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nonsynonymous substitution

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https://www.readbyqxmd.com/read/27921293/coloniality-and-migration-are-related-to-selection-on-mhc-genes-in-birds
#1
Piotr Minias, Linda A Whittingham, Peter O Dunn
The Major Histocompatibility Complex (MHC) plays a key role in pathogen recognition as a part of vertebrate adaptive immune system. The great diversity of MHC genes in natural populations is maintained by different forms of balancing selection and its strength should correlate with the diversity of pathogens to which a population is exposed and the rate of exposure. Despite this prediction, little is known about how the life-history characteristics affect selection at the MHC. Here, we examined whether the strength of balancing selection on MHC class II genes in birds (as measured with nonsynonymous nucleotide substitutions, dN) was related to their social or migratory behaviour, two life-history characteristics correlated with pathogen exposure...
December 6, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27914139/genetic-variations-of-the-kiss1r-gene-in-korean-girls-with-central-precocious-puberty
#2
Yeon Joung Oh, Young Jun Rhie, Hyo Kyoung Nam, Hye Ryun Kim, Kee Hyoung Lee
The timing of puberty onset varies greatly among individuals, and much of this variation is modulated by genetic factors. This study aimed to identify the kisspeptin receptor (KISS1R) gene variations and to investigate the associations between these variations and central precocious puberty (CPP). Korean girls with CPP (n = 194) and their healthy controls (n = 99) were included in this study. The entire coding region and the exon-intron boundaries (exon 1 through 5) of the KISS1R gene were directly sequenced...
January 2017: Journal of Korean Medical Science
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#3
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
https://www.readbyqxmd.com/read/27906615/polymorphism-in-exon-6-of-the-human-nt5e-gene-is-associated-with-aortic-valve-calcification
#4
Zdzislaw Kochan, Joanna Karbowska, Patrycja Gogga, Barbara Kutryb-Zajac, Ewa M Slominska, Ryszard T Smolenski
NT5E encodes ecto-5'-nucleotidase (e5NT, CD73) which hydrolyses extracellular AMP to adenosine. Adenosine has been shown to play a protective role against aortic valve calcification (AVC). We identified two nonsynonymous missense single nucleotide polymorphisms (c.1126A > G, p.T376A and c.1136T > C, p.M379T) in exon 6 of the human NT5E gene. Since both substitutions might affect e5NT activity and consequently alter extracellular adenosine levels, we evaluated the association between NT5E alleles and calcific aortic valve disease in 119 patients (95 patients with AVC and 24 controls)...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27903241/abundant-rna-editing-sites-of-chloroplast-protein-coding-genes-in-ginkgo-biloba-and-an-evolutionary-pattern-analysis
#5
Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang, Jianing Yu
BACKGROUND: RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, and the number of editing sites varies in terrestrial plants. Why and how RNA editing systems evolved remains a mystery. Ginkgo biloba is one of the oldest seed plants and has an important evolutionary position. Determining the patterns and distribution of RNA editing in the ancient plant provides insights into the evolutionary trend of RNA editing, and helping us to further understand their biological significance...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27886141/comprehensive-transcriptome-analysis-provides-evidence-of-local-thermal-adaptation-in-three-loaches-genus-misgurnus
#6
Shaokui Yi, Sai Wang, Jia Zhong, Weimin Wang
The geographic distribution of three Misgurnus species, M. anguillicaudatus, M. bipartitus, and M. mohoity, displays a specific pattern in China, coincident with temperature zones. In this study, we sequenced the transcriptomes of these three species and used the sequences to investigate the lineage-specific adaptations within the genus Misgurnus. In total, 51 orphan genes (19 in M. anguillicaudatus, 18 in M. bipartitus, and 14 in M. mohoity) that may contribute to the species-specific adaptations were identified...
November 24, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27847361/functional-characterization-of-adaptive-mutations-during-the-west-african-ebola-virus-outbreak
#7
Erik Dietzel, Gordian Schudt, Verena Krähling, Mikhail Matrosovich, Stephan Becker
: The Ebola virus (EBOV) outbreak in West Africa started in December 2013, claimed more than 11,000 lives, threatened to destabilize a whole region and showed how easily health crises can turn into humanitarian disasters. EBOV genomic sequences of the West African outbreak revealed nonsynonymous mutations, which induced considerable public attention, but their role in virus spread and disease remains obscure. In this study we investigated the functional significance of three nonsynonymous mutations that emerged early during the West African EBOV outbreak...
November 9, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27827323/sequence-variation-at-klk-and-wfdc-clusters-and-its-association-to-semen-hyperviscosity-and-other-male-infertility-phenotypes
#8
Patrícia Isabel Marques, Filipa Fonseca, Ana Sofia Carvalho, Diana A Puente, Isabel Damião, Vasco Almeida, Nuno Barros, Alberto Barros, Filipa Carvalho, Mikel Azkargorta, Felix Elortza, Hugo Osório, Rune Matthiesen, Victor Quesada, Susana Seixas
STUDY QUESTION: Are kallikreins (KLKs), the whey-acidic-protein four-disulfide core domain (WFDCs) and their neighbors, semenogelins (SEMGs), known to play a role in the cascade of semen coagulation and liquefaction, associated with male infertility? SUMMARY ANSWER: Several KLK and SEMG variants are overrepresented among hyperviscosity, asthenozoospermia and oligozoospermia, supporting an effect of abnormal semen liquefaction on the loss of semen quality and in lowering male reproductive fitness...
