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nonsynonymous substitution

T Fatima Mitterboeck, Jinzhong Fu, Sarah J Adamowicz
Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group...
August 19, 2016: Genome Génome / Conseil National de Recherches Canada
Akinori Suzuki, Hidero Komata, Shogo Iwashita, Shotaro Seto, Hironobu Ikeya, Mitsutoshi Tabata, Takashi Kitano
In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD) in the common ancestor of all vertebrates. In our previous work, where we analyzed details of the gene duplications process of this gene family, three nucleotide sequences belonging to this family were identified in Far Eastern brook lamprey (Lethenteron reissneri), and the phylogenetic positions of the genes were determined...
October 13, 2016: Molecular Phylogenetics and Evolution
Nicolas Rodrigue, Nicolas Lartillot
Codon substitution models have traditionally attempted to uncover signatures of adaptation within protein-coding genes by contrasting the rates of synonymous and nonsynonymous substitutions. Another modeling approach, known as the mutation-selection framework, attempts to explicitly account for selective patterns at the amino acid level, with some approaches allowing for heterogeneity in these patterns across codon sites. Under such a model, substitutions at a given position occur at the neutral or nearly-neutral rate when they are synonymous, or when they correspond to replacements between amino acids of similar fitness; substitutions from high to low (low to high) fitness amino acids have comparatively low (high) rates...
October 15, 2016: Molecular Biology and Evolution
Nararat Laopichienpong, Narongrit Muangmai, Lawan Chanhome, Sunutcha Suntrarachun, Panupon Twilprawat, Surin Peyachoknagul, Kornsorn Srikulnath
Snakes exhibit genotypic sex determination with female heterogamety (ZZ males and ZW females), and the state of sex chromosome differentiation also varies among lineages. To investigate the evolutionary history of homologous genes located in the non-recombining region of differentiated sex chromosomes in snakes, partial sequences of the gametologous CTNNB1 gene were analyzed for 12 species belonging to henophid (Cylindrophiidae, Xenopeltidae, and Pythonidae) and caenophid snakes (Viperidae, Elapidae, and Colubridae)...
October 14, 2016: Journal of Heredity
Horng-Yunn Dou, Yih-Yuan Chen, Ying-Tsong Chen, Jia-Ru Chang, Chien-Hsing Lin, Keh-Ming Wu, Ming-Shian Lin, Ih-Jen Su, Shih-Feng Tsai
To better understand the transmission and evolution of Mycobacterium tuberculosis (MTB) in Taiwan, six different MTB isolates (representatives of the Beijing ancient sublineage, Beijing modern sublineage, Haarlem, East-African Indian, T1, and Latin-American Mediterranean (LAM)) were characterized and their genomes were sequenced. Discriminating among large sequence polymorphisms (LSPs) that occur once versus those that occur repeatedly in a genomic region may help to elucidate the biological roles of LSPs and to identify the useful phylogenetic relationships...
2016: Evolutionary Bioinformatics Online
Kate Rockenbach, Justin C Havird, J Grey Monroe, Deborah A Triant, Douglas R Taylor, Daniel B Sloan
Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.e., positive selection) or simply a loss of functional constraint (i...
October 5, 2016: Genetics
Itamar Sela, Yuri I Wolf, Eugene V Koonin
Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Kye Hwa Lee, Su Youn Baik, Soo Youn Lee, Chan Hee Park, Paul J Park, Ju Han Kim
Despite substantial premarket efforts, a significant portion of approved drugs has been withdrawn from the market for safety reasons. The deleterious impact of nonsynonymous substitutions predicted by the SIFT algorithm on structure and function of drug-related proteins was evaluated for 2504 personal genomes. Both withdrawn (n = 154) and precautionary (Beers criteria (n = 90), and US FDA pharmacogenomic biomarkers (n = 96)) drugs showed significantly lower genomic deleteriousness scores (P < 0.001) compared to others (n = 752)...
2016: PloS One
Yujiao Zhao, Lihua Li, Dehong Ma, Jia Luo, Zhiqiang Ma, Xiaodan Wang, Yue Pan, Junying Chen, Juemin Xi, Jiajia Yang, Lijuan Qiu, Chunhai Bai, Liming Jiang, Xiyun Shan, Qiangming Sun
A total of 1067 serum samples were collected from febrile patients in Xishuangbanna, Yunnan, 2015. Of these, 852 cases were confirmed to be dengue NS1-positive. 76 structural protein genes were sequenced through RT-PCR based on the viral RNAs extracted from serum samples. Phylogenetic analysis revealed that all strains were classified as cosmopolitan genotype of DENV-2. After comparing with the DENV-2SS, 173 base substitutions were found in 76 sequences, resulting in 43 nonsynonymous mutations, of which 22 mutations existed among all samples...
September 29, 2016: Scientific Reports
Yuan Su, Diyan Li, Uma Gaur, Yan Wang, Nan Wu, Binlong Chen, Zhongxian Xu, Huadong Yin, Yaodong Hu, Qing Zhu
The sense of bitter taste plays a critical role in animals as it can help them to avoid intake of toxic and harmful substances. Previous research had revealed that chicken has only three bitter taste receptor genes (Tas2r1, Tas2r2 and Tas2r7). To better understand the genetic polymorphisms and importance of bitter taste receptor genes (Tas2rs) in chicken, here, we sequenced Tas2rs of 30 Sichuan domestic chickens and 30 Tibetan chickens. Thirteen single-nucleotide polymorphisms (SNPs) including three nonsynonymous mutations (m...
