scholarly journals Adaptive divergence in the bovine genome

2015 ◽  
Author(s):  
William Barendse ◽  
Sean McWilliam ◽  
Rowan J Bunch ◽  
Blair E Harrison
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Bovine Genome ◽  
Neutral Theory ◽  
Adaptive Divergence ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Adaptive Selection ◽  
Tropical Environments ◽  
Histocompatibility Complex

Cattle diverged during the Pleistocene into two subspecies, one in temperate and one in tropical environments. Here we have used next generation sequencing of the indicine subspecies of cattle and compared it to the taurine subspecies. Although 23.8 million single nucleotide polymorphisms (SNP) were found, the number of fixed amino acid substitutions between the taurine and indicine subspecies was low and consistent with the Haldane predictions for adaptive selection rather than with Neutral Theory. We noted 33 regions of enhanced divergence of nonsynonymous SNP between the subspecies, which included an increased rate of deleterious variants. Signals of positive selection were found for genes associated with immunity, including the Bovine Major Histocompatibility Complex, which also showed an increased rate of deleterious amino acid variants. The genes important in sensing the environment, especially the olfactory system, showed a network wide signal of positive selection.

scholarly journals Enrichment in conservative amino acid changes among fixed and standing missense variations in slowly evolving proteins

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9983
Author(s):  
Mingrui Wang ◽  
Dapeng Wang ◽  
Jun Yu ◽  
Shi Huang
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Rhesus Macaques ◽  
Neutral Theory ◽  
Evolutionary Rates ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Project Data ◽  
The Impact

The process of molecular evolution has many elements that are not yet fully understood. Evolutionary rates are known to vary among protein coding and noncoding DNAs, and most of the observed changes in amino acid or nucleotide sequences are assumed to be non-adaptive by the neutral theory of molecular evolution. However, it remains unclear whether fixed and standing missense changes in slowly evolving proteins are more or less neutral compared to those in fast evolving genes. Here, based on the evolutionary rates as inferred from identity scores between orthologs in human and Rhesus Macaques (Macaca mulatta), we found that the fraction of conservative substitutions between species was significantly higher in their slowly evolving proteins. Similar results were obtained by using four different methods of scoring conservative substitutions, including three that remove the impact of substitution probability, where conservative changes require fewer mutations. We also examined the single nucleotide polymorphisms (SNPs) by using the 1000 Genomes Project data and found that missense SNPs in slowly evolving proteins also had a higher fraction of conservative changes, especially for common SNPs, consistent with more non-conservative substitutions and hence stronger natural selection for SNPs, particularly rare ones, in fast evolving proteins. These results suggest that fixed and standing missense variants in slowly evolving proteins are more likely to be neutral.

Association of a region of bovine chromosome 1 (BTA1) with age at puberty in Angus bulls

2016 ◽  
Vol 28 (10) ◽  
pp. 1618 ◽  
Author(s):  
María E. Fernández ◽  
Alberto Prando ◽  
Andrés Rogberg-Muñoz ◽  
Pilar Peral-García ◽  
Andrés Baldo ◽  
...  
Keyword(s):  
Integration Site ◽  
Bovine Genome ◽  
Chromosome 1 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Complex Locus ◽  
Age At Puberty ◽  
Virus Integration ◽  
Ecotropic Virus ◽  
Larger Sample

Age at puberty is an important component of reproductive performance in cattle, so it is important to identify genes that contribute to the regulation of the onset of puberty and polymorphisms that explain differences between bulls. In a previous study, we found putative associations between age at puberty in Angus bulls and single-nucleotide polymorphisms (SNPs) in Chromosomes 1 and X. In the present work we aimed to confirm these findings in a larger sample of Angus bulls (n = 276). Four SNPs located in these regions were genotyped using SEQUENOM technology and the genotypes obtained were tested for association with age at puberty. The results showed that SNPs rs135953349 and rs110604205 on BTA1 were still significantly associated with age of puberty estimated at progressive sperm motility of 10% (P < 0.05). The association previously found on Chromosome X could not be confirmed. Analysis of the bovine genome revealed that the associated region (99.17–99.99 Mb) contained four predicted loci: myelodysplasia syndrome 1 (MDS1) and ecotropic virus integration site 1 (EVI1) complex locus (MECOM), eGF-like and EMI domain-containing 1 pseudogene-like (LOC100337483), microRNA mir-551b (MIR551B) and mCG140927-like (LOC100139843). The results obtained could contribute to the understanding of puberty regulation and could be useful for further identification and annotation of gene function in the context of reproduction.