November 7, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27822534/long-term-evolution-of-burkholderia-multivorans-during-a-chronic-cystic-fibrosis-infection-reveals-shifting-forces-of-selection
#9
Inês N Silva, Pedro M Santos, Mário R Santos, James E A Zlosnik, David P Speert, Sean W Buskirk, Eric L Bruger, Christopher M Waters, Vaughn S Cooper, Leonilde M Moreira
Burkholderia multivorans is an opportunistic pathogen capable of causing severe disease in patients with cystic fibrosis (CF). Patients may be chronically infected for years, during which the bacterial population evolves in response to unknown forces. Here we analyze the genomic and functional evolution of a B. multivorans infection that was sequentially sampled from a CF patient over 20 years. The population diversified into at least four primary, coexisting clades with distinct evolutionary dynamics. The average substitution rate was only 2...
May 2016: MSystems
https://www.readbyqxmd.com/read/27812361/transcriptome-analysis-of-green-peach-aphid-myzus-persicae-insight-into-developmental-regulation-and-inter-species-divergence
#10
Rui Ji, Yujun Wang, Yanbin Cheng, Meiping Zhang, Hong-Bin Zhang, Li Zhu, Jichao Fang, Keyan Zhu-Salzman
Green peach aphid (Myzus persicae) and pea aphid (Acyrthosiphon pisum) are two phylogenetically closely related agricultural pests. While pea aphid is restricted to Fabaceae, green peach aphid feeds on hundreds of plant species from more than 40 families. Transcriptome comparison could shed light on the genetic factors underlying the difference in host range between the two species. Furthermore, a large scale study contrasting gene expression between immature nymphs and fully developed adult aphids would fill a previous knowledge gap...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27808114/cassava-brown-streak-virus-has-a-rapidly-evolving-genome-implications-for-virus-speciation-variability-diagnosis-and-host-resistance
#11
Titus Alicai, Joseph Ndunguru, Peter Sseruwagi, Fred Tairo, Geoffrey Okao-Okuja, Resty Nanvubya, Lilliane Kiiza, Laura Kubatko, Monica A Kehoe, Laura M Boykin
Cassava is a major staple food for about 800 million people in the tropics and sub-tropical regions of the world. Production of cassava is significantly hampered by cassava brown streak disease (CBSD), caused by Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). The disease is suppressing cassava yields in eastern Africa at an alarming rate. Previous studies have documented that CBSV is more devastating than UCBSV because it more readily infects both susceptible and tolerant cassava cultivars, resulting in greater yield losses...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27792534/polymorphism-in-mitochondrial-coding-regions-of-mediterranean-loggerhead-turtles-evolutionary-relevance-and-structural-effects
#12
Andrea Novelletto, Letizia Testa, Federico Iacovelli, Paola Blasi, Luisa Garofalo, Toni Mingozzi, Mattia Falconi
We sequenced coding portions (1.6 kb) of the mtDNA in 170 loggerhead (Caretta caretta) turtles sampled in the central Mediterranean. The sequences spanned the entire ND1 and ND3 genes, the tRNAGly and tRNAArg, plus the 3' and 5' termini of COXIII and ND4L genes, respectively. Based on our sequencing results and published complete mitogenomes, we constructed a maximum parsimony phylogeny of C. caretta matrilines that sheds new light on the evolutionary relationships within the collection of lineages found in the Mediterranean and so far recognized by D-loop haplotypes only...
November 2016: Physiological and Biochemical Zoology: PBZ
https://www.readbyqxmd.com/read/27767335/rates-and-patterns-of-molecular-evolution-in-freshwater-versus-terrestrial-insects
#13
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
https://www.readbyqxmd.com/read/27746317/evolution-of-the-rh-gene-family-in-vertebrates-revealed-by-brown-hagfish-eptatretus-atami-genome-sequences
#14
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
https://www.readbyqxmd.com/read/27744408/detecting-adaptation-in-protein-coding-genes-using-a-bayesian-site-heterogeneous-mutation-selection-codon-substitution-model
#15
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
https://www.readbyqxmd.com/read/27742742/evolutionary-dynamics-of-the-gametologous-ctnnb1-gene-on-the-z-and-w-chromosomes-of-snakes
#16
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
https://www.readbyqxmd.com/read/27721649/genomics-study-of-mycobacterium-tuberculosis-strains-from-different-ethnic-populations-in-taiwan
#17
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
https://www.readbyqxmd.com/read/27707788/positive-selection-in-rapidly-evolving-plastid-nuclear-enzyme-complexes
#18
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
https://www.readbyqxmd.com/read/27702904/theory-of-prokaryotic-genome-evolution
#19
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
https://www.readbyqxmd.com/read/27690231/genome-sequence-variability-predicts-drug-precautions-and-withdrawals-from-the-market
#20
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
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