succumbing to it high. In this study, we aimed to evaluate the likely association between an individual’s ancestry and the extent of COVID-19 manifestation employing Europeans as the case study. We employed 10,215 ancient and modern genomes across the globe assessing 597,573 single nucleotide polymorphisms (SNPs). Pearson’s correlation coefficient (r) between various ancestry proportions of European genomes and COVID-19 death/recovery ratio was calculated and its significance was statistically evaluated. We found significant positive correlation (p=0.03) between European Mesolithic hunter gatherers (WHG) ancestral fractions and COVID-19 death/recovery ratio and a marginally significant negative correlation (p=0.06) between Neolithic Iranian ancestry fractions and COVID-19 death/recovery ratio. We further identified 404 immune response related single nucleotide polymorphisms (SNPs) by comparing publicly available 753 genomes from various European countries against 838 genomes from various Eastern Asian countries in a genome wide association study (GWAS). Prominently, we identified that SNPs associated with Interferon stimulated antiviral response, Interferon-stimulated gene 15 mediated antiviral mechanism and 2′-5′ oligoadenylate synthase mediated antiviral response show large differences in allele frequencies between Europeans and East Asians. Overall, to the best of our knowledge, this is the first study evaluating the likely association between genetic ancestry and COVID-19 manifestation. While our current findings improve our overall understanding of the COVID-19, we note that the development of effective therapeutics will benefit immensely from more detailed analyses of individual genomic sequence data from COVID-19 patients of varied ancestries.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide
Sign in / Sign up

Export Citation Format

Share Document