scholarly journals Molecular epidemiologic characteristics of hemagglutinin from five waves of avian influenza A (H7N9) virus infection, from 2013 to 2017, in Zhejiang Province, China

2021 ◽  
Author(s):  
Yi Sun ◽  
Haiyan Mao ◽  
Xiuyu Lou ◽  
Xinying Wang ◽  
Yin Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Zhejiang Province ◽  
Personal Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Amino Acid Mutations ◽  
Influenza Outbreaks ◽  
Epidemiological Characteristics ◽  
The Waves

AbstractThere have been five waves of influenza A (H7N9) epidemics in Zhejiang Province between 2013 and 2017. Although the epidemiological characteristics of the five waves have been reported, the molecular genetics aspects, including the phylogeny, evolution, and mutation of hemagglutinin (HA), have not been systematically investigated. A total of 154 H7N9 samples from Zhejiang Province were collected between 2013 and 2017 and sequenced using an Ion Torrent Personal Genome Machine. The starting dates of the waves were 16 March 2013, 1 July 2013, 1 July 2014, 1 July 2015, and 1 July 2016. Single-nucleotide polymorphisms (SNPs) and amino acid mutations were counted after the HA sequences were aligned. The evolution of H7N9 matched the temporal order of the five waves, among which wave 3 played an important role. The 55 SNPs and 14 amino acid mutations with high frequency identified among the five waves revealed the dynamic occurrence of mutation in the process of viral dissemination. Wave 3 contributed greatly to the subsequent epidemic of waves 4 and 5 of H7N9. Compared with wave 1, wave 5 was characterized by more mutations, including A143V and R148K, two mutations that have been reported to weaken the immune response. In addition, some amino acid mutations were observed in wave 5 that led to more lineages. It is necessary to strengthen the surveillance of subsequent H7N9 influenza outbreaks.

scholarly journals SINGLE-NUCLEOTIDE POLYMORPHISMS OF CALCIUM-SENSING RECEPTOR ENCODING GENE ASSOCIATED WITH CALCIUM KIDNEY STONE DISEASE IN BABYLON PROVINCE

2018 ◽  
Vol 11 (2) ◽  
pp. 417 ◽  
Author(s):  
Zahraa Isam ◽  
Rabab Omran ◽  
Ammad Hassan Mahmood
Keyword(s):  
Amino Acid ◽  
Single Nucleotide Polymorphisms ◽  
Kidney Stone ◽  
Stone Disease ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Calcium Sensing Receptor ◽  
Single Nucleotide ◽  
Kidney Stone Disease ◽  
Calcium Sensing

  Objective: The calcium-sensing receptor (CASR) is a G-protein-coupled receptor that is mainly expressed in the parathyroid and the kidneys where it regulates parathyroid hormone secretion and renal tubular calcium reabsorption. Inactivating and activating CASR gene due to mutations severally caused hypercalcemia or hypocalcemia disorders. The aim of the study was to investigate the risk factor of CASR rs1801725 (Ala986Ser) patients with renal disease.Method: The blood samples were collected from 100 patients and divided into two groups, each one containing 50 samples; chronic kidney disease and end-stage renal disease, who admitted Merjan Teaching Hospital in Babylon Province, Iraq, from February to July 2016. In addition, healthy persons as a control group (50 samples). Genotyping of CASR single-nucleotide polymorphisms (SNP) was performed using a polymerase chain reaction technique, followed by single-strand conformation polymorphism. Accordingly, these DNA polymorphisms were confirmed using DNA sequencing.Results: The conformational haplotypes of CASR, exon7 NCBI Primer3plus reference were obtained in three patterns, including two, three, and four bands, due to the presence SNPs within the studied region. These SNPs leads to change three amino acid residues of CASR, including amino acid substitutions were Ala 128→ Ser 128, Leu 155→Tye 155, and Leu 156→ Ser 156 that may affect or modified the tertiary structure of the receptor, subsequently the function like the affinity to calcium ion may be effected.Conclusion: These results suggest that the variants of CASR SNP, namely, rs1801725 might be involved in susceptibility to kidney stone disease.

Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

2010 ◽  
Vol 19 (5) ◽  
pp. 968-984 ◽  
Author(s):  
EVA-MARIA WILLING ◽  
PAUL BENTZEN ◽  
COCK van OOSTERHOUT ◽  
MARGARETE HOFFMANN ◽  
JOANNE CABLE ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Population History ◽  
Adaptive Divergence ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide
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