September 2016: Journal of Genetics
Kyong-Ah Yoon, Boyoung Park, Byung Il Lee, Moon Jung Yang, Sun-Young Kong, Eun Sook Lee
Purpose: Unclassified variants (UVs) of BRCA1 and BRCA2 genes are not defined as pathogenic for breast cancer, and their clinical significance currently remains undefined. Therefore, this study was conducted to identify potentially pathogenic unclassified variants by comparing their prevalence between breast cancer patients and controls. Methods: A total of 328 breast cancer patients underwent BRCA1/2 genetic screening at the National Cancer Center of Korea. Genetic variants of BRCA genes that were categorized as unclassified according to the Breast Cancer Information Core database were selected based on allelic frequency, after which candidate variants were genotyped in 421 healthy controls...
September 13, 2016: Cancer Research and Treatment: Official Journal of Korean Cancer Association
John H Hammond, Wesley P Hebert, Amanda Naimie, Kathryn Ray, Rachel D Van Gelder, Antonio DiGiandomenico, Prajna Lalitha, Muthiah Srinivasan, Nisha R Acharya, Thomas Lietman, Deborah A Hogan, Michael E Zegans
The Steroids for Corneal Ulcers Trial (SCUT) was a multicenter, international study of bacterial keratitis in which 101 Pseudomonas aeruginosa infections were treated. Twenty-two of 101 P. aeruginosa isolates collected had a colony morphology characteristic of a loss-of-function mutation in lasR, the gene encoding a quorum-sensing master regulator. Ulcers caused by these 22 strains were associated with larger areas of corneal opacification, worse vision, and a lower rate of vision recovery in response to treatment than ulcers caused by the other isolates...
September 2016: MSphere
Raja Kaliyappan, Sriram Viswanathan, Backiyarani Suthanthiram, Uma Subbaraya, Saraswathi Marimuthu Somasundram, Mayilvaganan Muthu
The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups...
2016: PloS One
Drake C Stenger, Rodrigo Krugner, Shahideh Nouri, Inmaculada Ferriol, Bryce W Falk, Mark S Sisterson
Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences...
November 2016: Virology
Justin C Havird, Daniel B Sloan
Eukaryotes rely on proteins encoded by the nuclear and mitochondrial (mt) genomes, which interact within multisubunit complexes such as oxidative-phosphorylation enzymes. Although selection is thought to be less efficient on the asexual mt genome, in bilaterian animals the ratio of nonsynonymous to synonymous substitutions (ω) is lower in mt- compared to nuclear-encoded OXPHOS subunits, suggesting stronger effects of purifying selection in the mt genome. Because high levels of gene expression constrain protein sequence evolution, one proposed resolution to this paradox is that mt genes are expressed more highly than nuclear genes...
August 25, 2016: Molecular Biology and Evolution
Lucy Peters, Emily Humble, Nicole Kröcker, Birgit Fuchs, Jaume Forcada, Joseph I Hoffman
Although the genetic basis of color variation has been extensively studied in humans and domestic animals, the genetic polymorphisms responsible for different color morphs remain to be elucidated in many wild vertebrate species. For example, hypopigmentation has been observed in numerous marine mammal species but the underlying mutations have not been identified. A particularly compelling candidate gene for explaining color polymorphism is the melanocortin 1 receptor (MC1R), which plays a key role in the regulation of pigment production...
August 2016: Ecology and Evolution
Jelli Venkatesh, Molly Jahn, Byoung-Cheorl Kang
The tomato Pto gene, which encodes a serine/threonine kinase (STK) domain-containing protein, confers resistance to bacterial speck disease caused by Pseudomonas syringae pv. tomato (Pst). In this study, in vivo recognition assays using PVX constructs showed that AvrPto was specifically recognized in the pepper genotypes. This AvrPto recognition caused a nonhost hypersensitive response (HR) and localization of the PVX::AvrPto fusion protein to inoculated pepper leaf tissues, which indicates the presence of a similar Pto recognition mechanism in pepper as in tomato...
2016: PloS One
Stephanie J Spielman, Suyang Wan, Claus O Wilke
Two broad paradigms exist for inferring [Formula: see text] the ratio of nonsynonymous to synonymous substitution rates, from coding sequences: (i) a one-rate approach, where [Formula: see text] is represented with a single parameter, or (ii) a two-rate approach, where [Formula: see text] and [Formula: see text] are estimated separately. The performances of these two approaches have been well studied in the specific context of proper model specification, i.e., when the inference model matches the simulation model...
October 2016: Genetics
Hoang van Tong, Nghiem Xuan Hoan, Bo Wang, Heiner Wedemeyer, C-Thomas Bock, Thirumalaisamy P Velavan
Hepatitis E virus (HEV) infection is a major cause of acute hepatitis and affects more than 20 million individuals, with three million symptomatic cases and 56,000 recognized HEV-related deaths worldwide. HEV is endemic in developing countries and is gaining importance in developed countries, due to increased number of autochthone cases. Although HEV replication is controlled by the host immune system, viral factors (especially specific viral genotypes and mutants) can modulate HEV replication, infection and pathogenesis...
September 2016: EBioMedicine
Collin P Jaeger, Melvin R Duvall, Bradley J Swanson, Christopher A Phillips, Michael J Dreslik, Sarah J Baker, Richard B King
Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations...
June 2016: Ecology and Evolution
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